PaperBLAST
PaperBLAST Hits for SwissProt::Q6DAR4 D-galactonate dehydratase family member ECA0189 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) (Erwinia carotovora subsp. atroseptica)) (399 a.a., MLPTIITDIE...)
Show query sequence
>SwissProt::Q6DAR4 D-galactonate dehydratase family member ECA0189 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) (Erwinia carotovora subsp. atroseptica))
MLPTIITDIECLVTRPDRHNLVTVVVHTNKNVTGYGCATFQQRPLAVKAMVDEYLKPLLL
GRDANHIEDLWHMMMVNAYWRNGPVINNAVAGVDMALWDIKGKLADMPLYHLFGGKSRDA
IAAYSHAASDTLDGLYQEVERLYAQGYRHIRCQLGFYGGNPDALHSTRQPTEGAYYDQDQ
YMANTLAMFRALREKYGDRFHILHDVHERLFPNQAVQFAKAVEVYRPYFIEDILPPAQNE
WLAQIRSQSAVPLATGELFNNPAEWQNLVINRQVDFIRCHVSQIGGITPALKLGAFCQNF
GVRLAWHCPPDMTPIGAAVNIHLNIHLHNAAIQEFVAYPENTRKVFPQAVEPENGYLYPI
ERPGIGVGIDLDAARQFPVVYRPHEWTQSRLPDGTMHTP
Running BLASTp...
Found 250 similar proteins in the literature:
IMAND_PECAS / Q6DAR4 D-galactonate dehydratase family member ECA0189 from Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) (Erwinia carotovora subsp. atroseptica) (see paper)
100% identity, 100% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro yes 1 A4W7D6 Pro yes 1 D0X4R4 Pro yes 1 A6AMN2 Pro yes 1 Q6DAR4 Pro yes 1 C6DI84 Pro yes 6 B8HCK2 Pro no 9 C9CN91 Pro yes 9 C8ZZN2 Pro yes 10 C7PW26 Pro no Singleton A6M2W4 Pro yes Singleton Q2CIN0 Pro yes...”
- “...C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and three cooperative agreements from the U.S. National Institutes of Health (P01GM071790, U54GM093342, U54GM074945, and U54GM094662). Molecular...”
IMAND_PECPW / D0KC90 D-galactonate dehydratase family member Pecwa_4254 from Pectobacterium parmentieri (strain WPP163) (Pectobacterium wasabiae (strain WPP163)) (see paper)
99% identity, 100% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...-strand UxuA? 1 A5KUH4 Pro yes 1 C9NUM5 Pro no 1 C9Y5D5 Pro yes 1 D0KC90 Pro yes 1 A4W7D6 Pro yes 1 D0X4R4 Pro yes 1 A6AMN2 Pro yes 1 Q6DAR4 Pro yes 1 C6DI84 Pro yes 6 B8HCK2 Pro no 9 C9CN91 Pro yes...”
- “...B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and three cooperative agreements from...”
IMAND_PECCP / C6DI84 D-galactonate dehydratase family member PC1_4063 from Pectobacterium carotovorum subsp. carotovorum (strain PC1) (see paper)
97% identity, 100% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro yes 1 D0X4R4 Pro yes 1 A6AMN2 Pro yes 1 Q6DAR4 Pro yes 1 C6DI84 Pro yes 6 B8HCK2 Pro no 9 C9CN91 Pro yes 9 C8ZZN2 Pro yes 10 C7PW26 Pro no Singleton A6M2W4 Pro yes Singleton Q2CIN0 Pro yes Singleton A8RQK7 Pro yes...”
- “...A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program...”
IMND1_VIBCR / C9NUM5 D-galactonate dehydratase family member VIC002985 from Vibrio coralliilyticus (strain ATCC BAA-450 / DSM 19607 / CCUG 48437 / LMG 20984 / YB1) (see paper)
76% identity, 100% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...(M 1 s 1 ) end of 7th -strand UxuA? 1 A5KUH4 Pro yes 1 C9NUM5 Pro no 1 C9Y5D5 Pro yes 1 D0KC90 Pro yes 1 A4W7D6 Pro yes 1 D0X4R4 Pro yes 1 A6AMN2 Pro yes 1 Q6DAR4 Pro yes 1 C6DI84 Pro yes...”
- “...B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and three cooperative...”
IMAND_VIBBS / A5KUH4 D-galactonate dehydratase family member VSWAT3_13707 from Vibrionales bacterium (strain SWAT-3) (see paper)
76% identity, 100% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
subunit: Homotetramer. - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...cat / K M (M 1 s 1 ) end of 7th -strand UxuA? 1 A5KUH4 Pro yes 1 C9NUM5 Pro no 1 C9Y5D5 Pro yes 1 D0KC90 Pro yes 1 A4W7D6 Pro yes 1 D0X4R4 Pro yes 1 A6AMN2 Pro yes 1 Q6DAR4 Pro yes...”
- “...ManD (blue), Cs ManD (tan), Uniprot ID Q8FHC7 (green), Uniprot ID B5R541 (magenta), Uniprot ID A5KUH4 (red), and Uniprot ID A6M2W4 (gray) showing the overall structural homology. The 150180s loops are conformationally distinct. Initially, the 150180s loops were proposed to contain the substrate specificity determinants in...”
3r25B / A5KUH4 Crystal structure of enolase superfamily member from vibrionales bacterium complexed with mg and glycerol in the active site
76% identity, 99% coverage
- Ligand: magnesium ion (3r25B)
IMND2_VIBCY / A6AMN2 D-galactonate dehydratase family member A1Q3065 from Vibrio campbellii (strain HY01) (see paper)
74% identity, 100% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro yes 1 D0KC90 Pro yes 1 A4W7D6 Pro yes 1 D0X4R4 Pro yes 1 A6AMN2 Pro yes 1 Q6DAR4 Pro yes 1 C6DI84 Pro yes 6 B8HCK2 Pro no 9 C9CN91 Pro yes 9 C8ZZN2 Pro yes 10 C7PW26 Pro no Singleton A6M2W4 Pro yes...”
- “...enzymatic activities of proteins with the following UniProt accession IDs: A4W7D6, A4WA78, A4XF23, A5KUH4, A5V6Z0, A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2,...”
4girB / D0X4R4 Crystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to mannonate dehydratase, with mg, ethylene glycol and sulfate bound (ordered loops, space group p41212)
73% identity, 97% coverage
- Ligand: magnesium ion (4girB)
IMAND_VIBH1 / D0X4R4 D-galactonate dehydratase family member VME_00770 from Vibrio harveyi (strain 1DA3) (see paper)
73% identity, 100% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
subunit: Homotetramer. - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro no 1 C9Y5D5 Pro yes 1 D0KC90 Pro yes 1 A4W7D6 Pro yes 1 D0X4R4 Pro yes 1 A6AMN2 Pro yes 1 Q6DAR4 Pro yes 1 C6DI84 Pro yes 6 B8HCK2 Pro no 9 C9CN91 Pro yes 9 C8ZZN2 Pro yes 10 C7PW26 Pro no...”
- “...from Vibrionales bacterium liganded with Mg 2+ and d -arabinonate (entry 3SBF), no-activity protein/Uniprot ID D0X4R4 from Vibrio harveyi liganded with Mg 2+ , Cl , glycerol, maleic acid, and malonic acid (entry 4GIS), no-activity protein/ Uniprot ID D0X4R4 from Vibrio harveyi liganded with Mg 2+...”
IMAND_CLOB8 / A6M2W4 D-galactonate dehydratase family member Cbei_4837 from Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052) (Clostridium acetobutylicum) (see paper)
71% identity, 100% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro no 9 C9CN91 Pro yes 9 C8ZZN2 Pro yes 10 C7PW26 Pro no Singleton A6M2W4 Pro yes Singleton Q2CIN0 Pro yes Singleton A8RQK7 Pro yes Singleton C6CVY9 Gly yes Singleton C9A1P5 Pro yes Singleton B5GCP6 Pro no 3 A6VRA1 0.020.001 160 Ala yes 3 E1V4Y0...”
- “...Uniprot ID Q8FHC7 (green), Uniprot ID B5R541 (magenta), Uniprot ID A5KUH4 (red), and Uniprot ID A6M2W4 (gray) showing the overall structural homology. The 150180s loops are conformationally distinct. Initially, the 150180s loops were proposed to contain the substrate specificity determinants in analogy with the 20s loops...”
3tjiA / A4W7D6 Crystal structure of an enolase from enterobacter sp. 638 (efi target efi-501662) with bound mg
A4W7D6 D-galactonate dehydratase family member Ent638_0932 from Enterobacter sp. (strain 638)
71% identity, 100% coverage
IMAND_CROTZ / C9Y5D5 D-galactonate dehydratase family member Ctu_1p00430 from Cronobacter turicensis (strain DSM 18703 / CCUG 55852 / LMG 23827 / z3032) (see paper)
70% identity, 100% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...) end of 7th -strand UxuA? 1 A5KUH4 Pro yes 1 C9NUM5 Pro no 1 C9Y5D5 Pro yes 1 D0KC90 Pro yes 1 A4W7D6 Pro yes 1 D0X4R4 Pro yes 1 A6AMN2 Pro yes 1 Q6DAR4 Pro yes 1 C6DI84 Pro yes 6 B8HCK2 Pro no...”
- “...B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and three cooperative agreements...”
IMAND_ENTCS / C9CN91 D-galactonate dehydratase family member ECAG_02205 from Enterococcus casseliflavus (strain EC10) (see paper)
68% identity, 100% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...Pro yes 1 Q6DAR4 Pro yes 1 C6DI84 Pro yes 6 B8HCK2 Pro no 9 C9CN91 Pro yes 9 C8ZZN2 Pro yes 10 C7PW26 Pro no Singleton A6M2W4 Pro yes Singleton Q2CIN0 Pro yes Singleton A8RQK7 Pro yes Singleton C6CVY9 Gly yes Singleton C9A1P5 Pro yes...”
- “...B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and three...”
3gy1B / A6M2W4 Crystal structure of putative mandelate racemase/muconate lactonizing protein from clostridium beijerinckii ncimb 8052
69% identity, 99% coverage
- Ligand: magnesium ion (3gy1B)
4hnlA / C8ZZN2 Crystal structure of enolase egbg_01401 (target efi-502226) from enterococcus gallinarum eg2
66% identity, 100% coverage
- Ligand: magnesium ion (4hnlA)
IMND1_ENTGE / C8ZZN2 D-galactonate dehydratase family member EGBG_01401 from Enterococcus gallinarum (strain EG2) (see paper)
66% identity, 100% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...Pro yes 1 C6DI84 Pro yes 6 B8HCK2 Pro no 9 C9CN91 Pro yes 9 C8ZZN2 Pro yes 10 C7PW26 Pro no Singleton A6M2W4 Pro yes Singleton Q2CIN0 Pro yes Singleton A8RQK7 Pro yes Singleton C6CVY9 Gly yes Singleton C9A1P5 Pro yes Singleton B5GCP6 Pro no...”
- “...638 liganded with Mg 2+ , Cl , and glycerol (entry 3TJI), no-activity protein/Uniprot ID C8ZZN2 from Enterococcus gallinarum EG2 liganded with Mg 2+ , Cl , and glycerol (entry 4HNL), low-activity ManD/Uniprot ID Q8FHC7 from Escherichia coli CFT073 complexed with Mg 2+ (entry 4IL2), the...”
IMND2_ENTGE / C9A1P5 D-galactonate dehydratase family member EGBG_02030 from Enterococcus gallinarum (strain EG2) (see paper)
51% identity, 99% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Cultivation of marine bacteria of the SAR202 clade.
Lim, Nature communications 2023 - “...four proteins that have been studied experimentally are indicated with black rectangles (UniProt ID: D8ADB5, C9A1P5, C6CBG9, and A8RQK7). We analyzed sequence divergence among the 80 COG4948 proteins of the JH545 genome by building a sequence similarity network (SSN) using the Enzyme Function Initiatives Enzyme Similarity...”
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...Pro yes Singleton Q2CIN0 Pro yes Singleton A8RQK7 Pro yes Singleton C6CVY9 Gly yes Singleton C9A1P5 Pro yes Singleton B5GCP6 Pro no 3 A6VRA1 0.020.001 160 Ala yes 3 E1V4Y0 0.030.006 20 0.050.004 20 Pro yes 3 B3PDB1 0.030.002 100 Ala yes 3 Cs ManD/Q1QT89 0.020.0005...”
- “...A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and...”
IMAND_ENTBW / A8RQK7 D-galactonate dehydratase family member CLOBOL_02770 from Enterocloster bolteae (strain ATCC BAA-613 / DSM 15670 / CCUG 46953 / JCM 12243 / WAL 16351) (Clostridium bolteae) (see paper)
47% identity, 98% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Cultivation of marine bacteria of the SAR202 clade.
Lim, Nature communications 2023 - “...have been studied experimentally are indicated with black rectangles (UniProt ID: D8ADB5, C9A1P5, C6CBG9, and A8RQK7). We analyzed sequence divergence among the 80 COG4948 proteins of the JH545 genome by building a sequence similarity network (SSN) using the Enzyme Function Initiatives Enzyme Similarity Tool (EFI-EST) 42...”
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...Pro yes 10 C7PW26 Pro no Singleton A6M2W4 Pro yes Singleton Q2CIN0 Pro yes Singleton A8RQK7 Pro yes Singleton C6CVY9 Gly yes Singleton C9A1P5 Pro yes Singleton B5GCP6 Pro no 3 A6VRA1 0.020.001 160 Ala yes 3 E1V4Y0 0.030.006 20 0.050.004 20 Pro yes 3 B3PDB1...”
- “...proteins with the following UniProt accession IDs: A4W7D6, A4WA78, A4XF23, A5KUH4, A5V6Z0, A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0,...”
4ihcB / C6CBG9 Crystal structure of probable mannonate dehydratase dd703_0947 (target efi-502222) from dickeya dadantii ech703
44% identity, 99% coverage
- Ligand: magnesium ion (4ihcB)
DGD_SALEP / B5R541 D-galactonate dehydratase family member SEN1436; D-gluconate dehydratase; EC 4.2.1.-; EC 4.2.1.39 from Salmonella enteritidis PT4 (strain P125109) (see paper)
SEN1436 putative dehydratase from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
43% identity, 94% coverage
- function: Has low D-gluconate dehydratase activity (in vitro), suggesting that it has no significant role in D-gluconate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:21612)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Homotetramer. - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro yes 4 B5RAG0 0.010.001 50 Pro yes 5 D4GJ14 0.040.003 120 Pro yes 5 B5R541 0.050.003 80 Pro yes 5 B5QBD4 0.020.0005 150 Pro yes 5 C6CBG9 0.040.002 50 0.030.002 60 Pro yes Singleton D9UNB2 0.0040.001 60 Pro yes 8 D7BPX0 0.010.002 40 Pro no...”
- “...the structures of Na ManD with d -mannonate in its active site (2QJM), Uniprot ID B5R541 with d -gluconate in its active site (3TWB), and unliganded Cs ManD (3BSM) (Figure 4 ). On the basis of this comparison, we hypothesized that the conserved His after the...”
- Investigating the physiological roles of low-efficiency D-mannonate and D-gluconate dehydratases in the enolase superfamily: pathways for the catabolism of L-gulonate and L-idonate
Wichelecki, Biochemistry 2014 - “...pathway that is encoded by genes proximal to that encoding a low-efficiency GlcD (Uniprot entry B5R541, Se GlcD; k cat / K M = 80 M 1 s 1 ) 7 (Figures 6 and 7 ). Figure 6 Genome neighborhoods of the previously described l -idonate...”
- In vitro reconstitution and characterisation of the oxidative D-xylose pathway for production of organic acids and alcohols
Boer, AMB Express 2019 - “...NCBI), and Haloferax volcanii ( Hv XylD, GI: 292493977, NCBI), the putative d -gluconate dehydratase SEN1436 from Salmonella enterica ( Se GluDHT, GI: 667467043, NCBI) the mandelate racemase/muconate lactonizing enzyme-like protein from Rubrobacter xylanophilus ( Rx MR/MLE, GI: 123368307, NCBI), and the d -galactonate dehydratase family...”
- Global Gene-expression Analysis of the Response of Salmonella Enteritidis to Egg White Exposure Reveals Multiple Egg White-imposed Stress Responses
Baron, Frontiers in microbiology 2017 - “...dgo genes. The SEN1433-5 genes form a putative operon adjacent to the functionally-related and divergent SEN1436 gene. They are induced by 5.17- to 33.38-fold (at 45 min, Table 11 ), similar to dgo and uxuAB-uxaC . The genes of the SEN1432-6 cluster specify three enzymes (two...”
- “...3.21 5.17 SEN1434 Hexonate sugar transporter n.s. 2.70 5.68 SEN1435 Gluconate 5-dehydrogenase n.s. 3.07 .40 SEN1436 D-galactonate dehydratase family member SEN1436 n.s. 10.30 33.38 Highlighted fold changes correspond to up-regulated (dark gray) and down-regulated (light gray) genes. (n.s.), fold changes with p > 0.05 . A...”
DGD_SALV4 / B5QBD4 D-galactonate dehydratase family member SeV_A0456; D-gluconate dehydratase; EC 4.2.1.-; EC 4.2.1.39 from Salmonella virchow (strain SL491) (see paper)
43% identity, 94% coverage
- function: Has low D-gluconate dehydratase activity (in vitro), suggesting that it has no significant role in D-gluconate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:21612)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro yes 5 D4GJ14 0.040.003 120 Pro yes 5 B5R541 0.050.003 80 Pro yes 5 B5QBD4 0.020.0005 150 Pro yes 5 C6CBG9 0.040.002 50 0.030.002 60 Pro yes Singleton D9UNB2 0.0040.001 60 Pro yes 8 D7BPX0 0.010.002 40 Pro no 2 Q1NAJ2 20.07 4200 Ala no...”
- “...IDs: A4W7D6, A4WA78, A4XF23, A5KUH4, A5V6Z0, A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This...”
JI728_13100 D-galactonate dehydratase from Salmonella enterica subsp. enterica serovar Gallinarum/Pullorum
43% identity, 94% coverage
- Integrated OMICs approach reveals energy metabolism pathway is vital for Salmonella Pullorum survival within the egg white
Kang, mSphere 2024 - “...amino acid metabolism, and carbohydrate metabolism were specifically affected. Additional upregulated functionally relevant genes (JI728_13095, JI728_13100, JI728_17960, JI728_10085, JI728_15605, and nhaA ) as mutants confirmed the susceptible phenotype. Furthermore, fim deletion resulted in an increased survival capacity in the egg white, consistent with the downregulated expression....”
- “...onto the transcriptomic data ( Fig. 2B ). Of note, one of the upregulated genes, JI728_13100, belongs to the carbohydrate metabolism in the KEGG database ( Fig. 1C ), which is associated with the enriched pathway pentose and glucuronate interconversions. Fig 2 Integrated OMICs to screen...”
3twbC / B5R541 Crystal structure of gluconate dehydratase (target efi-501679) from salmonella enterica subsp. Enterica serovar enteritidis str. P125109 complexed with magnesium and gluconic acid
43% identity, 94% coverage
- Ligands: magnesium ion; d-gluconic acid (3twbC)
DMGD_MUSP7 / C6CBG9 D-galactonate dehydratase family member Dd703_0947; D-gluconate dehydratase; D-mannonate dehydratase; EC 4.2.1.-; EC 4.2.1.39; EC 4.2.1.8 from Musicola paradisiaca (strain Ech703) (Dickeya paradisiaca) (Dickeya dadantii) (see paper)
42% identity, 94% coverage
- function: Has low dehydratase activity with D-mannonate and D- gluconate, suggesting that these are not physiological substrates and that it has no significant role in the in vivo degradation of these compounds. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
catalytic activity: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:21612)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Cultivation of marine bacteria of the SAR202 clade.
Lim, Nature communications 2023 - “...proteins that have been studied experimentally are indicated with black rectangles (UniProt ID: D8ADB5, C9A1P5, C6CBG9, and A8RQK7). We analyzed sequence divergence among the 80 COG4948 proteins of the JH545 genome by building a sequence similarity network (SSN) using the Enzyme Function Initiatives Enzyme Similarity Tool...”
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...Pro yes 5 B5R541 0.050.003 80 Pro yes 5 B5QBD4 0.020.0005 150 Pro yes 5 C6CBG9 0.040.002 50 0.030.002 60 Pro yes Singleton D9UNB2 0.0040.001 60 Pro yes 8 D7BPX0 0.010.002 40 Pro no 2 Q1NAJ2 20.07 4200 Ala no 2 Q9AAR4 10.006 12300 Ala no...”
- “...no-activity protein/Uniprot ID A6M2W4 from Clostridium beijerinckii liganded with Mg 2+ (entry 3S47), Uniprot ID C6CBG9 from Dickeya dadantii Ech703 liganded with Mg 2+ , formic acid, I , Cl , and glycerol (4IHC), no-activity protein/Uniprot ID A4W7D6 from Enterobacter sp. 638 liganded with Mg 2+...”
3t6cA / D4GJ14 Crystal structure of an enolase from pantoea ananatis (efi target efi- 501676) with bound d-gluconate and mg
43% identity, 95% coverage
- Ligands: magnesium ion; d-gluconic acid (3t6cA)
DGD_PANAM / D4GJ14 D-galactonate dehydratase family member RspA; D-gluconate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.39 from Pantoea ananatis (strain LMG 20103) (see paper)
43% identity, 94% coverage
- function: Has low D-gluconate dehydratase activity (in vitro), suggesting that it has no significant role in D-gluconate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:21612)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - In vitro reconstitution and characterisation of the oxidative D-xylose pathway for production of organic acids and alcohols
Boer, AMB Express 2019 - “...MR/MLE GI: 123368307 Dehydratase 4.2.1.- Rubrobacter xylanophilus His 6 -tag_C E. coli Pa GalDHT UniProt: D4GJ14 Dehydratase 4.2.1.- Pantoea ananatis His 6 -tag_N E. coli The NCBI/Uniprot identifier, function, EC number, microbial origin, purification tag and expression host are specified In this article, we present the...”
- “...and the d -galactonate dehydratase family member RspA from Pantoea ananatis ( Pa GalDHT, UniProt: D4GJ14). The dehydratases from H. marismortui, H. volcanii , and S. enterica were tagged with an N-terminal Strep-tag II, and a His 6 -tag was added to the C-terminal or N-terminal...”
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro yes 4 J7KNU2 0.010.001 20 Pro yes 4 B5RAG0 0.010.001 50 Pro yes 5 D4GJ14 0.040.003 120 Pro yes 5 B5R541 0.050.003 80 Pro yes 5 B5QBD4 0.020.0005 150 Pro yes 5 C6CBG9 0.040.002 50 0.030.002 60 Pro yes Singleton D9UNB2 0.0040.001 60 Pro yes...”
- “...red), Cs ManD (4F4R, low-activity, promiscuous for d -mannonate/ d -gluconate - blue), Uniprot ID D4GJ14 (3T6C, low-activity, d -gluconate specific - green), and Uniprot ID A4W7D6 (3TJI, no-activity - magenta). The metal binding and acid/base residues are superimposable. The Pro/Ala dimorphism is also shown. The...”
IMAND_CATAD / C7PW26 D-galactonate dehydratase family member Caci_4410 from Catenulispora acidiphila (strain DSM 44928 / JCM 14897 / NBRC 102108 / NRRL B-24433 / ID139908) (see paper)
42% identity, 92% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...Pro yes 6 B8HCK2 Pro no 9 C9CN91 Pro yes 9 C8ZZN2 Pro yes 10 C7PW26 Pro no Singleton A6M2W4 Pro yes Singleton Q2CIN0 Pro yes Singleton A8RQK7 Pro yes Singleton C6CVY9 Gly yes Singleton C9A1P5 Pro yes Singleton B5GCP6 Pro no 3 A6VRA1 0.020.001 160...”
- “...A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project...”
IMAND_STRSH / B5GCP6 D-galactonate dehydratase family member SSBG_02010 from Streptomyces sp. (strain SPB074) (see paper)
39% identity, 89% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...Pro yes Singleton A8RQK7 Pro yes Singleton C6CVY9 Gly yes Singleton C9A1P5 Pro yes Singleton B5GCP6 Pro no 3 A6VRA1 0.020.001 160 Ala yes 3 E1V4Y0 0.030.006 20 0.050.004 20 Pro yes 3 B3PDB1 0.030.002 100 Ala yes 3 Cs ManD/Q1QT89 0.020.0005 5 0.040.006 40 Pro...”
- “...accession IDs: A4W7D6, A4WA78, A4XF23, A5KUH4, A5V6Z0, A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4....”
MAND_STRS3 / D9UNB2 D-galactonate dehydratase family member SSLG_02014; D-mannonate dehydratase; EC 4.2.1.-; EC 4.2.1.8 from Streptomyces sp. (strain SPB78) (see paper)
39% identity, 89% coverage
- function: Has low D-mannonate dehydratase activity (in vitro), suggesting that this is not a physiological substrate and that it has no significant role in D-mannonate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...5 B5QBD4 0.020.0005 150 Pro yes 5 C6CBG9 0.040.002 50 0.030.002 60 Pro yes Singleton D9UNB2 0.0040.001 60 Pro yes 8 D7BPX0 0.010.002 40 Pro no 2 Q1NAJ2 20.07 4200 Ala no 2 Q9AAR4 10.006 12300 Ala no 2 Q9A4L8 0.650.02 1200 Ala no 2 B0T4L2...”
- “...B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and three cooperative agreements from the U.S. National Institutes of...”
IMAND_PAESJ / C6CVY9 D-galactonate dehydratase family member Pjdr2_1176 from Paenibacillus sp. (strain JDR-2) (see paper)
39% identity, 97% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...Pro no Singleton A6M2W4 Pro yes Singleton Q2CIN0 Pro yes Singleton A8RQK7 Pro yes Singleton C6CVY9 Gly yes Singleton C9A1P5 Pro yes Singleton B5GCP6 Pro no 3 A6VRA1 0.020.001 160 Ala yes 3 E1V4Y0 0.030.006 20 0.050.004 20 Pro yes 3 B3PDB1 0.030.002 100 Ala yes...”
- “...A5V6Z0, A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a...”
ESA_01752 hypothetical protein from Enterobacter sakazakii ATCC BAA-894
37% identity, 92% coverage
- Comparative analysis of genome sequences covering the seven cronobacter species
Joseph, PloS one 2012 - “...strains. Similarly, homologues were located for stringent starvation response (ESA_03615), carbon starvation sensing protein rspA (ESA_01752), and carbon starvation protein (ESA_00801) in all Cronobacter strains. However, an additional carbon starvation homologue (ESA_00339) was found in all Cronobacter strains except C. sakazakii 680 due to the long...”
ESA_01752 D-mannonate dehydratase ManD from Cronobacter sakazakii ATCC BAA-894
37% identity, 97% coverage
- Comparative analysis of genome sequences covering the seven cronobacter species
Joseph, PloS one 2012 - “...strains. Similarly, homologues were located for stringent starvation response (ESA_03615), carbon starvation sensing protein rspA (ESA_01752), and carbon starvation protein (ESA_00801) in all Cronobacter strains. However, an additional carbon starvation homologue (ESA_00339) was found in all Cronobacter strains except C. sakazakii 680 due to the long...”
IMAND_PSECP / B8HCK2 D-galactonate dehydratase family member Achl_0790 from Pseudarthrobacter chlorophenolicus (strain ATCC 700700 / DSM 12829 / CIP 107037 / JCM 12360 / KCTC 9906 / NCIMB 13794 / A6) (Arthrobacter chlorophenolicus) (see paper)
37% identity, 96% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...Pro yes 1 A6AMN2 Pro yes 1 Q6DAR4 Pro yes 1 C6DI84 Pro yes 6 B8HCK2 Pro no 9 C9CN91 Pro yes 9 C8ZZN2 Pro yes 10 C7PW26 Pro no Singleton A6M2W4 Pro yes Singleton Q2CIN0 Pro yes Singleton A8RQK7 Pro yes Singleton C6CVY9 Gly yes...”
- “...A4XF23, A5KUH4, A5V6Z0, A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported...”
AAur_0529 starvation sensing protein from Arthrobacter aurescens TC1
37% identity, 96% coverage
MAND_ENT38 / A4WA78 D-galactonate dehydratase family member Ent638_1932; D-mannonate dehydratase; EC 4.2.1.-; EC 4.2.1.8 from Enterobacter sp. (strain 638) (see paper)
36% identity, 97% coverage
- function: Has low D-mannonate dehydratase activity (in vitro), suggesting that this is not a physiological substrate and that it has no significant role in D-mannonate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Cs ManD/Q1QT89 0.020.0005 5 0.040.006 40 Pro yes 4 Q8FHC7 0.020.001 10 Pro yes 4 A4WA78 0.020.002 30 Pro yes 4 B1ELW6 0.020.001 20 Pro yes 4 D8ADB5 0.010.002 30 Pro yes 4 J7KNU2 0.010.001 20 Pro yes 4 B5RAG0 0.010.001 50 Pro yes 5 D4GJ14...”
- “...characterization of in vitro enzymatic activities of proteins with the following UniProt accession IDs: A4W7D6, A4WA78, A4XF23, A5KUH4, A5V6Z0, A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5,...”
MAND_PECCP / C6D9S0 D-galactonate dehydratase family member PC1_0802; D-mannonate dehydratase; EC 4.2.1.-; EC 4.2.1.8 from Pectobacterium carotovorum subsp. carotovorum (strain PC1) (see paper)
36% identity, 97% coverage
- function: Has low D-mannonate dehydratase activity (in vitro), suggesting that this is not a physiological substrate and that it has no significant role in D-mannonate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Paramixta manurensis gen. nov., sp. nov., a novel member of the family Erwiniaceae producing indole-3-acetic acid isolated from mushroom compost.
Kim, Scientific reports 2024 - “...PMPD1_3844 A0A0L7SVZ1 WP_052902905.1 87.2 0 Fructuronate reductase PMPD1_2875 A0A0U5L796 WP_067432173.1 78.8 0 Mannonate dehydratase PMPD1_2872 C6D9S0 WP_012773497.1 91.8 0 2-dehydro-3-deoxygluconokinase PMPD1_0039 A0A0L7SYX4 WP_052901041.1 84.9 0 2-dehydro-3-deoxyphosphogluconate aldolase (duplicate) PMPD1_2534 H3RFN6 WP_006120281.1 89.2 1.91E133 PMPD1_0571 A0A0A3YQQ3 WP_034896908.1 79.6 5.18E115 The ME phylogenetic tree shows that two DalD...”
t1426 starvation sensing protein RspA from Salmonella enterica subsp. enterica serovar Typhi Ty2
36% identity, 97% coverage
4e4fB / C6D9S0 Crystal structure of enolase pc1_0802 (target efi-502240) from pectobacterium carotovorum subsp. Carotovorum pc1
37% identity, 98% coverage
- Ligand: magnesium ion (4e4fB)
4fi4A / B0T0B1 Crystal structure of mannonate dehydratase prk15072 (target efi- 502214) from caulobacter sp. K31
39% identity, 96% coverage
- Ligand: magnesium ion (4fi4A)
MAND1_CAUSK / B0T0B1 D-mannonate dehydratase Caul1427; ManD; EC 4.2.1.8 from Caulobacter sp. (strain K31) (see paper)
39% identity, 97% coverage
- function: Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Prediction of enzymatic pathways by integrative pathway mapping.
Calhoun, eLife 2018 - “...compound, drug 2-keto-3-deoxy-D- gluconate Enzymatically synthesized CAS: 17510-99-5 Enzymatic synthesis by D-mannonate dehydratase (Uniprot ID B0T0B1). Verified via 1H-NMR Chemical compound, drug 2-keto-3-deoxy-D- gluconate-6- phosphate Enzymatically synthesized CAS: 884312-23-6 Enzymatic synthesis by D-mannonate dehydratase (Uniprot ID B0T0B1) and 1 M 2-keto-3-deoxy-D-gluconate kinase (Uniprot ID A4XF21). Verified...”
- “...10 mM MgCl 2 , 100 mM D-mannonate, and 1 M D-mannonate dehydratase (Uniprot ID B0T0B1). The reaction was left to proceed at 37C for 48 hr. Afterward, the enzyme was removed by filtration using 30,000 NMWL ultrafiltration membranes (Millipore). The identity of the product was...”
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Ala no 2 Q9A4L8 0.650.02 1200 Ala no 2 B0T4L2 0.30.01 1200 Ala no 2 B0T0B1 20.2 12100 0.0030.001 5 Ala no 2 A5V6Z0 40.2 2900 0.010.001 10 Ala no 2 Na ManD/A4XF23 1.30.1 3200 Ala no 7 G7TAD9 0.80.03 4400 Ala no Divergence in Activity...”
- “...for the following structures have been deposited in the Protein Data Bank: high-activity ManD/Uniprot ID B0T0B1 from Caulobacter sp. K31 liganded with Mg 2+ , Cl , and glycerol (entry 4FI4), high-activity ManD/EFI target 502209 from Caulobacter crescentus CB15 liganded with Mg 2+ , Cl ,...”
4il2B / Q8FHC7 Crystal structure of d-mannonate dehydratase (rspa) from e. Coli cft073 (efi target efi-501585)
E2348C_1665 starvation-sensing protein RspA from Escherichia coli O127:H6 str. E2348/69
36% identity, 97% coverage
MAND_ECOL6 / Q8FHC7 D-galactonate dehydratase family member RspA; D-mannonate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.8 from Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (see paper)
36% identity, 94% coverage
- function: Has low D-mannonate dehydratase activity (in vitro), suggesting that this is not a physiological substrate and that it has no significant role in D-mannonate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...B3PDB1 0.030.002 100 Ala yes 3 Cs ManD/Q1QT89 0.020.0005 5 0.040.006 40 Pro yes 4 Q8FHC7 0.020.001 10 Pro yes 4 A4WA78 0.020.002 30 Pro yes 4 B1ELW6 0.020.001 20 Pro yes 4 D8ADB5 0.010.002 30 Pro yes 4 J7KNU2 0.010.001 20 Pro yes 4 B5RAG0...”
- “...Information ). Figure 5 An overlay of Na ManD (blue), Cs ManD (tan), Uniprot ID Q8FHC7 (green), Uniprot ID B5R541 (magenta), Uniprot ID A5KUH4 (red), and Uniprot ID A6M2W4 (gray) showing the overall structural homology. The 150180s loops are conformationally distinct. Initially, the 150180s loops were...”
- Investigating the physiological roles of low-efficiency D-mannonate and D-gluconate dehydratases in the enolase superfamily: pathways for the catabolism of L-gulonate and L-idonate
Wichelecki, Biochemistry 2014 - “...This pathway is encoded by four genes: RspA , 7 a low-efficiency ManD (Uniprot entry Q8FHC7); RspB , annotated as an alcohol dehydrogenase (Uniprot entry Q8FHC8); RspC , annotated as a hypothetical metabolite transporter (Uniprot entry Q8FHC9); and RspD , annotated as an oxidoreductase (Uniprot entry...”
- “...of the gene cluster in E. coli CFT073. RspA (low-efficiency d -mannonate dehydratase, Uniprot entry Q8FHC7), RspB ( l -gulonate dehydrogenase, Uniprot entry Q8FHC8), and RspD (fructuronate reductase, Uniprot entry Q8FHD0) are colored green. The hypothetical metabolite transporter (RspC, Uniprot entry Q8FHC9) is colored red. Hypothetical...”
4kwsA / Q1QT89 Crystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with mg and glycerol
39% identity, 98% coverage
- Ligand: magnesium ion (4kwsA)
PMPD1_2872 D-mannonate dehydratase ManD from Paramixta manurensis
36% identity, 97% coverage
DMGD_HALED / E1V4Y0 D-galactonate dehydratase family member RspA; D-gluconate dehydratase; D-mannonate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.39; EC 4.2.1.8 from Halomonas elongata (strain ATCC 33173 / DSM 2581 / NBRC 15536 / NCIMB 2198 / 1H9) (see paper)
38% identity, 96% coverage
- function: Has low dehydratase activity with D-mannonate and D- gluconate, suggesting that these are not physiological substrates and that it has no significant role in the in vivo degradation of these compounds. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
catalytic activity: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:21612)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...Singleton C9A1P5 Pro yes Singleton B5GCP6 Pro no 3 A6VRA1 0.020.001 160 Ala yes 3 E1V4Y0 0.030.006 20 0.050.004 20 Pro yes 3 B3PDB1 0.030.002 100 Ala yes 3 Cs ManD/Q1QT89 0.020.0005 5 0.040.006 40 Pro yes 4 Q8FHC7 0.020.001 10 Pro yes 4 A4WA78 0.020.002...”
- “...C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and three cooperative agreements from the U.S. National Institutes of Health...”
MAND_SALG2 / B5RAG0 D-galactonate dehydratase family member RspA; D-mannonate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.8 from Salmonella gallinarum (strain 287/91 / NCTC 13346) (see paper)
36% identity, 97% coverage
- function: Has low D-mannonate dehydratase activity (in vitro), suggesting that this is not a physiological substrate and that it has no significant role in D-mannonate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro yes 4 D8ADB5 0.010.002 30 Pro yes 4 J7KNU2 0.010.001 20 Pro yes 4 B5RAG0 0.010.001 50 Pro yes 5 D4GJ14 0.040.003 120 Pro yes 5 B5R541 0.050.003 80 Pro yes 5 B5QBD4 0.020.0005 150 Pro yes 5 C6CBG9 0.040.002 50 0.030.002 60 Pro yes...”
- “...A4WA78, A4XF23, A5KUH4, A5V6Z0, A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was...”
DMGD_CHRSD / Q1QT89 D-galactonate dehydratase family member ManD; D-gluconate dehydratase; D-mannonate dehydratase; EC 4.2.1.-; EC 4.2.1.39; EC 4.2.1.8 from Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11) (see paper)
38% identity, 97% coverage
- function: Has low dehydratase activity with D-mannonate and D- gluconate, suggesting that these are not physiological substrates and that it has no significant role in the in vivo degradation of these compounds. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
catalytic activity: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:21612)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...into the active site of the member from Chromohalobacter salexigens ( Cs ManD) (Uniprot ID Q1QT89) that dehydrates both d -mannonate and d -gluconate (PDB code 3BSM). This was accomplished by superposing the structures of Na ManD with d -mannonate in its active site (2QJM), Uniprot...”
- “...-tartaric acid (entry 3V4B), the P317A mutant of promiscuous ManD/GlcD from Chromohalobacter salexigens (Uniprot ID Q1QT89) liganded with Mg 2+ and d -gluconate (entry 3QKF), promiscuous ManD/GlcD/Uniprot ID Q1QT89 from Chromohalobacter salexigens DSM 3043 liganded with Na + , Cl , and glycerol (4F4R), promiscuous ManD/GlcD/Uniprot...”
- Investigating the physiological roles of low-efficiency D-mannonate and D-gluconate dehydratases in the enolase superfamily: pathways for the catabolism of L-gulonate and L-idonate
Wichelecki, Biochemistry 2014 - “...source. However, we were unable to demonstrate a physiological requirement for the ManD (Uniprot entry Q1QT89; Cs ManD 9 ) that catalyzes the dehydration of d -mannonate ( k cat / K M = 5 M 1 s 1 ) and d -gluconate ( k cat...”
RspA / b1581 mandelate racemase/muconate lactonizing enzyme family protein RspA from Escherichia coli K-12 substr. MG1655 (see 5 papers)
RSPA_ECOLI / P38104 Starvation-sensing protein RspA from Escherichia coli (strain K12) (see 2 papers)
rspA / RF|NP_416098 starvation-sensing protein rspA from Escherichia coli K12 (see 6 papers)
b1581 predicted dehydratase from Escherichia coli str. K-12 substr. MG1655
NJ74_RS12400 starvation-sensing protein RspA from Escherichia coli DH5[alpha]
36% identity, 97% coverage
- function: Probably involved in the degradation of homoserine lactone (HSL) or of a metabolite of HSL that signals starvation
- Metabolic shift of Escherichia coli under salt stress in the presence of glycine betaine
Metris, Applied and environmental microbiology 2014 - “...b4014 b4014 b2684 b0678 b1482 b4376 b1896 b1897 b0133 b3403 b1062 b3310 b1581 b2464 b2104 b2465 b0740 b1414 b2898 b3003 b3153 b3011 2 2 2 2 2 2 2 2 2 2 2 2 2...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase
Sutter, Journal of bacteriology 2016 - “...A4XF23), E. coli (GenBank accession number P38104), and Streptomyces coelicolor (GenBank accession number P95726); promiscuous gluconate/ galactonate...”
- Metabolomic and proteomic insights into carbaryl catabolism by Burkholderia sp. C3 and degradation of ten N-methylcarbamates.
Seo, Biodegradation 2013 - “...30/4 Q02755 Sensors/regulators HTH-type transcriptional regulator (PcaQ) 26/4 P0A4T6 Sensors/regulators Starvation sensing protein (RspA) 20/3 P38104 Sensors/regulators, stress GTP pyrophosphokinase (RelA) 35/3 P0AG20 Sensors/regulators, stress ADA regulatory protein (Ada) 51/5 P26189 Sensors/regulators, stress 60 kDa chaperonin 1 (GroL) 46/6 Q00767 Stress Chaperone protein (DnaK) 54/7 Q9L7P1...”
- The Effects and Toxicity of Different Pyrene Concentrations on Escherichia coli Using Transcriptomic Analysis
Zhu, Microorganisms 2024 - “...fold (NJ74_RS00655, NJ74_RS17475, NJ74_RS04535, novel0293, NJ74_RS01070, novel0385, NJ74_RS11870, NJ74_RS08950, NJ74_RS04260, NJ74_RS11935, novel0132, NJ74_RS11920, NJ74_RS09985, NJ74_RS12985, NJ74_RS12400, NJ74_RS10665, novel0325, NJ74_RS07890, NJ74_RS12055, NJ74_RS21540, NJ74_RS17855, NJ74_RS04415, novel0200, NJ74_RS12045, NJ74_RS07895; Table 1 ). With regard to energy metabolism, many genes that were mostly up-regulated in this pathway belong to the...”
- “...NJ74_RS11920 yihR Aldose 1-epimerase NJ74_RS09985 agaV N-acetylgalactosamine PTS system EIIB component NJ74_RS12985 ydiF Acetate CoA-transferase NJ74_RS12400 rspA Mannonate dehydratase NJ74_RS10665 aldA Lactaldehyde dehydrogenase/glycolaldehyde dehydrogenase NJ74_RS09990 kbaZ D-tagatose-1,6-bisphosphate aldolase subunit GatZ/KbaZ novel0325 - Formate dehydrogenase major subunit NJ74_RS07890 gatZ D-tagatose-1,6-bisphosphate aldolase subunit GatZ/KbaZ NJ74_RS12055 rhaB Rhamnulokinase NJ74_RS17855...”
SACE_4937 mandelate racemase/starvation sensing protein from Saccharopolyspora erythraea NRRL 2338
36% identity, 95% coverage
3thuA / Q1NAJ2 Crystal structure of an enolase from sphingomonas sp. Ska58 (efi target efi-501683) with bound mg
38% identity, 98% coverage
- Ligand: magnesium ion (3thuA)
MAND_ESCAT / B1ELW6 D-galactonate dehydratase family member RspA; D-mannonate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.8 from Escherichia albertii (strain TW07627) (see paper)
36% identity, 97% coverage
- function: Has low D-mannonate dehydratase activity (in vitro), suggesting that this is not a physiological substrate and that it has no significant role in D-mannonate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro yes 4 Q8FHC7 0.020.001 10 Pro yes 4 A4WA78 0.020.002 30 Pro yes 4 B1ELW6 0.020.001 20 Pro yes 4 D8ADB5 0.010.002 30 Pro yes 4 J7KNU2 0.010.001 20 Pro yes 4 B5RAG0 0.010.001 50 Pro yes 5 D4GJ14 0.040.003 120 Pro yes 5 B5R541...”
- “...following UniProt accession IDs: A4W7D6, A4WA78, A4XF23, A5KUH4, A5V6Z0, A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8,...”
3v3wA / B3PDB1 Crystal structure of an enolase from the soil bacterium cellvibrio japonicus (target efi-502161) with bound mg and glycerol
37% identity, 98% coverage
- Ligand: magnesium ion (3v3wA)
MAND_ECOMS / D8ADB5 D-galactonate dehydratase family member RspA; D-mannonate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.8 from Escherichia coli (strain MS 21-1) (see paper)
36% identity, 94% coverage
- function: Has low D-mannonate dehydratase activity (in vitro), suggesting that this is not a physiological substrate and that it has no significant role in D-mannonate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Cultivation of marine bacteria of the SAR202 clade.
Lim, Nature communications 2023 - “...The four proteins that have been studied experimentally are indicated with black rectangles (UniProt ID: D8ADB5, C9A1P5, C6CBG9, and A8RQK7). We analyzed sequence divergence among the 80 COG4948 proteins of the JH545 genome by building a sequence similarity network (SSN) using the Enzyme Function Initiatives Enzyme...”
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro yes 4 A4WA78 0.020.002 30 Pro yes 4 B1ELW6 0.020.001 20 Pro yes 4 D8ADB5 0.010.002 30 Pro yes 4 J7KNU2 0.010.001 20 Pro yes 4 B5RAG0 0.010.001 50 Pro yes 5 D4GJ14 0.040.003 120 Pro yes 5 B5R541 0.050.003 80 Pro yes 5 B5QBD4...”
- “...B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and three cooperative agreements from the U.S. National Institutes...”
MAND_CELJU / B3PDB1 D-galactonate dehydratase family member RspA; D-mannonate dehydratase; Starvation sensing protein RspA homolog; EC 4.2.1.-; EC 4.2.1.8 from Cellvibrio japonicus (strain Ueda107) (Pseudomonas fluorescens subsp. cellulosa) (see paper)
37% identity, 97% coverage
- function: Has low D-mannonate dehydratase activity (in vitro), suggesting that this is not a physiological substrate and that it has no significant role in D-mannonate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...3 A6VRA1 0.020.001 160 Ala yes 3 E1V4Y0 0.030.006 20 0.050.004 20 Pro yes 3 B3PDB1 0.030.002 100 Ala yes 3 Cs ManD/Q1QT89 0.020.0005 5 0.040.006 40 Pro yes 4 Q8FHC7 0.020.001 10 Pro yes 4 A4WA78 0.020.002 30 Pro yes 4 B1ELW6 0.020.001 20 Pro...”
- “...2+ , Cl , CO 3 2 , and glycerol (entry 3VCN), low-activity ManD/Uniprot ID B3PDB1 from Cellvibrio japonicus Ueda107 liganded with Mg 2+ , Cl , 2-[ N -cyclohexylamino]ethane sulfonic acid, and glycerol (entry 3V3W), low-activity ManD/Uniprot ID B3PDB1 from Cellvibrio japonicus Ueda107 liganded with...”
MAND_SPHSS / Q1NAJ2 D-mannonate dehydratase; ManD; EC 4.2.1.8 from Sphingomonas sp. (strain SKA58) (see paper)
38% identity, 98% coverage
- function: Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro yes Singleton D9UNB2 0.0040.001 60 Pro yes 8 D7BPX0 0.010.002 40 Pro no 2 Q1NAJ2 20.07 4200 Ala no 2 Q9AAR4 10.006 12300 Ala no 2 Q9A4L8 0.650.02 1200 Ala no 2 B0T4L2 0.30.01 1200 Ala no 2 B0T0B1 20.2 12100 0.0030.001 5 Ala no...”
- “...enterica serovar Enteritidis str. P125109 liganded with Cl and glycerol (entry 3TWB), high-activity ManD/Uniprot ID Q1NAJ2 from Sphingomonas sp. SKA58 liganded with Mg 2+ , Cl , and glycerol (entry 3THU), no-activity protein/Uniprot ID A5KUH4 from Vibrionales bacterium liganded with Mg 2+ , and glycerol (entry...”
MAND1_CAUVC / Q9A4L8 D-mannonate dehydratase CC2812; ManD; EC 4.2.1.8 from Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15) (Caulobacter crescentus) (see paper)
YP_002518276 bifunctional D-altronate/D-mannonate dehydratase from Caulobacter vibrioides NA1000
CC2812 mandelate racemase / muconate lactonizing enzyme family from Caulobacter crescentus CB15
37% identity, 98% coverage
- function: Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Identification of the in vivo function of the high-efficiency D-mannonate dehydratase in Caulobacter crescentus NA1000 from the enolase superfamily.
Wichelecki, Biochemistry 2014 - GeneRIF: the ManD activity of B8H1R9 is essential for the metabolic function that is currently unknown.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro no 2 Q1NAJ2 20.07 4200 Ala no 2 Q9AAR4 10.006 12300 Ala no 2 Q9A4L8 0.650.02 1200 Ala no 2 B0T4L2 0.30.01 1200 Ala no 2 B0T0B1 20.2 12100 0.0030.001 5 Ala no 2 A5V6Z0 40.2 2900 0.010.001 10 Ala no 2 Na ManD/A4XF23 1.30.1...”
- “...C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and three cooperative agreements from the U.S. National Institutes of Health (P01GM071790, U54GM093342, U54GM074945, and U54GM094662). Molecular graphics and...”
- Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media
Hottes, Journal of bacteriology 2004 - “...xylosidase/arabinosidase, xylB CC2811, -glucuronidasea,c CC2812, mandelate racemase/muconatelactonizing enzyme familyc CC3054, xylosidase/arabinosidase, xarBa,c...”
MAND_MARMS / A6VRA1 D-galactonate dehydratase family member Mmwyl1_0037; D-mannonate dehydratase; EC 4.2.1.-; EC 4.2.1.8 from Marinomonas sp. (strain MWYL1) (see paper)
36% identity, 97% coverage
- function: Has low D-mannonate dehydratase activity (in vitro), suggesting that this is not a physiological substrate and that it has no significant role in D-mannonate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...Pro yes Singleton C6CVY9 Gly yes Singleton C9A1P5 Pro yes Singleton B5GCP6 Pro no 3 A6VRA1 0.020.001 160 Ala yes 3 E1V4Y0 0.030.006 20 0.050.004 20 Pro yes 3 B3PDB1 0.030.002 100 Ala yes 3 Cs ManD/Q1QT89 0.020.0005 5 0.040.006 40 Pro yes 4 Q8FHC7 0.020.001...”
- “...of proteins with the following UniProt accession IDs: A4W7D6, A4WA78, A4XF23, A5KUH4, A5V6Z0, A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89,...”
MSMEG_2909 starvation-sensing protein RspA from Mycobacterium smegmatis str. MC2 155
37% identity, 98% coverage
- Dynamic Transcriptional Landscape of Mycobacterium smegmatis under Cold Stress
Grigorov, International journal of molecular sciences 2023 - “...by qRT-PCR. The results confirmed that the transcription profiles of the selected genes (MSMEG_0158, MSMEG_1972, MSMEG_2909, MSMEG_3722, MSMEG_4793, and MSMEG_6159) obtained by qRT-PCR ( Figure 5 a) coincided with those obtained by RNA-seq ( Figure 5 b). To reveal the functional enrichment of genes in the...”
MAND2_CAUSK / B0T4L2 D-mannonate dehydratase Caul1835; ManD; EC 4.2.1.8 from Caulobacter sp. (strain K31) (see paper)
37% identity, 97% coverage
- function: Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Ala no 2 Q9AAR4 10.006 12300 Ala no 2 Q9A4L8 0.650.02 1200 Ala no 2 B0T4L2 0.30.01 1200 Ala no 2 B0T0B1 20.2 12100 0.0030.001 5 Ala no 2 A5V6Z0 40.2 2900 0.010.001 10 Ala no 2 Na ManD/A4XF23 1.30.1 3200 Ala no 7 G7TAD9 0.80.03...”
- “...the following UniProt accession IDs: A4W7D6, A4WA78, A4XF23, A5KUH4, A5V6Z0, A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7,...”
P95726 SpaA protein from Streptomyces coelicolor
39% identity, 95% coverage
MAND2_CAUVC / Q9AAR4 D-mannonate dehydratase CC0532; ManD; EC 4.2.1.8 from Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15) (Caulobacter crescentus) (see paper)
A0A0H3C643 mannonate dehydratase (EC 4.2.1.8) from Caulobacter vibrioides (see paper)
4gmeA / Q9AAR4 Crystal structure of mannonate dehydratase (target efi-502209) from caulobacter crescentus cb15 complexed with magnesium and d-mannonate
YP_002515939 mannonate dehydratase from Caulobacter vibrioides NA1000
CC0532 mandelate racemase/muconate lactonizing enzyme family from Caulobacter crescentus CB15
36% identity, 97% coverage
- function: Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Ligands: magnesium ion; carbonate ion (4gmeA)
- Identification of the in vivo function of the high-efficiency D-mannonate dehydratase in Caulobacter crescentus NA1000 from the enolase superfamily.
Wichelecki, Biochemistry 2014 - GeneRIF: the in vivo functional characterization of a high-efficiency ManD from Caulobacter crescentus NA1000 by in vivo discovery of its essential role in d-glucuronate metabolism. This in vivo functional annotation may be extended to ~50 additional proteins.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...Pro yes 8 D7BPX0 0.010.002 40 Pro no 2 Q1NAJ2 20.07 4200 Ala no 2 Q9AAR4 10.006 12300 Ala no 2 Q9A4L8 0.650.02 1200 Ala no 2 B0T4L2 0.30.01 1200 Ala no 2 B0T0B1 20.2 12100 0.0030.001 5 Ala no 2 A5V6Z0 40.2 2900 0.010.001 10...”
- “...D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and three cooperative agreements from the U.S. National Institutes of Health (P01GM071790, U54GM093342, U54GM074945, and U54GM094662). Molecular graphics and analyses were...”
- Role of the extracytoplasmic function sigma factor RpoE4 in oxidative and osmotic stress responses in Rhizobium etli
Martínez-Salazar, Journal of bacteriology 2009 - “...in S. meliloti and to CC3475, CC3476, CC3477, CC0938, CC0532, and CC2626 in C. crescentus, respectively. In addition, between the R. etli RpoE4 and S. meliloti...”
DGD_STRBB / D7BPX0 D-galactonate dehydratase family member SBI_01856; D-gluconate dehydratase; EC 4.2.1.-; EC 4.2.1.39 from Streptomyces bingchenggensis (strain BCW-1) (see paper)
36% identity, 95% coverage
- function: Has low D-gluconate dehydratase activity (in vitro), suggesting that it has no significant role in D-gluconate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:21612)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...5 C6CBG9 0.040.002 50 0.030.002 60 Pro yes Singleton D9UNB2 0.0040.001 60 Pro yes 8 D7BPX0 0.010.002 40 Pro no 2 Q1NAJ2 20.07 4200 Ala no 2 Q9AAR4 10.006 12300 Ala no 2 Q9A4L8 0.650.02 1200 Ala no 2 B0T4L2 0.30.01 1200 Ala no 2 B0T0B1...”
- “...B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and three cooperative agreements from the U.S. National...”
MAND_RHIWR / A5V6Z0 D-mannonate dehydratase; ManD; EC 4.2.1.8 from Rhizorhabdus wittichii (strain DSM 6014 / CCUG 31198 / JCM 15750 / NBRC 105917 / EY 4224 / RW1) (Sphingomonas wittichii) (see paper)
38% identity, 97% coverage
- function: Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...2 B0T4L2 0.30.01 1200 Ala no 2 B0T0B1 20.2 12100 0.0030.001 5 Ala no 2 A5V6Z0 40.2 2900 0.010.001 10 Ala no 2 Na ManD/A4XF23 1.30.1 3200 Ala no 7 G7TAD9 0.80.03 4400 Ala no Divergence in Activity Members with different in vitro activities are assumed...”
- “...vitro enzymatic activities of proteins with the following UniProt accession IDs: A4W7D6, A4WA78, A4XF23, A5KUH4, A5V6Z0, A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9,...”
MAND_XANOB / G7TAD9 D-mannonate dehydratase; ManD; EC 4.2.1.8 from Xanthomonas oryzae pv. oryzicola (strain BLS256) (see paper)
36% identity, 93% coverage
- function: Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...A5V6Z0 40.2 2900 0.010.001 10 Ala no 2 Na ManD/A4XF23 1.30.1 3200 Ala no 7 G7TAD9 0.80.03 4400 Ala no Divergence in Activity Members with different in vitro activities are assumed to have different in vivo functions. Physiologically, the dehydration of d -mannonate to 2-keto-3-deoxy- d...”
- “...C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and three cooperative agreements from the U.S. National Institutes of Health (P01GM071790,...”
IMAND_OCEGH / Q2CIN0 D-galactonate dehydratase family member OG2516_05608 from Oceanicola granulosus (strain ATCC BAA-861 / DSM 15982 / KCTC 12143 / HTCC2516) (see paper)
38% identity, 96% coverage
- function: Has no detectable activity with D-mannonate and with a panel of 70 other acid sugars (in vitro), in spite of the conservation of the residues that are expected to be important for catalytic activity and cofactor binding. May have evolved a divergent function.
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki, Biochemistry 2014 - “...Pro yes 9 C8ZZN2 Pro yes 10 C7PW26 Pro no Singleton A6M2W4 Pro yes Singleton Q2CIN0 Pro yes Singleton A8RQK7 Pro yes Singleton C6CVY9 Gly yes Singleton C9A1P5 Pro yes Singleton B5GCP6 Pro no 3 A6VRA1 0.020.001 160 Ala yes 3 E1V4Y0 0.030.006 20 0.050.004 20...”
- “...C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2, E1V4Y0, G7TAD9, J7KNU2, Q1NAJ2, Q1QT89, Q2CIN0, Q6DAR4, Q8FHC7, Q9A4L8, and Q9AAR4. This research was supported by a program project grant and three cooperative agreements from the U.S. National Institutes of Health (P01GM071790, U54GM093342, U54GM074945, and U54GM094662)....”
MAND_NOVAD / A4XF23 D-mannonate dehydratase; ManD; RspA homolog; EC 4.2.1.8 from Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199) (see 2 papers)
2qjjA / A4XF23 Crystal structure of d-mannonate dehydratase from novosphingobium aromaticivorans (see paper)
36% identity, 97% coverage
- function: Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro).
catalytic activity: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:20097)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Homotetramer. - Ligand: magnesium ion (2qjjA)
- Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase
Sutter, Journal of bacteriology 2016 - “...from Novosphingobium aromaticivorans (UniProt accession number A4XF23), E. coli (GenBank accession number P38104), and Streptomyces coelicolor (GenBank...”
- Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
Wichelecki, Biochemistry 2014 - “...d -mannonate to 2-keto-3-deoxy- d -mannonate (equivalently, 2-keto-3-deoxy- d -gluconate) (EC 4.2.1.8 and Unitprot ID A4XF23). The Mg 2+ -binding residues located at the ends of the third, fourth, and fifth -strands are Asp 210, Glu 236, and Glu 262, respectively. The general base that abstracts...”
- “...of in vitro enzymatic activities of proteins with the following UniProt accession IDs: A4W7D6, A4WA78, A4XF23, A5KUH4, A5V6Z0, A6AMN2, A6M2W4, A6VRA1, A8RQK7, B0T0B1, B0T4L2, B1ELW6, B3PDB1, B5GCP6, B5QBD4, B5R541, B5RAG0, B8HCK2, C6CBG9, C6CVY9, C6DI84, C7PW26, C8ZZN2, C9A1P5, C9CN91, C9NUM5, C9Y5D5, D0KC90, D0X4R4, D4GJ14, D7BPX0, D8ADB5, D9UNB2,...”
3rraB / B2UCA8 Crystal structure of enolase prk14017 (target efi-500653) from ralstonia pickettii 12j with magnesium bound
31% identity, 86% coverage
- Ligand: magnesium ion (3rraB)
SPC_3914 galactonate dehydratase from Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
29% identity, 93% coverage
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...galactose-1-phosphate uridylyltransferase ( SPC_0771 ), an UDP-galactose 4-epimerase ( SPC_0772 ), a galactonate dehydratase ( SPC_3914 ), and a 2-oxo-3-deoxygalactonate kinase ( SPC_3916 ). Among these, notably, the expression of alpha-galactosidase ( SPC_4361 ) was strongly inhibited (0.009-fold) ( p < 0.05), which is an exoglycosidase...”
- “...SPC_4361 0.009 Alpha-galactosidase SPC_0771 0.051 Galactose-1-phosphate uridylyltransferase SPC_0772 0.087 UDP-galactose 4-epimerase SPC_3916 0.199 2-oxo-3-deoxygalactonate kinase SPC_3914 0.397 Galactonate dehydratase SPC_2404 2.237 6-phosphofructokinase isozyme SPC_1977 2.93 Glucose-1-phosphate uridylyltransferase SPC_1252 32.911 Glucokinase plants-12-00890-t005_Table 5 Table 5 The major altered metabolic pathways in S. aureus ATCC25923 mediated by Fragment...”
YidU / b4478 D-galactonate dehydratase (EC 4.2.1.140; EC 4.2.1.6) from Escherichia coli K-12 substr. MG1655 (see 5 papers)
dgoD / Q6BF17 D-galactonate dehydratase (EC 4.2.1.140) from Escherichia coli (strain K12) (see 5 papers)
DGOD_ECOLI / Q6BF17 D-galactonate dehydratase; GalD; EC 4.2.1.6 from Escherichia coli (strain K12) (see 3 papers)
Q6BF17 galactonate dehydratase (EC 4.2.1.6) from Escherichia coli (see paper)
dgoD / RF|YP_026237 D-galactonate dehydratase; EC 4.2.1.6 from Escherichia coli K12 (see 6 papers)
YP_026237 D-galactonate dehydratase from Escherichia coli str. K-12 substr. MG1655
NJ74_RS04415 galactonate dehydratase from Escherichia coli DH5[alpha]
29% identity, 88% coverage
- function: Catalyzes the dehydration of D-galactonate to 2-keto-3-deoxy- D-galactonate.
catalytic activity: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O (RHEA:18649)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
disruption phenotype: Deletion mutant cannot grow on D-galactonate. - A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids.
Babbitt, Science (New York, N.Y.) 1995 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on complete protein
- The Effects and Toxicity of Different Pyrene Concentrations on Escherichia coli Using Transcriptomic Analysis
Zhu, Microorganisms 2024 - “...NJ74_RS11870, NJ74_RS08950, NJ74_RS04260, NJ74_RS11935, novel0132, NJ74_RS11920, NJ74_RS09985, NJ74_RS12985, NJ74_RS12400, NJ74_RS10665, novel0325, NJ74_RS07890, NJ74_RS12055, NJ74_RS21540, NJ74_RS17855, NJ74_RS04415, novel0200, NJ74_RS12045, NJ74_RS07895; Table 1 ). With regard to energy metabolism, many genes that were mostly up-regulated in this pathway belong to the sulfate reduction pathway and are regulated via...”
- “...gatZ D-tagatose-1,6-bisphosphate aldolase subunit GatZ/KbaZ NJ74_RS12055 rhaB Rhamnulokinase NJ74_RS17855 fadB 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase/3-hydroxybutyryl-CoA epimerase/enoyl-CoA isomerase NJ74_RS04415 dgoD Galactonate dehydratase NJ74_RS12045 rhaD Rhamnulose-1-phosphate aldolase NJ74_RS07895 gatY Tagatose 1,6-diphosphate aldolase GatY/KbaY novel0200 - Fumarate reductase flavoprotein subunit...”
STM3828 galactonate dehydratase in bifunctional: 2-oxo-3-deoxygalactonate 6-phosphate aldolase and galactonate dehydratase from Salmonella typhimurium LT2
SEN3644 galactonate dehydratase (ec 4.1.2.21) (ec 4.2.1.6) from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
29% identity, 93% coverage
- Mapping and regulation of genes within Salmonella pathogenicity island 12 that contribute to in vivo fitness of Salmonella enterica Serovar Typhimurium
Tomljenovic-Berube, Infection and immunity 2013 - “...1.63E22 1.83E15 2.07E20 4.71E43 3.41E23 1.05E16 2.49E12 STM1214 STM3828 STM0701 STM0152 ycfR dgoA speF aceE 3.18 3.17 3.12 3.06 3.53E09 2.88E39 2.87E76 1.88E108...”
- Salmonella serovar identification using PCR-based detection of gene presence and absence
Arrach, Journal of clinical microbiology 2008 - “...STM3775, STM3780, STM3782, STM3822, STM3823, STM3826, STM3828, STM3831, STM3833, STM3834, STM3860, STM4012, STM4032, STM4046, STM4052, STM4067, STM4068,...”
- Global Gene-expression Analysis of the Response of Salmonella Enteritidis to Egg White Exposure Reveals Multiple Egg White-imposed Stress Responses
Baron, Frontiers in microbiology 2017 - “...isomerase A 3.01 2.24 2.15 tktA Transketolase 2.94 2.91 3.17 D-GALACTONATE UTILIZATION dgoA D-galactonate dehydratase (SEN3644) 5.87 26.22 24.85 dgoD 2-dehydro-3-deoxy-6-phosphogalactonate aldolase (SEN3645) 6.67 23.93 22.03 dgoK 2-dehydro-3-deoxygalactonokinase 9.47 34.35 31.13 dgoR Galactonate operon transcriptional repressor 8.96 28.70 27.13 dgoT D-galactonate transporter n.s. 10.77 13.59 dkgB...”
Halxa_3608 galactonate dehydratase from Halopiger xanaduensis SH-6
30% identity, 88% coverage
- Complete genome sequence of Halopiger xanaduensis type strain (SH-6(T))
Anderson, Standards in genomic sciences 2012 - “...Galactose is probably metabolized via the De Ley-Doudoroff pathway as a galactonate dehydratase is present (Halxa_3608). Adjacent to this gene are a possible alpha-galactosidase (Halxa_3609) and a kinase and aldolase that may take part in this pathway (Halxa_3607, Halxa_3606). Xylose utilization appears to be via the...”
HVO_A0331 mandelate racemase/muconate lactonizing enzyme family protein from Haloferax volcanii DS2
30% identity, 90% coverage
Hlac_2866 Mandelate racemase/muconate lactonizing protein from Halorubrum lacusprofundi ATCC 49239
30% identity, 93% coverage
- Cloning, overexpression, purification, and characterization of a polyextremophilic β-galactosidase from the Antarctic haloarchaeon Halorubrum lacusprofundi
Karan, BMC biotechnology 2013 - “...sugar transport system permease component; Hlac_2864, sugar permease; Hlac_2865, ABC-type sugar transport system; ATPase component; Hlac_2866, L-alanine-DL-glutamate epimerase and related enzymes of enolase; Hlac_2867, short-chain dehydrogenase/reductase SDR; Hlac_2868, -galactosidase; Hlac_2869, -galactosidase; Hlac_2870, sugar kinase, and Hlac_2871 and 2872, IS200 family and IS605 OrB family transposases. The...”
- Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes
Anderson, PloS one 2011 - “...and aldolase (Hlac_2860) are close on the chromosome to each other and to galactonate dehydratase (Hlac_2866), beta-galactosidase (Hlac_2868), and a probable alpha-galactosidase (Hlac_2869), suggesting that the kinase and aldolase may be involved in the utilization of galactose via the De Ley-Doudoroff pathway. Similarly, H. volcanii has...”
BPHYT_RS16405 galactonate dehydratase [EC: 4.2.1.6] from Burkholderia phytofirmans PsJN
28% identity, 98% coverage
- mutant phenotype: Specifically important for: D-Galactose. galactonate is an intermediate in galactose oxidation
RHE_RS18905 galactonate dehydratase from Rhizobium etli CFN 42
29% identity, 93% coverage
- Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network
Taboada-Castro, Frontiers in microbiology 2022 - “...enzyme dgoD , galactonate dehydratase [EC:4.2.1.6] for catalysis of D-galactonate to 2-dehydro-3-deoxy-D-galactonate in MM the RHE_RS18905 and in bacteroid RHE_RS24515 proteins were expressed ( Table 1 ), showing multiplicity for two different enzymes of the same pathway. These data showed that the same enzymatic reactions are...”
- “...transport system ATP-binding protein K02031 Bacteroid RHE_RS28270 ddpD; peptide/nickel transport system ATP-binding protein K01684 MM RHE_RS18905 dgoD; galactonate dehydratase [EC:4.2.1.6] K01684 Bacteroid RHE_RS24515 dgoD; galactonate dehydratase [EC:4.2.1.6] K00064 MM RHE_RS02500 E1.1.1.122; D-threo-aldose 1-dehydrogenase [EC:1.1.1.122] K00064 Bacteroid RHE_RS28605 E1.1.1.122; D-threo-aldose 1-dehydrogenase [EC:1.1.1.122] K01092 MM RHE_RS17960 E3.1.3.25, IMPA,...”
CH_124262 putative galactonate dehydratase from Magnaporthe grisea 70-15 (see 2 papers)
26% identity, 98% coverage
C9ZDW7 Putative dehydratase from Streptomyces scabiei (strain 87.22)
28% identity, 92% coverage
Pc12g13310 uncharacterized protein from Penicillium rubens
26% identity, 98% coverage
CIRMBP1228_02728 galactonate dehydratase from Enterococcus cecorum
26% identity, 98% coverage
ABD05_RS19805 mandelate racemase/muconate lactonizing enzyme family protein from Burkholderia pyrrocinia
27% identity, 88% coverage
G3YE52 galactonate dehydratase (EC 4.2.1.6) from Aspergillus niger (see paper)
26% identity, 96% coverage
G3Y8T6 galactonate dehydratase (EC 4.2.1.6) from Aspergillus niger (see paper)
26% identity, 93% coverage
VT47_09395 galactonate dehydratase from Pseudomonas syringae pv. syringae
28% identity, 86% coverage
PSHAa0287 putative mandelate racemase/muconate lactonizing enzyme family from Pseudoalteromonas haloplanktis TAC125
26% identity, 91% coverage
RL3858 putative mandelate racemase/muconate lactonising family protein from Rhizobium leguminosarum bv. viciae 3841
30% identity, 92% coverage
RHE_RS24515 mandelate racemase/muconate lactonizing enzyme family protein from Rhizobium etli CFN 42
29% identity, 92% coverage
- Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network
Taboada-Castro, Frontiers in microbiology 2022 - “...dehydratase [EC:4.2.1.6] for catalysis of D-galactonate to 2-dehydro-3-deoxy-D-galactonate in MM the RHE_RS18905 and in bacteroid RHE_RS24515 proteins were expressed ( Table 1 ), showing multiplicity for two different enzymes of the same pathway. These data showed that the same enzymatic reactions are performed in MM and...”
- “...ddpD; peptide/nickel transport system ATP-binding protein K01684 MM RHE_RS18905 dgoD; galactonate dehydratase [EC:4.2.1.6] K01684 Bacteroid RHE_RS24515 dgoD; galactonate dehydratase [EC:4.2.1.6] K00064 MM RHE_RS02500 E1.1.1.122; D-threo-aldose 1-dehydrogenase [EC:1.1.1.122] K00064 Bacteroid RHE_RS28605 E1.1.1.122; D-threo-aldose 1-dehydrogenase [EC:1.1.1.122] K01092 MM RHE_RS17960 E3.1.3.25, IMPA, suhB; myo-inositol-1(or 4)-monophosphatase [EC:3.1.3.25] K01092 MM RHE_RS22570...”
STM14_2807 mandelate racemase/muconate lactonizing enzyme family protein from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STM2273 putative dehydratase protein from Salmonella typhimurium LT2
24% identity, 94% coverage
- Integrative DNA methylome and transcriptome analysis reveals DNA adenine methylation is involved in Salmonella enterica Typhimurium response to oxidative stress
Zhang, Microbiology spectrum 2023 - “...Hypothetical protein STM14_1904 STM14_2065 0.83 0.04 Hypothetical protein STM14_2065 STM14_2272 0.98 0.00066 Phage-tail assembly-like protein STM14_2807 0.77 0.044 Putative dehydratase STM14_3294 smpB 0.89 0.007 SsrA-binding protein STM14_3338 fljB 0.78 0.038 Flagellin STM14_4269 0.83 0.022 Hypothetical protein STM14_4269 STM14_5330 cybC 0.94 0.0049 Cytochrome b562 STM14_0076 0.88 0.024...”
- Genetic Determinants in Salmonella enterica Serotype Typhimurium Required for Overcoming In Vitro Stressors in the Mimicking Host Environment
Mandal, Microbiology spectrum 2021 - “...for either in vitro or in vivo systemic infection were STM14_1138, STM14_4880, STM14_4992, STM14_5184, STM14_2759, STM14_2807, STM14_3334, STM14_4825, STM14_5299, and STM14_5300. CONCLUSION A recent study by Kroger et al. presented transcriptomes of S. Typhimurium under 22 distinct infection-relevant environmental conditions in vitro . The study found...”
- Evolution of Variable Number Tandem Repeats and Its Relationship with Genomic Diversity in Salmonella Typhimurium
Fu, Frontiers in microbiology 2016 - “...Propanediol diffusion facilitator Y D L2187 yehU STM2159 Two component sensor kinase G D L2183 STM2273 Dehydratase G R L2187 asrC STM2550 Anaerobic sulfite reductase subunit C I S L2173 STM2767 DNA/RNA helicase E G L2179/2182 iroC STM2774 ABC transporter ATP-binding protein D G L2174 STM2922...”
- An allele of gyrA prevents Salmonella enterica serovar Typhimurium from using succinate as a carbon source
Schmitz, Journal of bacteriology 2006 - “...strains with insertions in rcsB, yojN, apbE, ompC, STM2273, STM2274, or STM2275 generated two phenotypic classes (Suc and Suc) when the succinate-negative...”
- Characterization of Salmonella enterica subspecies I genovars by use of microarrays
Porwollik, Journal of bacteriology 2004 - “...to STM0042, STM0649 to STM0652, STM2132 to STM2135, STM2273 to STM2275, STM2573 to STM2575, and STM3547 to STM3550. All six operons are probably involved...”
4e6mA / Q8ZNH1 Crystal structure of putative dehydratase protein from salmonella enterica subsp. Enterica serovar typhimurium (salmonella typhimurium)
24% identity, 94% coverage
- Ligand: magnesium ion (4e6mA)
HVO_A0267 mandelate racemase/muconate lactonizing enzyme family protein from Haloferax volcanii DS2
27% identity, 89% coverage
SSO26655 / Q97VG1 D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (see paper)
SSO2665 mandelate racemase/muconate lactonizing enzyme family protein from Saccharolobus solfataricus P2
SSO2665 Muconate cycloisomerase related protein from Sulfolobus solfataricus P2
28% identity, 92% coverage
- Structure and function of aldopentose catabolism enzymes involved in oxidative non-phosphorylative pathways
Ren, Biotechnology for biofuels and bioproducts 2022 - “...], while Sso3124 S. solfataricus dehydratase [ 30 ] participates in d -arabinose degradation, and Sso2665 S. solfataricus dehydratase participates in degradation of d -xylonate and l -arabinonate [ 37 ]. Based on sequence comparison, it can be predicted that archaeal aldopentonate dehydratases contain a typical...”
- “...7 -barrel. Both H. volcanii and Sso3124 S. solfataricus dehydratases are characterized as homo-octamers, whereas Sso2665 S. solfataricus dehydratase is active as a tetramer [ 30 , 69 ]. The N-terminal domain is primarily responsible for determining substrate specificity and the C-terminal domain is responsible for...”
- Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation
Bräsen, Microbiology and molecular biology reviews : MMBR 2014 - “...identified, i.e., xylonate dehydratase (XAD) (putatively SSO2665) and arbinonate dehydratase (AraD; SSO3124) (see below) (291). Sequence comparison revealed...”
- “...The enzyme was proposed to be encoded by SSO2665, although the coding function has not clearly been demonstrated (291). The D-arabinonate dehydratase (SSO3124)...”
B3Q5L5 Putative racemase protein from Rhizobium etli (strain CIAT 652)
RHECIAT_PC0000418 putative racemase protein from Rhizobium etli CIAT 652
27% identity, 92% coverage
araD / Q97U96 D-arabinonate dehydratase subunit (EC 4.2.1.5) from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (see paper)
ARAD_SACS2 / Q97U96 Arabinonate dehydratase; EC 4.2.1.5 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (Sulfolobus solfataricus) (see paper)
Q97U96 Arabinonate dehydratase (EC 4.2.1.5) from Saccharolobus solfataricus (see paper)
SSO3124 Mandelate racemase /muconate lactonizing enzyme related protein (MR/MLE) from Sulfolobus solfataricus P2
SSO3124 arabinonate dehydratase from Saccharolobus solfataricus P2
26% identity, 88% coverage
- function: Catalyzes the dehydration of D-arabinonate to 2-keto-3-deoxy- D-arabinonate. Participates in a pentose oxidation pathway that converts D-arabinonate to 2-oxoglutarate.
catalytic activity: D-arabinonate = 2-dehydro-3-deoxy-D-arabinonate + H2O (RHEA:21836)
cofactor: Mg(2+)
subunit: Homooctamer. - Structure and function of aldopentose catabolism enzymes involved in oxidative non-phosphorylative pathways
Ren, Biotechnology for biofuels and bioproducts 2022 - “...H. volcanii is reported to catalyze d -xylonate and d -gluconate [ 69 ], while Sso3124 S. solfataricus dehydratase [ 30 ] participates in d -arabinose degradation, and Sso2665 S. solfataricus dehydratase participates in degradation of d -xylonate and l -arabinonate [ 37 ]. Based on...”
- “...a C-terminal modified TIM-barrel domain, known as a (/) 7 -barrel. Both H. volcanii and Sso3124 S. solfataricus dehydratases are characterized as homo-octamers, whereas Sso2665 S. solfataricus dehydratase is active as a tetramer [ 30 , 69 ]. The N-terminal domain is primarily responsible for determining...”
- Novel non-phosphorylative pathway of pentose metabolism from bacteria
Watanabe, Scientific reports 2019 - “...II pathway from S. solfataricus 19 , 20 , D-arabinose 1-dehydrogenase (SSO1300) and D-arabinonate dehydratase (SSO3124) belong to the medium-chain dehydrogenase/reductase (COG1063) and enolase superfamilies (cd00308), respectively, which differ from bacteria (Fig. 1c ), indicating their convergent evolution. The archaeal D-arabinose pathway partially overlaps with the...”
- Metabolic reconstruction and experimental verification of glucose utilization in Desulfurococcus amylolyticus DSM 16532
Reischl, Folia microbiologica 2018 - “...et al. 2006 ) and genes for arabinose degradation found in S. solfataricus , e.g., SSO3124, SSO3117 and SSO3118 (Peng et al. 2011 ) or SSO3107, SSO1303 (Brouns et al. 2006 ), could not be detected in the genome of D. amylolyticus . Only a homolog...”
- Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation
Bräsen, Microbiology and molecular biology reviews : MMBR 2014 - “...(XAD) (putatively SSO2665) and arbinonate dehydratase (AraD; SSO3124) (see below) (291). Sequence comparison revealed that SsoGAD (GnaD) belongs to the...”
- “...clearly been demonstrated (291). The D-arabinonate dehydratase (SSO3124) from Sul. solfataricus (SsoAraD) seems to be specific for D-arabinose degradation. The...”
- D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii
Johnsen, The Journal of biological chemistry 2009 - “...also includes the archaeal D-arabinoate dehydratase, araD (SSO3124), from S. solfataricus, as well as characterized and putative archaeal gluconate dehydratases...”
- “...SSO3198; GAD of S. solfataricus, Pto0485, P. torridus, SSO3124, AraD of S. solfataricus. homologous genes in sugar utilizputative orthologs in S. solfataricus...”
Atu4196 hypothetical protein from Agrobacterium tumefaciens str. C58 (Cereon)
A9CG74 Mandelate racemase/muconate lactonizing enzyme C-terminal domain-containing protein from Agrobacterium fabrum (strain C58 / ATCC 33970)
26% identity, 98% coverage
- Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58
Groninger-Poe, Biochemistry 2014 - “...library of 77 acid sugars for high-throughput screening, one protein (UniProt entry A9CG74; locus tag Atu4196) showed activity with both m- galactarate and d -galacturonate. Two families of galactarate dehydratases had been discovered previously in the ENS, GalrD/TalrD [Yew, W. S., et al. (2007) Biochemistry 46...”
- “...describe the assignment of the in vitro enzymatic activity to UniProt entry A9CG74 (locus tag Atu4196), a functionally uncharacterized member of the MR subgroup, which is encoded by the A. tumefaciens C58 genome. Screening of A9CG74 with a library of acid sugars and a semicarbazide assay...”
- Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58
Groninger-Poe, Biochemistry 2014 - “...dehydratases. Using a library of 77 acid sugars for high-throughput screening, one protein (UniProt entry A9CG74; locus tag Atu4196) showed activity with both m- galactarate and d -galacturonate. Two families of galactarate dehydratases had been discovered previously in the ENS, GalrD/TalrD [Yew, W. S., et al....”
- “...1154611558]; these have different active site acid/base catalysis and have no activity with d -galacturonate. A9CG74 dehydrates m- galactarate to form 2-keto-3-deoxy-galactarate but does not dehydrate d -galacturonate as expected. Instead, when A9CG74 is incubated with d -galacturonate, 3-deoxy- d - xylo -hexarate or 3-deoxy- d...”
B9JNP7 Isomerase protein from Rhizobium rhizogenes (strain K84 / ATCC BAA-868)
Arad_7740 isomerase protein from Agrobacterium radiobacter K84
Arad_7740 galactarate dehydratase from Rhizobium rhizogenes K84
25% identity, 98% coverage
H16_B0217 L-Alanine-DL-glutamate epimerase or related enzyme of enolase superfamily from Ralstonia eutropha H16
Q0K4Q6 L-Alanine-DL-glutamate epimerase or related enzyme of enolase superfamily from Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)
H16_B0217 L-rhamnonate dehydratase from Cupriavidus necator H16
26% identity, 91% coverage
- Characterization of an l-Ascorbate Catabolic Pathway with Unprecedented Enzymatic Transformations
Stack, Journal of the American Chemical Society 2020 - “...catabolism ( Supplementary Table S3 ). 8 In the P. aeruginosa pathway, an ortholog of H16_B0217 (LyxD) catalyzes the dehydration of L-lyxonate to form 2-keto-3-deoxy-L-lyxonate (Kdl). The subsequent dehydration of Kdl is catalyzed by a member (KdlD) of the fumarylacetoacetate hydrolase superfamily (FAH) to form -ketoglutarate...”
- Characterization of an l-Ascorbate Catabolic Pathway with Unprecedented Enzymatic Transformations
Stack, Journal of the American Chemical Society 2020 - “...DhaL, DHA lactonase Q0K1W7 DkgM, DKG mutase Q0K1W5 ClxL, Clyx lactonase Q0K4Q7 ClxD, Clx decarboxylase Q0K4Q6 LyxD, L-lyxonate dehydratase Q0K4R0 KdlD, Kdl dehydratase Q0K4R1 KgsD, Kgs dehydrogenase...”
3rcyF Crystal structure of mandelate racemase/muconate lactonizing enzyme- like protein from roseovarius sp. Tm1035
23% identity, 93% coverage
- Ligands: magnesium ion; alpha-d-ribofuranose (3rcyF)
lyxD / Q9I1Q2 L-lyxonate dehydratase (EC 4.2.1.176) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
Q9I1Q2 L-lyxonate dehydratase (EC 4.2.1.176) from Pseudomonas aeruginosa (see paper)
PA2215 hypothetical protein from Pseudomonas aeruginosa PAO1
DBX28_14890 L-lyxonate dehydratase from Pseudomonas aeruginosa
25% identity, 91% coverage
- A non-classical LysR-type transcriptional regulator PA2206 is required for an effective oxidative stress response in Pseudomonas aeruginosa
Reen, PloS one 2013 - “...hypothetical protein 2.2 PA2206 probable transcriptional regulator 6.4 PA2214 major facilitator superfamily (MFS) transporter 2.2 PA2215 hypothetical protein 3.8 PA2216 hypothetical protein 2.7 PA2426 pvdS sigma factor 5.3 PA2594 hypothetical protein 3.3 PA2761 hypothetical protein 2.2 PA3229 hypothetical protein 3.0 PA3515 hypothetical protein 2.0 PA3516 probable...”
- “...3A ). Furthermore, hydrogen peroxide sensitivity assays revealed comparable zones of inhibition in PA2206 and PA2215 mutants (a PA2214 mutant was not available from the mutant collection), both of which were significantly more sensitive than wild-type ( Table S2 ). Therefore, to investigate whether these loci...”
- PA2663 (PpyR) increases biofilm formation in Pseudomonas aeruginosa PAO1 through the psl operon and stimulates virulence and quorum-sensing phenotypes
Attila, Applied microbiology and biotechnology 2008 (PubMed)- “...molecule transport (PA0326, PA1541, PA1632, PA1971, PA2214, PA2215, PA2678, and PA3407). Phenotype arrays also showed that PA2663 represses growth on D-gluconic...”
- “...porin OprP precursor Heme acquisition protein 4.9 4.0 4.3 PA2215 4.6 PA2678 PA3279 PA3407 4.3 4.3 2.6 oprP hasAp Complete analysis deposited at the NCBI Gene...”
- Integrated Comparative Genomic Analysis and Phenotypic Profiling of Pseudomonas aeruginosa Isolates From Crude Oil
Xu, Frontiers in microbiology 2020 - “...3171792 3173375 CDS aldehyde dehydrogenase [NADP(+)] + 1SD DBX28_14885 3173504 3174499 CDS FAH family protein DBX28_14890 3174527 3175702 CDS L-rhamnonate dehydratase DBX28_14895 3175733 3177055 CDS MFS transporter Difference in RLs Production Among the Three Strains is Not at Genomic Level Our previous study described that three...”
3sjnA / A8H9D1 Crystal structure of enolase spea_3858 (target efi-500646) from shewanella pealeana with magnesium bound
26% identity, 94% coverage
- Ligand: magnesium ion (3sjnA)
Hlac_1300 Mandelate racemase/muconate lactonizing protein from Halorubrum lacusprofundi ATCC 49239
B9LNF4 Mandelate racemase/muconate lactonizing protein from Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34)
24% identity, 86% coverage
- Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase
Sutter, Journal of bacteriology 2016 - “...H. volcanii (HVO_1488) (A), H. lacusprofundi (Hlac_1300), Haloarcula marismortui (rrnAC0575), H. volcanii (HVO_B0038A) (UniProt accession number D4GP40) (B),...”
- “...homologs from the haloarchaea H. lacusprofundi (2 homologs, Hlac_1300 [91%] and Hlac_2242 [77%]) and H. marismortui (rrnAC0575 [88%]) and also to XAD from H....”
- Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi
Liao, Scientific reports 2016 - “...1.7 ns One carbon metabolism Hlac_1238 formate dehydrogenase, alpha subunit (FdhA) 1.5 2.0 Carbohydrate metabolism Hlac_1300 gluconate dehydratase (GnaD) 1.6 ns 2.3 ns Hlac_1672 glyceraldehyde-3-phosphate dehydrogenase, type II (Gap2) 0.4 ns 0.6 ns Hlac_1891 NAD-dependent epimerase/dehydratase (possible glycosylation of S-layer protein) 1.7 ns 1.8 ns Hlac_2371...”
- d-Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species
Johnsen, Journal of bacteriology 2020 (secret)
F8D4H7 Galactonate dehydratase from Halopiger xanaduensis (strain DSM 18323 / JCM 14033 / SH-6)
23% identity, 86% coverage
Atu0270 mandelate racemase / muconate lactonizing enzyme family protein from Agrobacterium tumefaciens str. C58 (Cereon)
26% identity, 94% coverage
4e5tA Crystal structure of a putative mandelate racemase/muconate lactonizing enzyme (target psi-200750) from labrenzia alexandrii dfl- 11
25% identity, 99% coverage
- Ligand: magnesium ion (4e5tA)
RL3864 putative mandelate racemase/muconate lactonising family protein from Rhizobium leguminosarum bv. viciae 3841
26% identity, 92% coverage
2ox4C / Q5NN22 Crystal structure of putative dehydratase from zymomonas mobilis zm4
25% identity, 90% coverage
- Ligand: magnesium ion (2ox4C)
3bjsB / Q120Q7 Crystal structure of a member of enolase superfamily from polaromonas sp. Js666
25% identity, 96% coverage
- Ligand: magnesium ion (3bjsB)
rrnAC0575 mandelate racemase/muconate lactonizing enzyme family from Haloarcula marismortui ATCC 43049
Q5V4G3 Mandelate racemase/muconate lactonizing enzyme family from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
23% identity, 86% coverage
- d-Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species
Johnsen, Journal of bacteriology 2020 (secret) - Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase
Sutter, Journal of bacteriology 2016 - “...(A), H. lacusprofundi (Hlac_1300), Haloarcula marismortui (rrnAC0575), H. volcanii (HVO_B0038A) (UniProt accession number D4GP40) (B), and Halorubrum...”
- “...Hlac_1300 [91%] and Hlac_2242 [77%]) and H. marismortui (rrnAC0575 [88%]) and also to XAD from H. volcanii (HVO_B0038A [76%]). Less sequence identity (about...”
- D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii
Johnsen, The Journal of biological chemistry 2009 - “...found in the sugarutilizing halophiles, H. marismortui, rrnAC0575, and H. lacusprofundi, Hlac_2242, respectively, suggesting functional XAD in these organisms....”
- “...XAD of H. volcanii; Hlac_2242, H. lacusprofundi; rrnAC0575, H. volcanii and its comparison with marismortui, SSO3198; GAD of S. solfataricus, Pto0485,...”
F8D4X4 Galactonate dehydratase from Halopiger xanaduensis (strain DSM 18323 / JCM 14033 / SH-6)
23% identity, 86% coverage
D4GYD4 gluconate dehydratase (EC 4.2.1.39) from Haloferax volcanii (see paper)
HVO_1488 mandelate racemase/muconate lactonizing enzyme family protein from Haloferax volcanii DS2
23% identity, 86% coverage
- d-Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species
Johnsen, Journal of bacteriology 2020 (secret) - Discovery of a novel transcriptional regulator of sugar catabolism in archaea
Johnsen, Molecular microbiology 2023 - “...in Haloferax volcanii . -galactosidase activity (mU/mg) Induction (fold) Promotor of Strain CAS CAS+D-glucose gad (HVO_1488) wt 48 18 471 84 9.8 gfcR 47 22 58 30 1.2 gapl (HVO_0481) wt 218 21 585191 2.7 gfcR 220 44 221 60 1.0 pykA (HVO_0806) wt 65 24...”
- Glucose Metabolism and Acetate Switch in Archaea: the Enzymes in Haloferax volcanii
Kuprat, Journal of bacteriology 2021 (secret) - Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase
Sutter, Journal of bacteriology 2016 - “...and the encoding gene, gad, was identified as HVO_1488. GAD catalyzed the specific dehydration of gluconate and did not utilize galactonate at significant...”
- “...of recombinant GDH, KDPGA, and GAD. HVO_1083, HVO_0950, and HVO_1488 were amplified, and each PCR product was cloned into pTA963, a shuttle vector for E. coli...”
ACI_STRCO / Q9RKF7 3,6-anhydro-alpha-L-galactonate cycloisomerase; AHGA cycloisomerase; EC 5.5.1.25 from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (see paper)
SCO3480 racemase from Streptomyces coelicolor A3(2)
27% identity, 90% coverage
- function: Involved in the degradation of 3,6-anhydro-L-galactose, which is the major monomeric sugar of red macroalgae (PubMed:33820885). Catalyzes the isomerization of 3,6-anhydrogalactonate (AHGA) to 2-keto- 3-deoxy-galactonate (KDGal) (PubMed:33820885).
catalytic activity: 3,6-anhydro-L-galactonate = 2-dehydro-3-deoxy-L-galactonate (RHEA:21512)
cofactor: Mg(2+) - NADP+-Dependent Dehydrogenase SCO3486 and Cycloisomerase SCO3480: Key Enzymes for 3,6-Anhydro-L-Galactose Catabolism in Streptomyces coelicolor A3(2)
Tsevelkhorloo, Journal of microbiology and biotechnology 2021 - “...and Bioengineering (BB) Microbial Genetics, Physiology, and Metabolism NADP + -Dependent Dehydrogenase SCO3486 and Cycloisomerase SCO3480 : Key Enzymes for 3,6-Anhydro-L-Galactose Catabolism in Streptomyces coelicolor A3(2) Tsevelkhorloo Maral 1 Kim Sang Hoon 2 Kang Dae-Kyung 2 Lee Chang-Ro 1 Hong Soon-Kwang 1 * 1 Department of...”
- “...gram-positive soil bacterium. Based on genomic data, the SCO3486 protein (492 amino acids) and the SCO3480 protein (361 amino acids) of S. coelicolor A3(2) showed identity with H2IFE7.1 (40% identity) encoding AHG dehydrogenase and H2IFX0.1 (42% identity) encoding 3,6-anhydro-L-galactonate cycloisomerase, respectively, which are involved in the...”
2o56A / Q8ZKY6 Crystal structure of a member of the enolase superfamily from salmonella typhimurium
24% identity, 90% coverage
- Ligand: magnesium ion (2o56A)
STM3833 putative mandelate racemase / muconate lactonizing enzyme family from Salmonella typhimurium LT2
24% identity, 90% coverage
- Expression of Pyridoxal 5'-Phosphate-Independent Racemases Can Reduce 2-Aminoacrylate Stress in Salmonella enterica
Hodge-Hanson, Journal of bacteriology 2018 - “...annotated as putative PLP-independent mandelate racemases (STM3697 and STM3833). 137 Proteins from E. coli and S. enterica were tested to determine if multicopy...”
- Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage
Octavia, Journal of clinical microbiology 2015 - “...STM1618 recG STM3744 btuB STM4130 dcuA STM4325 yjiE STM4511 STM3833 yihV STM4024.S STM3021 rfaK STM3714 flhC STM1924.S yhdG STM3384 a b Locus Product COGb Amino...”
- Exposure to sub-inhibitory concentrations of cefotaxime enhances the systemic colonization of Salmonella Typhimurium in BALB/c mice
Molina-Quiroz, Open biology 2015 - “...ribose and galactose sensor receptor STM1187 rluC 23S rRNA pseudouridylate synthase STM0765 putative cation transporter STM3833 putative mandelate racemase/muconate lactonizing enzyme family STM0565 putative periplasmic protein STM1931 araH putative intracellular protease/amidase 3.4. Exposure to a sub-inhibitory concentration of cefotaxime during aerobic growth induces a switch to...”
- Salmonella serovar identification using PCR-based detection of gene presence and absence
Arrach, Journal of clinical microbiology 2008 - “...STM3782, STM3822, STM3823, STM3826, STM3828, STM3831, STM3833, STM3834, STM3860, STM4012, STM4032, STM4046, STM4052, STM4067, STM4068, STM4072, STM4074,...”
3ck5A / Q9RKF7 Crystal structure of a racemase from streptomyces coelicolor a3(2) with bound magnesium
28% identity, 90% coverage
- Ligand: magnesium ion (3ck5A)
G4RJQ1 gluconate dehydratase (EC 4.2.1.39) from Thermoproteus tenax (see paper)
25% identity, 87% coverage
xacD / D4GP40 D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) from Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (see 3 papers)
XAD_HALVD / D4GP40 D-xylonate dehydratase; XAD; EC 4.2.1.82 from Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (Halobacterium volcanii) (see 2 papers)
D4GP40 xylonate dehydratase (EC 4.2.1.82) from Haloferax volcanii (see paper)
HVO_B0038A D-xylonate dehydratase from Haloferax volcanii DS2
25% identity, 90% coverage
- function: NADP-dependent D-xylose dehydrogenase involved in the degradation of D-xylose, a major component of hemicelluloses such as xylan. Catalyzes the third reaction in the xylose utilization pathway through dehydratation of D-xylonate into 2-dehydro-3-deoxy-D-xylonate.
catalytic activity: D-xylonate = 2-dehydro-3-deoxy-D-arabinonate + H2O (RHEA:19157)
subunit: Homooctamer.
disruption phenotype: Impairs growth on D-xylose as sole energy and carbon substrate. - d-Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species
Johnsen, Journal of bacteriology 2020 (secret) - Biochemical routes for uptake and conversion of xylose by microorganisms
Zhao, Biotechnology for biofuels 2020 - “...by sequentially catalytic reaction, involving the enzymes of xylose dehydrogenase (HVO_B0028), xylonolactonase (HVO_B0030), xylonate dehydratase (HVO_B0038A), 2-keto-3-deoxy-xylonate dehydratase (HVO_B0027), and -ketoglutarate semialdehyde dehydrogenase (HVO_B0039) [ 55 ]. The related genes in H. volcanii are clustered and transcriptionally regulated by a putative IclR-like regulator HVO_B0040 (designated XacR)...”
- Alone at last! - Heterologous expression of a single gene is sufficient for establishing the five-step Weimberg pathway in Corynebacterium glutamicum
Brüsseler, Metabolic engineering communications 2019 - “...archaeon Haloferax volcanii , naturally having the Weimberg pathway, requires the activity of both dehydratases (HVO_B0038A and HVO_B0027) for growth on d -xylose containing media ( Johnsen etal., 2009 ). In our experiments, microbial synthesis of -ketoglutarate from a d -glucose/ d -xylose mixture with engineered...”
- Exploring D-xylose oxidation in Saccharomyces cerevisiae through the Weimberg pathway
Wasserstrom, AMB Express 2018 - “...xylD, xylX and xylA was replaced with the counterpart from the halophilic archaeon H. volcanii (HVO_B0038A, xad_Hv), generating strain TMB4531. The same three phase-set up as previously described for TMB4530 was used to test d -xylose conversion with a low simultaneous d -glucose co-consumption. In the...”
- Metabolic reconstruction and experimental verification of glucose utilization in Desulfurococcus amylolyticus DSM 16532
Reischl, Folia microbiologica 2018 - “...which forms L-arabinoate, could be detected. Furthermore, no H. volcanii homologs for arabinose degradation (e.g. HVO_B0038A, HVO_B0027, or HVO_B0039 (Johnsen et al. 2013 ) could be identified in the genome of D. amylolyticus . Concerning utilization of disaccharides by D. amylolyticus , sucrose could be split...”
- Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase
Sutter, Journal of bacteriology 2016 - “...was analyzed by SDS-PAGE and MALDI-TOF analysis, yielding HVO_B0038A as the encoding gene; HVO_B0038A codes for XAD, which uses both xylonate and gluconate as...”
- “...RNA isolation and RT-PCR analysis. RNA for xad (HVO_B0038A) transcript analysis was prepared from exponentially grown H. volcanii gad mutant cells. Cells were...”
- Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation
Bräsen, Microbiology and molecular biology reviews : MMBR 2014 - “...conversion of L-arabinonate to KGSA, i.e., XAD (HVO_B0038A), KDXD (HVO_B0027), and -KGSADH (HVO_0039), suggesting that either these enzymes are promiscuous or...”
- “...Among these genes, HVO_B0027, HVO_B0028, HVO_B0038A, and HVO_B0039, encoding 2-keto-3-deoxyxylonate dehydratase (KDXD), xylose dehydrogenase (XDH), xylonate...”
- L-Arabinose degradation pathway in the haloarchaeon Haloferax volcanii involves a novel type of L-arabinose dehydrogenase
Johnsen, Extremophiles : life under extreme conditions 2013 (PubMed)- “...analyses of transcripts and deletion mutants as HVO_B0038A, HVO_B0027 and HVO_B0039 recently reported to be involved in D-xylonate conversion to a-ketoglutarate...”
- “...degree of nucleotide sequence identity (85 %) of HVO_B0038A to HVO_1488, RT-PCR was performed for transcript analysis of HVO_B0038A. RNA was treated with DNaseI...”
- More
- Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase
Sutter, Journal of bacteriology 2016 - “...(rrnAC0575), H. volcanii (HVO_B0038A) (UniProt accession number D4GP40) (B), and Halorubrum lacusprofundi (Hlac_2242) are shown. Sutter et al. 2260 jb.asm.org...”
GAD_THETE / Q704D2 D-gluconate dehydratase; EC 4.2.1.39 from Thermoproteus tenax (see 2 papers)
gad / CAF18462.1 gluconate dehydratase from Thermoproteus tenax (see paper)
25% identity, 70% coverage
- function: Involved in the degradation of glucose via the Entner- Doudoroff pathway. Catalyzes the dehydration of gluconate to produce 2- keto-3-deoxygluconate (KDG). It is not able to use D-galactonate as substrate.
catalytic activity: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:21612)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
Bpet3300 putative racemase from Bordetella petrii DSM 12804
26% identity, 73% coverage
2pp1A / Q8ZL58 Crystal structure of l-talarate/galactarate dehydratase from salmonella typhimurium lt2 liganded with mg and l-lyxarohydroxamate (see paper)
23% identity, 97% coverage
- Ligands: magnesium ion; (2r,3s,4r)-2,3,4-trihydroxy-5-(hydroxyamino)-5-oxopentanoic acid (2pp1A)
TAGAD_SALTY / Q8ZL58 L-talarate/galactarate dehydratase; TalrD/GalrD; StTGD; EC 4.2.1.156; EC 4.2.1.42 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 2 papers)
Q8ZL58 L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) from Salmonella enterica subsp. enterica serovar Typhimurium (see 2 papers)
NP_462597 putative mandelate racemase from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
STM3697 putative mandelate racemase / muconate lactonizing enzyme family from Salmonella typhimurium LT2
SL1344_3662 L-talarate/galactarate dehydratase from Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
23% identity, 97% coverage
- function: Catalyzes the efficient dehydration of both L-talarate (also called L-altrarate) and galactarate to 5-keto-4-deoxy-D-glucarate (5- KDG) (PubMed:17649980, PubMed:29248502). Also catalyzes the epimerization of L-talarate to galactarate; epimerization occurs in competition with dehydration. Is required for the utilization of L- talarate as a carbon source. Also functions in galactarate utilization. Is not active on other acid sugars (PubMed:17649980).
catalytic activity: L-altrarate = 5-dehydro-4-deoxy-D-glucarate + H2O (RHEA:44028)
catalytic activity: galactarate = 5-dehydro-4-deoxy-D-glucarate + H2O (RHEA:16005)
catalytic activity: L-altrarate = galactarate (RHEA:64172)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Homooctamer; tetramer of dimers.
disruption phenotype: Cells lacking this gene lose the ability to grow on L-talarate as carbon source, and are impaired in the ability to utilize galactarate as carbon source. - Evolution of enzymatic activities in the enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2.
Yew, Biochemistry 2007 (PubMed)- GeneRIF: STM3697 catalyzes the efficient dehydration of both l-talarate and galactarate.
- Expression of Pyridoxal 5'-Phosphate-Independent Racemases Can Reduce 2-Aminoacrylate Stress in Salmonella enterica
Hodge-Hanson, Journal of bacteriology 2018 - “...136 ORFs annotated as putative PLP-independent mandelate racemases (STM3697 and STM3833). 137 Proteins from E. coli and S. enterica were tested to determine if...”
- Characterization of a novel Agrobacterium tumefaciens galactarolactone cycloisomerase enzyme for direct conversion of D-galactarolactone to 3-deoxy-2-keto-L-threo-hexarate
Andberg, The Journal of biological chemistry 2012 - “...The Salmonella typhimurium LT2 L-talarate/galactarate dehydratase gene (STM3697) (15) optimized for E. coli expression was synthesized by GeneArt, and amplified...”
- Salmonella serovar identification using PCR-based detection of gene presence and absence
Arrach, Journal of clinical microbiology 2008 - “...STM3638, STM3639, STM3658, STM3673, STM3678, STM3691, STM3697, STM3753, STM3770, STM3775, STM3780, STM3782, STM3822, STM3823, STM3826, STM3828, STM3831,...”
- Evolution of enzymatic activities in the enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2
Yew, Biochemistry 2007 (PubMed)- “...by the Salmonella typhimurium LT2 genome (GI:16766982; STM3697). Like the homologous mandelate racemase, L-fuconate dehydratase, and D-tartrate dehydratase, the...”
- “...of the eighth -strand. We discovered the function of STM3697 by screening a library of acid sugars; it catalyzes the efficient dehydration of both L-talarate...”
- speG Is Required for Intracellular Replication of Salmonella in Various Human Cells and Affects Its Polyamine Metabolism and Global Transcriptomes
Fang, Frontiers in microbiology 2017 - “...involved in the succinate reductase complex (Table 2A ). Moreover, narK, malK, ybfM , SL1344_2997, SL1344_3662, dctA, hutU , and hutH as well as five genes encoding hypothetical proteins were significantly upregulated (Table 2A ). Thus, speG could be involved in suppression of the expression of...”
- “...protein 3.343 ybf M SL1344_0669 Putative outer membrane protein 2.372 SL1344_2997 SL1344_2997 Acetyl-CoA acetyltransferase 2.089 SL1344_3662 SL1344_3662 Putative racemase 1.552 SL1344_0211 SL1344_0211 Hypothetical protein 1.495 dctA SL1344_3579 C4-dicarboxylate transport protein 1.454 SL1344_2940 SL1344_2940 Hypothetical protein 1.319 hutU SL1344_0767 Urocanate hydratase 1.237 SL1344_3732 SL1344_3732 Hypothetical protein 1.227...”
B9LRU5 Mandelate racemase/muconate lactonizing protein from Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34)
Hlac_2242 Mandelate racemase/muconate lactonizing protein from Halorubrum lacusprofundi ATCC 49239
25% identity, 91% coverage
- d-Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species
Johnsen, Journal of bacteriology 2020 (secret) - Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase
Sutter, Journal of bacteriology 2016 - “...(UniProt accession number D4GP40) (B), and Halorubrum lacusprofundi (Hlac_2242) are shown. Sutter et al. 2260 jb.asm.org FIG 9 Proposed pathway of glucose...”
- “...haloarchaea H. lacusprofundi (2 homologs, Hlac_1300 [91%] and Hlac_2242 [77%]) and H. marismortui (rrnAC0575 [88%]) and also to XAD from H. volcanii (HVO_B0038A...”
- D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii
Johnsen, The Journal of biological chemistry 2009 - “...halophiles, H. marismortui, rrnAC0575, and H. lacusprofundi, Hlac_2242, respectively, suggesting functional XAD in these organisms. The enzymes belongs to the...”
- “...superfamily) is marked. HVO_B0038A, XAD of H. volcanii; Hlac_2242, H. lacusprofundi; rrnAC0575, H. volcanii and its comparison with marismortui, SSO3198; GAD of...”
Atu1406 isomerase/lactonizing enzyme from Agrobacterium tumefaciens str. C58 (Cereon)
25% identity, 90% coverage
G0HPX2 Mandelate racemase/muconate lactonizing family protein from Haloarcula hispanica (strain ATCC 33960 / DSM 4426 / JCM 8911 / NBRC 102182 / NCIMB 2187 / VKM B-1755)
23% identity, 86% coverage
lra3 / Q1NEI8 L-rhamnonate dehydratase (EC 4.2.1.90) from Sphingomonas sp. (strain SKA58) (see paper)
RHMD_SPHSS / Q1NEI8 L-rhamnonate dehydratase; RhamD; SpLRA3; EC 4.2.1.90 from Sphingomonas sp. (strain SKA58) (see paper)
27% identity, 90% coverage
- function: Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy- L-rhamnonate (KDR) (PubMed:19187228). Shows also activity with L- lyxonate and L-mannonate, with much lower catalytic efficiency (PubMed:19187228). Catalyzes the third step in an alternative pathway for rhamnose utilization that does not involve phosphorylated intermediates (PubMed:19187228).
catalytic activity: L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O (RHEA:23080)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Homooctamer; tetramer of dimers.
RhmD / b2247 L-rhamnonate dehydratase (EC 4.2.1.90) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
rhmD / P77215 L-rhamnonate dehydratase (EC 4.2.1.90) from Escherichia coli (strain K12) (see paper)
RHMD_ECOLI / P77215 L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 from Escherichia coli (strain K12) (see paper)
P77215 L-rhamnonate dehydratase (EC 4.2.1.90) from Escherichia coli K-12 (see paper)
b2247 predicted enolase from Escherichia coli str. K-12 substr. MG1655
25% identity, 89% coverage
- function: Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy- L-rhamnonate (KDR). Can also dehydrate L-lyxonate, L-mannonate and D- gulonate, although less efficiently, but not 2-keto-4-hydroxyheptane- 1,7-dioate.
catalytic activity: L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O (RHEA:23080)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Homooctamer; tetramer of dimers. - DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli
DeLisa, Journal of bacteriology 2001 - “...5-fold repressed, notably b2650 (27.8-fold), thiH (19.2-fold), and b2247 (15.2-fold). The entire dataset of induction ratios for all 4,290 annotated E. coli...”
- “...8.4 b2247 ................................................................................... 15.2 b2650...”
BPSS2072 mandelate racemase / muconate lactonizing enzyme from Burkholderia pseudomallei K96243
25% identity, 94% coverage
- Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in Northeast Thailand
Seng, Nature communications 2024 - “...Notably, we observed that a cluster of genes specific to lineage 1 ( BPSS2060 to BPSS2072 ) formed a mosaic structure within a putative metabolic island known as GI 16 30 . Although several variations of GI 16 have been reported (GI16, GI16.1, GI16.2, GI16a, GI16b,...”
- “...specific to dominant lineages. For example, the mosaic structure of GI 16 ( BPSS2060 to BPSS2072 ), specific to lineage 1 (Supplementary data 3 ), contains genes involved in alternative nutrient catabolism and anabolism ( BPSS2060 , BPSS2065 , BPSS2067 , BPSS2068 , and BPSS2072 ),...”
- Genetic diversity, determinants, and dissemination ofBurkholderia pseudomalleilineages implicated in melioidosis in northeast Thailand
Seng, 2023
ST2366 396aa long hypothetical dgoA protein from Sulfolobus tokodaii str. 7
25% identity, 90% coverage
F8DCB2 Galactonate dehydratase from Halopiger xanaduensis (strain DSM 18323 / JCM 14033 / SH-6)
23% identity, 91% coverage
A0NP48 L-lyxonate dehydratase (EC 4.2.1.176) from Roseibium aggregatum (see paper)
3stpA / A0NP48 Crystal structure of a putative galactonate dehydratase
23% identity, 91% coverage
- Ligand: magnesium ion (3stpA)
- Discovery of a novel L-lyxonate degradation pathway in Pseudomonas aeruginosa PAO1.
Ghasempur, Biochemistry 2014 - “...10 mM maltose). The gene encoding the LyxD from Labrenzia aggregata IAM 12614 (UniProt ID A0NP48) was cloned into expression vector pNIC28-BSA4 by PCR and the ligation-independent cloning method as previously described. 7 The resulting plasmid was transformed into BL21(DE3) E. coli containing the pRIL plasmid...”
- “..., Table 2. Crystallization and Data Collection LyxD from L. aggregata IAM 12614 (UniProt ID A0NP48) was crystallized by the sitting drop vapor diffusion method using Hampton Research crystallization screens. The protein solution (0.5 L; 12 mg/mL) was mixed with an equal volume of reservoir solution...”
BB4687 putative mandelate racemase from Bordetella bronchiseptica RB50
27% identity, 88% coverage
3ozmA / A0A0H3LT39 Crystal structure of enolase superfamily member from bordetella bronchiseptica complexed with mg, m-xylarate and l-lyxarate
27% identity, 88% coverage
- Ligands: magnesium ion; d-xylaric acid (3ozmA)
5xd8B / H2IFX0 Crystal structure analysis of 3,6-anhydro-l-galactonate cycloisomerase (see paper)
25% identity, 85% coverage
- Ligand: magnesium ion (5xd8B)
Saci_0885 conserved Prokaryal protein from Sulfolobus acidocaldarius DSM 639
26% identity, 93% coverage
RHMD_POLSJ / Q12DF1 L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 from Polaromonas sp. (strain JS666 / ATCC BAA-500) (see paper)
25% identity, 82% coverage
- function: Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy- L-rhamnonate (KDR).
catalytic activity: L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O (RHEA:23080)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Homooctamer; tetramer of dimers.
aci / H2IFX0 3,6-anhydro-L-galactonate cycloisomerase (EC 5.5.1.25) from Vibrio sp. (strain EJY3) (see paper)
ACI_VIBSJ / H2IFX0 3,6-anhydro-alpha-L-galactonate cycloisomerase; AHGA cycloisomerase; EC 5.5.1.25 from Vibrio sp. (strain EJY3) (see paper)
H2IFX0 3,6-anhydro-L-galactonate cycloisomerase (EC 5.5.1.25) from Vibrio sp. (see paper)
VEJY3_09370 3,6-anhydro-alpha-L-galactonate cycloisomerase from Vibrio sp. EJY3
25% identity, 84% coverage
- function: Involved in the degradation of 3,6-anhydro-L-galactose, which is the major monomeric sugar of red macroalgae. Catalyzes the isomerization of 3,6-anhydrogalactonate (AHGA) to 2-keto-3-deoxy- galactonate (KDGal).
catalytic activity: 3,6-anhydro-L-galactonate = 2-dehydro-3-deoxy-L-galactonate (RHEA:21512)
cofactor: Mg(2+) - Characterization of Agarolytic Pathway in a Terrestrial Bacterium Cohnella sp. LGH
Li, Frontiers in microbiology 2022 - “...the 3,6-anhydro-L-galactose dehydrogenase VejAHGD (accession NO. H2IFE7 ) and the 3,6-anhydrogalactonate cycloisomerase VejACI (accession NO. H2IFX0 ). In strain LGH, CL4996 shared 44.5% sequence identity to VejAHGD and was present the same aldehyde dehydrogenase family domain (accession NO. pfam00171 ) as VejAHGD ( Supplementary Figure 3...”
- Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria
Ficko-Blean, Nature communications 2017 - “...provided new insights. Indeed, Vibrio 3,6-anhydro- l -galactose dehydrogenase (VEJY3_09240) and 3,6-anhydro- l -galactonate cycloisomerase (VEJY3_09370) are distantly related to ZGAL_3155 and ZGAL_3156 (35% and 31% sequence identity, respectively). We thus hypothesized that ZGAL_3155 and ZGAL_3156 could catalyze similar reactions but on the D enantiomer of...”
3sqsA / A8LS88 Crystal structure of a putative mandelate racemase/muconate lactonizing protein from dinoroseobacter shibae dfl 12
24% identity, 91% coverage
- Ligand: magnesium ion (3sqsA)
A8LS88 Putative mandelate racemase/muconate lactonizing protein from Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12)
24% identity, 91% coverage
- Discovery of a novel L-lyxonate degradation pathway in Pseudomonas aeruginosa PAO1.
Ghasempur, Biochemistry 2014 - “...one from Verminephrobacter eiseniae (UniProt ID A1WLE4) and the second from Dianorosiobacter shabila (UniProt ID A8LS88), were screened for dehydration activity on a library of di- and monoacid sugars using the semicarbazide assay. 3 After a 16 h incubation at 30 C, both proteins quantitatively converted...”
- “...810 3 d -gulonate 20.4 10.2 210 3 l -mannonate NA NA 0.08 LyxD-wild type A8LS88 l -lyxonate 20.2 0.20.05 110 4 d -gulonate 30.3 10.3 310 3 l -mannonate NA NA 0.04 (B) LyxD-Y216F A8LS88 l -lyxonate 20.3 0.20.05 110 4 LyxD-R179Q A8LS88 l -lyxonate...”
5olcC / G0L7B8 Crystal structure of the 3,6-anhydro-d-galactonate cycloisomerase from zobellia galactanivorans (see paper)
24% identity, 90% coverage
- Ligand: magnesium ion (5olcC)
Ta0085m Galactonate dehydratase from Thermoplasma acidophilum DSM 1728
24% identity, 88% coverage
GAD_PICTO / Q6L1T2 D-gluconate/D-galactonate dehydratase; GAD; GNAD; EC 4.2.1.140; EC 4.2.1.39; EC 4.2.1.6 from Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828 / KAW 2/3) (see paper)
Q6L1T2 gluconate/galactonate dehydratase (EC 4.2.1.140); gluconate dehydratase (EC 4.2.1.39) from Picrophilus torridus (see paper)
PTO0485 gluconate/galactonate dehydratase from Picrophilus torridus DSM 9790
WP_011177286 mandelate racemase/muconate lactonizing enzyme family protein from Picrophilus oshimae DSM 9789
23% identity, 88% coverage
- function: Involved in the degradation of glucose and galactose via the nonphosphorylative variant of Entner-Doudoroff pathway. Catalyzes the dehydration of gluconate to produce 2-keto-3-deoxygluconate (KDG). It is also able to catalyze the dehydration of galactonate to produce 2- keto-3-deoxygalactonate (KDGal).
catalytic activity: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:21612)
catalytic activity: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:21612)
catalytic activity: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O (RHEA:18649)
catalytic activity: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O (RHEA:18649)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Homooctamer. - Efficacy of signal peptide predictors in identifying signal peptides in the experimental secretome of Picrophilous torridus, a thermoacidophilic archaeon
Singhal, PloS one 2021 - “...PTO0604 19 Q6KZE9 Iron(III) dicitrate ABC transporter extracellular binding protein/integral component of membrane PTO1318 20 Q6L1T2 D-gluconate/D-galactonate dehydratase/D-gluconate catabolic process PTO0485 21 Q6KZT9 ABC transporter extracellular solute-binding protein/membrane component PTO1178 22 Q6L2S5 Uncharacterized protein PTO0142 23 Q6L2L9 Uncharacterized protein PTO0198 24 Q6L268 Hypothetical membrane protein PTO0349...”
- “...involved in the various KEGG pathways. S.No. KEGG pathway Protein accession number 1. Carbon metabolism Q6L1T2, Q6L0C3, Q6L0B7, Q6KZF2, Q6KZA7 2. Microbial metabolism in diverse environments Q6L1T2, Q6L0C3, Q6L0B7, Q6KZF2, Q6KZA7 3. Biosynthesis of antibiotics Q6L0C3, Q6L0B7, Q6KZA7 4. Biosynthesis of secondary metabolites Q6L0C3, Q6L0B7, Q6KZA7...”
- Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase
Sutter, Journal of bacteriology 2016 - “...acidophilum (Ta0085m), P. torridus (GenBank accession number Q6L1T2), S. solfataricus (GenBank accession number Q97U27), and S. acidocaldarius (Saci_0885); GAD...”
- Efficacy of signal peptide predictors in identifying signal peptides in the experimental secretome of Picrophilous torridus, a thermoacidophilic archaeon
Singhal, PloS one 2021 - “...ABC transporter extracellular binding protein/integral component of membrane PTO1318 20 Q6L1T2 D-gluconate/D-galactonate dehydratase/D-gluconate catabolic process PTO0485 21 Q6KZT9 ABC transporter extracellular solute-binding protein/membrane component PTO1178 22 Q6L2S5 Uncharacterized protein PTO0142 23 Q6L2L9 Uncharacterized protein PTO0198 24 Q6L268 Hypothetical membrane protein PTO0349 25 Q6L1Y4 Uncharacterized protein PTO0433...”
- Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase
Sutter, Journal of bacteriology 2016 - “...for the GADs of S. solfataricus (SSO3198), P. torridus (Pto0485), and T. tenax (TTX1156). H. volcanii GAD also showed moderate sequence identity (22%) to the...”
- Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation
Bräsen, Microbiology and molecular biology reviews : MMBR 2014 - “...Sul. solfataricus (SSO3198) and also from Pic. torridus (Pto0485) extracts, and the characterization revealed that both enzymes, like the GDHs, are promiscuous...”
- The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase
Reher, Journal of bacteriology 2010 - “...GAD is a homooctamer of 44-kDa subunits, encoded by Pto0485. KDG aldolase, KDGA, is a homotetramer of 32-kDa subunits. This enzyme was highly specific for KDG...”
- “...mass fingerprinting of the purified enzyme, a single ORF, Pto0485, was identified in the genome of P. torridus; the matched peptides cover 34% of the protein....”
- D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii
Johnsen, The Journal of biological chemistry 2009 - “...with marismortui, SSO3198; GAD of S. solfataricus, Pto0485, P. torridus, SSO3124, AraD of S. solfataricus. homologous genes in sugar utilizputative orthologs...”
- The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase.
Reher, Journal of bacteriology 2010 - GeneRIF: Gluconate dehydratase (GAD) is a homooctamer of 44-kDa subunits, encoded by Pto0485.
2qq6B / Q1AYK7 Crystal structure of mandelate racemase/muconate lactonizing enzyme- like protein from rubrobacter xylanophilus dsm 9941
24% identity, 80% coverage
- Ligand: magnesium ion (2qq6B)
RHMD_SALTY / Q8ZNF9 L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
Q8ZNF9 L-rhamnonate dehydratase (EC 4.2.1.90) from Salmonella enterica subsp. enterica serovar Typhimurium (see paper)
3d46A / Q8ZNF9 Crystal structure of l-rhamnonate dehydratase from salmonella typhimurium complexed with mg and l-tartrate
25% identity, 88% coverage
- function: Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy- L-rhamnonate (KDR). Can also dehydrate L-lyxonate and L-mannonate, although less efficiently, but not 2-keto-4-hydroxyheptane-1,7-dioate.
catalytic activity: L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O (RHEA:23080)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Homooctamer; tetramer of dimers. - Ligand: magnesium ion (3d46A)
SM_b21107 dehydratase involved in L-fucose catabolism from Sinorhizobium meliloti 1021
23% identity, 92% coverage
- mutant phenotype: # Specifically important in carbon source L-Fucose. T. Lukk's 2009 thesis reported that this protein had weak activity as a L-fuconate dehydratase, which was the expected substrate. The fitness data shows that two other dehydratases are involved in fucose catabolism as well (see SMc02776 and SM_b21110), so the pathway is probably more complicated.
A1WLE4 Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein from Verminephrobacter eiseniae (strain EF01-2)
25% identity, 91% coverage
- Discovery of a novel L-lyxonate degradation pathway in Pseudomonas aeruginosa PAO1
Ghasempur, Biochemistry 2014 - “...Identification Using the Acid Sugar Library Two uncharacterized proteins, one from Verminephrobacter eiseniae (UniProt ID A1WLE4) and the second from Dianorosiobacter shabila (UniProt ID A8LS88), were screened for dehydration activity on a library of di- and monoacid sugars using the semicarbazide assay. 3 After a 16...”
- “...m (mM) k cat / K m (M 1 s 1 ) (A) LyxD-wild type A1WLE4 l -lyxonate 30.3 0.40.1 810 3 d -gulonate 20.4 10.2 210 3 l -mannonate NA NA 0.08 LyxD-wild type A8LS88 l -lyxonate 20.2 0.20.05 110 4 d -gulonate 30.3 10.3...”
3cb3A / Q12GE3 Crystal structure of l-talarate dehydratase from polaromonas sp. Js666 complexed with mg and l-glucarate
24% identity, 92% coverage
- Ligands: magnesium ion; l-glucaric acid (3cb3A)
SPO2414 mandelate racemase/muconate lactonizing enzyme family protein from Ruegeria pomeroyi DSS-3
25% identity, 83% coverage
- Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium
Chan, Frontiers in microbiology 2012 - “...0.3 0.3 SPO2271 fabF 3-oxoacyl-(acyl carrier protein) synthase II 0.5 0.3 SPO2373 Hypothetical protein 0.1 SPO2414 Mandelate racemase/muconate lactonizing enzyme family protein 0.3 SPO2556 Allantoate amidohydrolase 0.2 SPO2592 Beta-lactamase, putative 1.0 0.3 SPO2616 tgt Queuine tRNA-ribosyltransferase 0.7 0.3 SPO3012 Inositol-1-monophosphatase, putative 0.1 0.2 SPO3156 l -threonine...”
3ekgA / C1DMY1 Crystal structure of l-rhamnonate dehydratase from azotobacter vinelandii complexed with mg and l-tartrate
27% identity, 88% coverage
- Ligand: magnesium ion (3ekgA)
GAD_SACS2 / Q97U27 D-gluconate/D-galactonate dehydratase; GAD; GNAD; EC 4.2.1.140; EC 4.2.1.39; EC 4.2.1.6 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (Sulfolobus solfataricus) (see 2 papers)
Q97U27 gluconate/galactonate dehydratase (EC 4.2.1.140) from Saccharolobus solfataricus (see paper)
SSO3198 mandelate racemase/muconate lactonizing enzyme family protein from Saccharolobus solfataricus P2
SSO3198 Muconate cycloisomerase related protein from Sulfolobus solfataricus P2
25% identity, 89% coverage
- function: Involved in the degradation of glucose and galactose via the branched variant of the Entner-Doudoroff pathway. Catalyzes the dehydration of gluconate to produce 2-keto-3-deoxygluconate (KDG). It is also able to catalyze the dehydration of galactonate to produce 2- keto-3-deoxygalactonate (KDGal).
catalytic activity: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:21612)
catalytic activity: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:21612)
catalytic activity: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O (RHEA:18649)
catalytic activity: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O (RHEA:18649)
cofactor: Mg(2+) Co(2+) Mn(2+) Ni(2+) (Binds 1 Mg(2+) ion per subunit. Can also use divalent metal ions such as Co(2+), Mn(2+) and Ni(2+).)
subunit: Monomer or homooctamer. - Utilization of Phenol as Carbon Source by the Thermoacidophilic Archaeon Saccharolobus solfataricus P2 Is Limited by Oxygen Supply and the Cellular Stress Response
Wolf, Frontiers in microbiology 2020 - “...Transposase ISC1778 0.18 0.02 2.32E-12 Sso3194 1.2.1.9 Non-phosphorylating NAD(P)-dependent glyceraldehyde 3-phosphate dehydrogenase 0.23 0.06 1.99E-10 Sso3198 4.2.1.140 Gluconate/galactonate dehydratase 0.24 0.01 2.59E-09 Sso2182 1.1.1.42 Isocitrate dehydrogenase (NADP + ) 0.39 0.04 7.94E-05 Sso3197 4.1.2.20/4.1.2.21 Bifunctional 2-keto-3-deoxy-(6-phospho)gluconate/galactonate aldolase 0.44 0.01 6.58E-04 Genes which are not significantly regulated...”
- A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function.
Holliday, Database : the journal of biological databases and curation 2020 - “...and type. EFDs shown in this figure are the same as those describing UniProtKB protein Q97U27 (EFD:51, gluconate dehydratase family) and UniProtKB protein P11444 (EFD:94, mandelate racemase family) in Figure S1 . Though each of the two EFDs shown has multiple functional residues, only one is...”
- Protein phosphorylation and its role in archaeal signal transduction.
Esser, FEMS microbiology reviews 2016 (no snippet) - Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase
Sutter, Journal of bacteriology 2016 - “...22%) was found for the GADs of S. solfataricus (SSO3198), P. torridus (Pto0485), and T. tenax (TTX1156). H. volcanii GAD also showed moderate sequence identity...”
- Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation
Bräsen, Microbiology and molecular biology reviews : MMBR 2014 - “...enzyme was purified to homogeneity from Sul. solfataricus (SSO3198) and also from Pic. torridus (Pto0485) extracts, and the characterization revealed that both...”
- “...protein phosphorylation in Sul. solfataricus is GAD (SSO3198); only phosphorylated GAD was shown to be active (289). The previously reported phosphorylation...”
- Global analysis of viral infection in an archaeal model system
Maaty, Frontiers in microbiology 2012 - “...(Figure 2 C). Another protein known to be regulated by phosphorylation is d -gluconate dehydratase (SSO3198), a key enzyme in the non-phosphorylated EntnerDoudoroff pathway (Kim and Lee, 2005 ). We found this to be up-regulated at 48h and to appear in multiple positions on the gels....”
- "Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus
Zaparty, Extremophiles : life under extreme conditions 2010 - “...Arabinose ABC transporter, arabinose binding protein 1.51 (0.61) SSO3120 Metabolite transport protein, putative 1.69 (0.94) SSO3198 Muconate cycloisomerase related protein 1.28 (0.49) SSO6391 SSU ribosomal protein S14AB (rps14AB) 1.44 (0.53) SSO6401 LSU ribosomal protein L23AB (rpl23AB) 1.85 (0.64) SSO2088 Peptidase, putative 1.12 (0.12) SSO0316 Superoxide dismutase...”
- “...) also do not show differential expression between the two conditions with the exception of SSO3198 coding for gluconate dehydratase and SSO3194 encoding the non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase (GAPN) (Table 3 ). The encoding genes are twofold down-regulated at 80C. They are located in the ED...”
- Metabolism of pentose sugars in the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius
Nunn, The Journal of biological chemistry 2010 - “...solfataricus genome using the gluconate dehydratase gene sequence (SSO3198). The gene was cloned into pET3a and pET19b vectors (Novagen, Nottingham, UK) using...”
- The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase
Reher, Journal of bacteriology 2010 - “...enzyme showed high sequence identity (44%) to GAD (SSO3198) from S. solfataricus. Both GADs share a similar subunit size and an octameric oligomeric structure...”
- D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii
Johnsen, The Journal of biological chemistry 2009 - “...rrnAC0575, H. volcanii and its comparison with marismortui, SSO3198; GAD of S. solfataricus, Pto0485, P. torridus, SSO3124, AraD of S. solfataricus. homologous...”
- More
F6450_06750 mandelate racemase/muconate lactonizing enzyme family protein from Photobacterium damselae subsp. damselae
26% identity, 91% coverage
MS144 putative racemase from Microscilla sp. PRE1
24% identity, 81% coverage
RL3866 putative madelate racemase/muconate lactonising family protein from Rhizobium leguminosarum bv. viciae 3841
24% identity, 93% coverage
BAB1_0242 Mandelate racemase/muconate lactonizing enzyme from Brucella melitensis biovar Abortus 2308
24% identity, 90% coverage
gci / A9CEQ8 D-galactarolactone cycloisomerase monomer (EC 5.5.1.27) from Agrobacterium fabrum (strain C58 / ATCC 33970) (see paper)
GCI_AGRFC / A9CEQ8 D-galactarolactone cycloisomerase; EC 5.5.1.27 from Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58)) (see 2 papers)
A9CEQ8 D-galactarolactone cycloisomerase (EC 5.5.1.27) from Agrobacterium tumefaciens (see paper)
4hpnA / A9CEQ8 Crystal structure of a proposed galactarolactone cycloisomerase from agrobacterium tumefaciens, target efi-500704, with bound ca, ordered loops (see paper)
Atu3139 hypothetical protein from Agrobacterium tumefaciens str. C58 (Cereon)
25% identity, 93% coverage
- function: Catalyzes the ring opening of D-galactaro-1,4-lactone to yield 5-keto-4-deoxy-D-glucarate (KDG) via a beta-elimination reaction. This is a step in the oxidative degradation pathway of D-galacturonate, which allows A.tumefaciens to utilize D-galacturonate as a sole carbon source. To a lesser extent, can also use D-glucaro-1,4-lactone as substrate to produce KDG, but cannot use D-galactaro-1,5-lactone, D- glucaro-6,3-lactone and linear D-glucarate.
catalytic activity: D-glucaro-1,4-lactone = 5-dehydro-4-deoxy-D-glucarate + H(+) (RHEA:45604)
catalytic activity: D-galactaro-1,4-lactone = 5-dehydro-4-deoxy-D-glucarate + H(+) (RHEA:45600)
cofactor: Mg(2+)
subunit: Homooctamer. - Ligand: calcium ion (4hpnA)
- Purification, crystallization and structural elucidation of D-galactaro-1,4-lactone cycloisomerase from Agrobacterium tumefaciens involved in pectin degradation
Vetting, Acta crystallographica. Section F, Structural biology communications 2016 - “...production The gene encoding AtGCI (UniProt accession A9CEQ8, gene locus Atu3139) was amplified via the polymerase chain reaction (PCR) from genomic...”
- “...Spectrometry Laboratory (UIUC) for determining the mass of A9CEQ8 by electrospray ionization. This research used the resources of the Advanced Photon Source, a...”
- Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58
Groninger-Poe, Biochemistry 2014 - “...tumefaciens C58 is a source of novel sugar catabolic pathways. For example, Gci (UniProt entry A9CEQ8; locus tag Atu3139), a member of the MR subgroup of the ENS, recently was shown to catalyze the novel cycloisomerization of d -galactaro-1,4-lactone (-galactarolactone) to 5-keto-4-deoxy- d -galactarate in a...”
- Purification, crystallization and structural elucidation of D-galactaro-1,4-lactone cycloisomerase from Agrobacterium tumefaciens involved in pectin degradation
Vetting, Acta crystallographica. Section F, Structural biology communications 2016 - “...gene encoding AtGCI (UniProt accession A9CEQ8, gene locus Atu3139) was amplified via the polymerase chain reaction (PCR) from genomic DNA isolated from A....”
- Involvement of Agrobacterium tumefaciens Galacturonate Tripartite ATP-Independent Periplasmic (TRAP) Transporter GaaPQM in Virulence Gene Expression
Zhao, Applied and environmental microbiology 2016 - “...cycloisomerase (encoded by gene locus Atu3139) (27) catalyzes the ring opening of galactaro-1,4-lactone to form 3-deoxy-2-keto-L-threo-hexarate,...”
- Galactaro δ-lactone isomerase: lactone isomerization by a member of the amidohydrolase superfamily
Bouvier, Biochemistry 2014 - “...member of the functionally diverse enolase superfamily. 2 This enzyme, designated d -galactarolactone cycloisomerase (Gci, Atu3139), catalyzes the ring opening of d -galactaro-1,4-lactone to yield 2-keto-3-deoxy- l - threo -hexarate [hereafter designated 5-keto-4-deoxy- d -galactarate or 5-keto-4-deoxy- d -glucarate (KDG)] via a -elimination reaction that is...”
- “...semialdehyde, which is oxidized to -ketoglutarate, an intermediate in the citric acid cycle. 1 4 Atu3139 is located in a gene cluster that includes Atu3138 and Atu3140 (Figure 1 B); the transcription of the genes in this cluster is upregulated when d -galacturonate is the carbon...”
- Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58
Groninger-Poe, Biochemistry 2014 - “...a source of novel sugar catabolic pathways. For example, Gci (UniProt entry A9CEQ8; locus tag Atu3139), a member of the MR subgroup of the ENS, recently was shown to catalyze the novel cycloisomerization of d -galactaro-1,4-lactone (-galactarolactone) to 5-keto-4-deoxy- d -galactarate in a pathway for degradation...”
- Characterization of a novel Agrobacterium tumefaciens galactarolactone cycloisomerase enzyme for direct conversion of D-galactarolactone to 3-deoxy-2-keto-L-threo-hexarate
Andberg, The Journal of biological chemistry 2012 - “...the genome sequence of A. tumefaciens strain C58, the Atu3139 gene was identified. As the gene was not annotated, we called it gci for galactarolactone...”
- “...verify that we had identified the right gene, the gci (Atu3139) gene was expressed in the pBAT4 vector in E. coli BL21(DE3), and the crude cell extract was...”
Q1QUN5 Mandelate racemase/muconate lactonizing enzyme from Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11)
25% identity, 93% coverage
4h1zB / Q92ZS5 Crystal structure of putative isomerase from sinorhizobium meliloti, open loop conformation (target efi-502104)
26% identity, 72% coverage
- Ligand: magnesium ion (4h1zB)
Swit_0975 muconate cycloisomerase from Sphingomonas wittichii RW1
24% identity, 94% coverage
- Genome-wide analysis of Sphingomonas wittichii RW1 behaviour during inoculation and growth in contaminated sand
Moreno-Forero, The ISME journal 2015 - “...transition to sand with DBF (both SAL-DBF and DBF-DBF ) include a group of genes (Swit_0975 to Swit_0978) previously implicated in degradation of salicylate ( Coronado et al. , 2012 ), three genes (Swit_3144, Swit_3256 and Swit_3044) for TonB-dependent receptors, which may be associated with uptake...”
- “...2.6 2.3 3.5 2.6 1.4 1.1 Swit_0652 Methylmalonate-semialdehyde dehydrogenase 4.2 4.5 6.5 1.1 6.2 1.9 Swit_0975 Muconate cycloisomerase 21.7 21.1 6.3 1.5 1.9 1.1 Swit_0976 Muconolactone Delta-isomerase 12.9 11.9 4.5 1.7 5.4 1.2 Swit_0977 Catechol 1,2-dioxygenase 11.4 12.9 9.8 1.1 2.6 1.6 Swit_1124 Glutaredoxin 3.7 4.3...”
SiRe_2246 mandelate racemase/muconate lactonizing enzyme family protein from Saccharolobus islandicus REY15A
23% identity, 82% coverage
- Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress
Chiu, Frontiers in microbiology 2023 - “...UDP-sulfoquinovose synthase, Agl3 SiRe_2623 2.38 AMP-dependent synthetase and ligase SiRe_2451 1.94 Mandelate racemase (MR) subfamily SiRe_2246 N/A 1.62 Aminotransferase class V SiRe_0032 1.17 Conserved hypothetical protein SiRe_2599 1.15 Conserved hypothetical protein SiRe_2391 3.31 Formate dehydrogenase, alpha subunit SiRe_2464 2.58 Thioredoxin/glutaredoxin-like protein SiRe_1684 N/A 2.19 Heat shock...”
7mqxE / P11444 P. Putida mandelate racemase forms an oxobenzoxaborole adduct with 2- formylphenylboronic acid (see paper)
26% identity, 72% coverage
- Ligands: magnesium ion; (3s)-2,1-benzoxaborole-1,3(3h)-diol (7mqxE)
mdlA / P11444 mandelate racemase (EC 5.1.2.2) from Pseudomonas putida (see paper)
MANR_PSEPU / P11444 Mandelate racemase; MR; EC 5.1.2.2 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see 4 papers)
R9RJF1 mandelate racemase (EC 5.1.2.2) from Pseudomonas aeruginosa (see paper)
26% identity, 72% coverage
4hcdA / Q7CSI0 Crystal structure of d-glucarate dehydratase from agrobacterium tumefaciens complexed with magnesium
25% identity, 92% coverage
- Ligand: magnesium ion (4hcdA)
NBT05_09125 mandelate racemase/muconate lactonizing enzyme family protein from Aquimarina sp. ERC-38
22% identity, 79% coverage
- Agarolytic Pathway in the Newly Isolated Aquimarina sp. Bacterial Strain ERC-38 and Characterization of a Putative β-agarase
Kang, Marine biotechnology (New York, N.Y.) 2023 - “...2-Dehydro-3-deoxy-D-gluconate 5-dehydrogenase 4Z9Y_A EC 1.1.1.127 47.5% Aq1858 NBT05_09120 3,6-Anhydro-alpha-L-galactose dehydrogenase 6J75_A EC 1.2.1.92 69.3% Aq1859 NBT05_09125 3,6-Anhydro-L-galactonate cycloisomerase 5XD7_A EC 5.5.1.25 69.1% Each -agarase, Aq1828, Aq1829, Aq1830, Aq1832, Aq1839, and Aq1840, had a signal peptide at the N-terminal. When the proteins were compared against the PDB...”
3i4kA / Q8NN12 Crystal structure of muconate lactonizing enzyme from corynebacterium glutamicum
24% identity, 90% coverage
- Ligand: magnesium ion (3i4kA)
NCgl2318 muconate/chloromuconate family cycloisomerase from Corynebacterium glutamicum ATCC 13032
24% identity, 90% coverage
- Metabolic engineering of Corynebacterium glutamicum for the production of cis, cis-muconic acid from lignin
Becker, Microbial cell factories 2018 - “...(Sci-Ed Software, Denver, USA) was used. The genetic construct for deletion of the catB gene (NCgl2318) in the genome of C. glutamicum comprised a DNA fragment, lacking 703bp of the target gene and 500bp-sized flanking regions as homologous recombination sites. For overexpression of the catA gene...”
- “...primers that were used in the present work for genome-based deletion of the catB gene (NCgl2318) and integration of the tuf -promoter for overexpression of the catA gene (NCgl2319) in Corynebacterium glutamicum Name Sequence Use AT [C] catB TS1 FW 5-TTAACAATTGGGATCCTCTAGACCCACTCCAGAGCATTGGGGTGTTT-3 Amplification of TS1; TS1 FW+...”
TFDD_DELAC / Q9RNZ9 Chloromuconate cycloisomerase; EC 5.5.1.7 from Delftia acidovorans (Pseudomonas acidovorans) (Comamonas acidovorans) (see paper)
BJN34_37385 muconate cycloisomerase family protein from Cupriavidus necator
24% identity, 82% coverage
3n4eA / A1AYL4 Crystal structure of mandelate racemase/muconate lactonizing protein from paracoccus denitrificans pd1222
23% identity, 87% coverage
- Ligand: calcium ion (3n4eA)
3tteA / A4YVM8 Crystal structure of enolase brado_4202 (target efi-501651) from bradyrhizobium complexed with magnesium and mandelic acid
25% identity, 74% coverage
- Ligands: magnesium ion; (s)-mandelic acid (3tteA)
P11452 Chloromuconate cycloisomerase from Pseudomonas putida
23% identity, 83% coverage
CGS9114_RS08660 muconate/chloromuconate family cycloisomerase from Corynebacterium glutamicum S9114
24% identity, 90% coverage
SMa1461 Putative muconate cycloisomerase from Sinorhizobium meliloti 1021
23% identity, 89% coverage
3i6tB / Q28SI7 Crystal structure of muconate cycloisomerase from jannaschia sp.
24% identity, 90% coverage
- Ligand: magnesium ion (3i6tB)
4h83F / A4AFX2 Crystal structure of mandelate racemase/muconate lactonizing enzyme (efi target:502127)
23% identity, 90% coverage
- Ligand: bicarbonate ion (4h83F)
FN1586 O-succinylbenzoate-CoA synthase from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
24% identity, 77% coverage
- Autoaggregation response of Fusobacterium nucleatum
Merritt, Applied and environmental microbiology 2009 - “...RT-r Fn0796 RT-f Fn0796 RT-r Fn0941 RT-f Fn0941 RT-r Fn1586 RT-f Fn1586 RT-r Fn1803 RT-f Fn1803 RT-r Fn1900 RT-f Fn1900 RT-r Fn1988 RT-f Fn1988 RT-r Fn1989 RT-f...”
- “...FN0271 FN0271 FN0650 FN0650 FN0796 FN0796 FN0941 FN0941 FN1586 FN1586 FN1803 FN1803 FN1900 FN1900 FN1988 FN1988 FN1989 FN1989 FN2077 FN2077 using the...”
2qgyA Crystal structure of an enolase from the environmental genome shotgun sequencing of the sargasso sea
20% identity, 90% coverage
- Ligand: magnesium ion (2qgyA)
3my9A / A8HTB8 Crystal structure of a muconate cycloisomerase from azorhizobium caulinodans
23% identity, 70% coverage
- Ligand: magnesium ion (3my9A)
clcB / Q706U0 chloromuconate cycloisomerase subunit (EC 5.5.1.7; EC 5.5.1.11) from Pseudomonas putida (see 5 papers)
clcB / CAE92860.1 chloromuconate cycloisomerase from Pseudomonas putida (see 3 papers)
PKB_3274, PKB_3623 muconate cycloisomerase family protein from Pseudomonas knackmussii B13
23% identity, 83% coverage
- Combinatorial pathway balancing provides biosynthetic access to 2-fluoro-cis,cis-muconate in engineered Pseudomonas putida
Wirth, Chem catalysis 2021 - “...catA and catB (>30% homology) were found in identical copies ( PKB_3273 / PKB_3622 and PKB_3274 / PKB_3623 ) as part of an extended genome duplication ( Figure1 B). This DNA segment, clc , had been previously recognized as a self-transferable element conferring the ability to...”
- “...catB (>30% homology) were found in identical copies ( PKB_3273 / PKB_3622 and PKB_3274 / PKB_3623 ) as part of an extended genome duplication ( Figure1 B). This DNA segment, clc , had been previously recognized as a self-transferable element conferring the ability to degrade chloroaromatics....”
3u4fA / A3SMJ4 Crystal structure of a mandelate racemase (muconate lactonizing enzyme family protein) from roseovarius nubinhibens
23% identity, 87% coverage
- Ligand: magnesium ion (3u4fA)
3fxgA / D0VX14 Crystal structure of rhamnonate dehydratase from gibberella zeae complexed with mg
24% identity, 82% coverage
- Ligand: magnesium ion (3fxgA)
4mggA / A0NXQ8 Crystal structure of an enolase (mandelate racemase subgroup) from labrenzia aggregata iam 12614 (target nysgrc-012903) with bound mg, space group p212121
22% identity, 86% coverage
- Ligand: magnesium ion (4mggA)
C3HPD_ROSAI / A0NXQ8 Cis-3-hydroxy-L-proline dehydratase; c3LHyp dehydratase; c3LHypD; EC 4.2.1.171 from Roseibium aggregatum (strain ATCC 25650 / DSM 13394 / JCM 20685 / NBRC 16684 / NCIMB 2208 / IAM 12614 / B1) (Stappia aggregata) (see paper)
A0NXQ8 cis-L-3-hydroxyproline dehydratase (EC 4.2.1.171) from Roseibium aggregatum (see paper)
22% identity, 86% coverage
- function: Catalyzes the dehydration of cis-3-hydroxy-L-proline (c3LHyp) to Delta(1)-pyrroline-2-carboxylate (Pyr2C). Is likely involved in a degradation pathway that converts c3LHyp to L-proline, which allows L.aggregata to grow on c3LHyp as a sole carbon source. Also catalyzes the epimerization of c3LHyp to trans-3-hydroxy-D-proline (t3DHyp), a competing reaction occurring from the same enolate anion intermediate. L-proline, t3LHyp, t4LHyp, c4DHyp and their methylated derivatives are not substrates.
catalytic activity: cis-3-hydroxy-L-proline = 1-pyrroline-2-carboxylate + H2O (RHEA:47624)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily.
Zhang, Journal of the American Chemical Society 2015 (PubMed)
A3LZU6 L-rhamnonate dehydratase (EC 4.2.1.90) from Scheffersomyces stipitis (see 2 papers)
XP_001386433 L-rhamnonate dehydratase from Scheffersomyces stipitis CBS 6054
21% identity, 75% coverage
BCAS0498 muconate cycloisomerase I 2 from Burkholderia cenocepacia J2315
23% identity, 90% coverage
- Identification of functions linking quorum sensing with biofilm formation in Burkholderia cenocepacia H111
Inhülsen, MicrobiologyOpen 2012 - “...aidA ) 138.1 7.8 Cell envelope biogenesis BCAL1813 5.3 4.1 n.d. BCAM2720 4.4 2.3 n.d. BCAS0498 4.9 2.4 n.d. Signal transduction and secondary metabolites BCAM0028 5.1 n.d. n.d. BCAM1870 ( cepI ) 27.0 n.d. n.d. Transport and metabolism BCAL0121 ( aqpZ ) 3.3 n.d. n.d. BCAL0358...”
- “...BCAL1678BCAL1681, BCAL1813, BCAL1921, BCAL3178, BCAL3179, BCAL3285, BCAM0028, BCAM0030, BCAM0393, BCAM0835, BCAM2140BCAM2143, BCAM2308, BCAM2720, BCAS0236, and BCAS0498 ( Table 1 ). We found that a large proportion of the QS-regulated proteins was not among the QS-regulated genes identified by the microarray analysis, suggesting that expression of many...”
CD1389 putative chloromuconate cycloisomerase from Clostridium difficile 630
22% identity, 88% coverage
3i6eA / Q5LM96 Crystal structure of muconate lactonizing enzyme from ruegeria pomeroyi.
25% identity, 68% coverage
- Ligand: magnesium ion (3i6eA)
4h19A / Q7CU39 Crystal structure of an enolase (mandelate racemase subgroup, target efi-502087) from agrobacterium tumefaciens, with bound mg and d- ribonohydroxamate, ordered loop
24% identity, 86% coverage
- Ligands: calcium ion; magnesium ion; (2r,3r,4r)-n,2,3,4,5-pentakis(oxidanyl)pentanamide (4h19A)
1nu5A / P27099 Crystal structure of pseudomonas sp. P51 chloromuconate lactonizing enzyme (see paper)
24% identity, 69% coverage
- Ligand: manganese (ii) ion (1nu5A)
tcbD / P27099 chloromuconate cycloisomerase subunit (EC 5.5.1.11; EC 5.5.1.7) from Pseudomonas sp. (strain P51) (see 2 papers)
TCBD_PSESQ / P27099 Chloromuconate cycloisomerase; Muconate cycloisomerase II; EC 5.5.1.7 from Pseudomonas sp. (strain P51) (see paper)
24% identity, 69% coverage
tfdDI / P05404 chloromuconate cycloisomerase subunit (EC 5.5.1.7; EC 5.5.1.11) from Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197) (see 5 papers)
2chrA / P05404 A re-evaluation of the crystal structure of chloromuconate cycloisomerase (see paper)
P05404 Chloromuconate cycloisomerase from Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)
24% identity, 69% coverage
3tcsB / Q161M1 Crystal structure of a putative racemase from roseobacter denitrificans
22% identity, 87% coverage
- Ligands: magnesium ion; d-alanine (3tcsB)
4dn1A / A9CL63 Crystal structure of an enolase (mandelate racemase subgroup member) from agrobacterium tumefaciens (target efi-502088) with bound mg and formate
23% identity, 88% coverage
- Ligand: magnesium ion (4dn1A)
Pc21g04400 uncharacterized protein from Penicillium rubens
23% identity, 75% coverage
- Studying the Gene Expression of Penicillium rubens Under the Effect of Eight Essential Oils
Kisová, Antibiotics (Basel, Switzerland) 2020 - “...Pc12g13500 and Pc20g04410); fructose and mannose metabolisms (Pc16g12970, Pc22g09390, Pc21g05470, Pc20g01550, Pc13g12020, Pc12g09190, Pc12g13500, Pc21g04410, Pc21g04400 and Pc16g10970) and galactose metabolism (Pc12g13500, Pc14g00310, Pc12g07810 and Pc20g04410). The dominant gene in each group is 6-phosphofructokinase (Pc12g13500). It is responsible for transferring phosphorus-containing groups. In contrast, low levels...”
NCU09034 mandelate racemase/muconate lactonizing enzyme family protein from Neurospora crassa OR74A
22% identity, 72% coverage
- The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus
Wu, Proceedings of the National Academy of Sciences of the United States of America 2020 - “...mutant, sut-28 cells failed to activate expression of the rhamnose catabolic gene l -rhamnonate dehydratase (NCU09034) ( Fig. 4 C ). The expression of sut-28 was higher in cre-1 cells compared to WT when exposed to l -rhamnose or l -rhamnose and glucose ( SI Appendix...”
- “...in FGSC2489 and sut-28 strains after induction on pectin. ( C ) Relative expression of NCU09034 ( l -rhamnonate dehydratase) relative to actin (NCU04173) in FGSC2489 (WT), sut-28 , and pdr-1 strains after induction on rhamnose. ( D ) Rhamnose uptake in FGSC2489 and cre-1 strains...”
- The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in Neurospora crassa
Thieme, Biotechnology for biofuels 2017 - “...- 1 (NCU02369) and genes encoding the unsaturated rhamnogalacturonyl hydrolase GH105-1 (NCU02654), the LRA3 homolog NCU09034, the -galactosidases GH35-1 (NCU00642) and GH35-2 (NCU04623), and the l -arabinitol 4-dehydrogenase ARD-1 (NCU00643). Fig.3 Scatterplots and clustering of RNA-seq data from WT and pdr - 1 . Scatterplot diagram...”
- “...- 1 , two putative lra4 homologs (NCU03086, NCU05037), the putative lra3 and rha1 homologs (NCU09034 and NCU09035, respectively), the putative gaaB/lgd1 homolog (NCU07064), ard - 1 (NCU00643), and the GCY protein-coding gene NCU01906. In particular, the failed induction of the endo-PG-encoding gh28 - 1 and...”
- Identification of Allorecognition Loci in Neurospora crassa by Genomics and Evolutionary Approaches
Zhao, Molecular biology and evolution 2015 - “...actual gene size. Three genes were conserved and syntenic in all species (NCU09035, alcohol dehydrogenase; NCU09034, mandelate racemase; NCU09033, C6 transcription factor). Checkered brown boxes show conservation of genes between species within the het-e genetic interval in species outside of the Sordariomycetes. Gene 111 stands for...”
An13g00920 uncharacterized protein from Aspergillus niger
23% identity, 77% coverage
3t8qB / A9D2J3 Crystal structure of mandelate racemase/muconate lactonizing enzyme family protein from hoeflea phototrophica
23% identity, 74% coverage
- Ligand: magnesium ion (3t8qB)
SSO1303 Mandelate racemase /muconate lactonizing enzyme related protein (MR/MLE) from Sulfolobus solfataricus P2
24% identity, 55% coverage
- Metabolic reconstruction and experimental verification of glucose utilization in Desulfurococcus amylolyticus DSM 16532
Reischl, Folia microbiologica 2018 - “...S. solfataricus , e.g., SSO3124, SSO3117 and SSO3118 (Peng et al. 2011 ) or SSO3107, SSO1303 (Brouns et al. 2006 ), could not be detected in the genome of D. amylolyticus . Only a homolog of the 2-keto-3-deoxy-D-arabinonate dehydratase (COG3970), which is responsible for arabinose degradation,...”
- Carbohydrate hydrolysis and transport in the extreme thermoacidophile Sulfolobus solfataricus
Lalithambika, Applied and environmental microbiology 2012 - “...(DSM1617). (C) PCR analysis of the site of duplication from Sso1303 (primer P3) to Sso1388 (P4) (Table 3). Lanes: 1, strain P2; 2, strain 98/2. (D) Analysis of...”
- “...were determined by PCR using a forward primer for Sso1303 and a reverse primer for Sso1388, resulting in a 6.875-kb amplicon (Fig. 1C) rather than the nearly...”
3fv9C / A3SNG0 Crystal structure of putative mandelate racemase/muconatelactonizing enzyme from roseovarius nubinhibens ism complexed with magnesium
21% identity, 89% coverage
- Ligand: magnesium ion (3fv9C)
C3HPD_ANCN5 / D7A0Y2 Cis-3-hydroxy-L-proline dehydratase; c3LHyp dehydratase; c3LHypD; EC 4.2.1.171 from Ancylobacter novellus (strain ATCC 8093 / DSM 506 / JCM 20403 / CCM 1077 / IAM 12100 / NBRC 12443 / NCIMB 10456) (Starkeya novella) (see paper)
22% identity, 86% coverage
- function: Catalyzes the dehydration of cis-3-hydroxy-L-proline (c3LHyp) to Delta(1)-pyrroline-2-carboxylate (Pyr2C). May be involved in a degradation pathway that converts c3LHyp to L-proline, which would allow S.novella to grow on c3LHyp as a sole carbon source.
catalytic activity: cis-3-hydroxy-L-proline = 1-pyrroline-2-carboxylate + H2O (RHEA:47624)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
JJQ59_20615 muconate/chloromuconate family cycloisomerase from Cupriavidus necator
24% identity, 76% coverage
PMI19_01186 muconate cycloisomerase family protein from Pseudomonas sp. GM16
22% identity, 94% coverage
- Mechanism for Utilization of the Populus-Derived Metabolite Salicin by a Pseudomonas-Rahnella Co-Culture
Dahal, Metabolites 2023 - “...PMI19_01135 catechol 1,2-dioxygenase Yes (up) PMI19_01184 catechol 1,2-dioxygenase Yes 6.8 PMI19_03945 catechol 1,2-dioxygenase No (up) PMI19_01186 muconate cycloisomerase Yes (up) PMI19_03943 muconate cycloisomerase - ND PMI19_01185 muconolactone delta-isomerase Yes (up) PMI19_03944 muconolactone delta-isomerase - ND PMI19_04396 3-oxoadipate enol-lactonase Yes (up) PMI19_04846 3-oxoadipate enol-lactonase - ND PMI19_01175...”
BJN34_24340 muconate/chloromuconate family cycloisomerase from Cupriavidus necator
25% identity, 76% coverage
- Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses
Moriuchi, Frontiers in microbiology 2019 - “...BJN34_08555 (C1), 18150 (C1), 26685 (C2), 28970 (C2), 30600 (C2) catB K01856 EC:5.5.1.1 Muconate cycloisomerase BJN34_24340 (C2) catC K03464 EC:5.3.3.4 Muconolactone isomerase BJN34_29745 (C2) catD K01055 EC:3.1.1.24 3-oxoadipate enol-lactonase BJN34_29740 (C2) 3-oxoadipate pcaI K01031 EC:2.8.3.6 3-oxoadipate CoA-transferase, alpha subunit BJN34_21015 (C2) pcaJ K01032 EC:2.8.3.6 3-oxoadipate CoA-transferase,...”
- “...transcriptional regulator. Two catR homologs were identified upstream of catA (BJN34_08555) on Chr1 and catB (BJN34_24340) on Chr2, respectively, in the NH9 genome. Because catechol degradation is one of the central pathways in the metabolism of a variety of aromatic compounds (Broderick, 1999 ), the acquisition...”
O33949 Muconate cycloisomerase 1-2 from Acinetobacter lwoffii
22% identity, 72% coverage
catB2 / BAA75210.1 muconate cycloisomerase from Frateuria sp. ANA-18 (see paper)
23% identity, 72% coverage
PMI19_03943 muconate cycloisomerase family protein from Pseudomonas sp. GM16
21% identity, 94% coverage
- Mechanism for Utilization of the Populus-Derived Metabolite Salicin by a Pseudomonas-Rahnella Co-Culture
Dahal, Metabolites 2023 - “...PMI19_01184 catechol 1,2-dioxygenase Yes 6.8 PMI19_03945 catechol 1,2-dioxygenase No (up) PMI19_01186 muconate cycloisomerase Yes (up) PMI19_03943 muconate cycloisomerase - ND PMI19_01185 muconolactone delta-isomerase Yes (up) PMI19_03944 muconolactone delta-isomerase - ND PMI19_04396 3-oxoadipate enol-lactonase Yes (up) PMI19_04846 3-oxoadipate enol-lactonase - ND PMI19_01175 3-oxoadipate CoA-transferase, alpha subunit Yes...”
3sn0A / Q13PB7 Crystal structure of putative l-alanine-dl-glutamate epimerase from burkholderia xenovorans strain lb400 bound to magnesium and fumarate
24% identity, 71% coverage
- Ligands: magnesium ion; fumaric acid (3sn0A)
LOC411307 mitochondrial enolase superfamily member 1 from Apis mellifera
20% identity, 82% coverage
catB / A0F0B3 muconate cycloisomerase (EC 5.5.1.1) from Pseudomonas reinekei (see paper)
21% identity, 76% coverage
YITF_BACSU / O06741 Putative isomerase YitF; EC 5.-.-.- from Bacillus subtilis (strain 168)
BSU10970 putative enolase superfamily enzyme from Bacillus subtilis subsp. subtilis str. 168
24% identity, 63% coverage
HYEP_ENTFA / Q834W6 Hydrophobic dipeptide epimerase; EC 5.1.1.- from Enterococcus faecalis (strain ATCC 700802 / V583) (see paper)
3jvaB / Q834W6 Crystal structure of dipeptide epimerase from enterococcus faecalis v583 (see paper)
24% identity, 56% coverage
- function: Catalyzes the epimerization of L-Ile-L-Tyr to L-Ile-D-Tyr (in vitro). Catalyzes the epimerization of dipeptides, with a preference for substrates with a hydrophobic or basic amino acid in the first position, followed by an aromatic residue in the second position. Has epimerase activity with L-Ile-L-Tyr, L-Val-L-Tyr and L-Arg-L-Tyr (in vitro).
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Ligand: magnesium ion (3jvaB)
2ggeD / O06741 Crystal structure of mandelate racemase/muconate lactonizing enzyme from bacillus subtilis complexed with mg++ at 1.8 a
25% identity, 63% coverage
- Ligand: magnesium ion (2ggeD)
MENC_GEOKU / B1A612 o-succinylbenzoate synthase; OSB synthase; OSBS; 4-(2'-carboxyphenyl)-4-oxybutyric acid synthase; N-acylamino acid racemase; NAAAR; N-succinylamino acid racemase; NSAAR; NSAR; o-succinylbenzoic acid synthase; EC 4.2.1.113; EC 5.1.1.- from Geobacillus kaustophilus (see paper)
24% identity, 80% coverage
- function: Converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1- carboxylate (SHCHC) to 2-succinylbenzoate (OSB) (By similarity). Also acts as a N-succinylamino acid racemase (NSAR) that catalyzes the racemization of various N-succinylamino acids, including N-succinyl- alanine and N-succinyl-phenylalanine (Ref.1). Can catalyze the racemization of a broad range of N-acylamino acids, including N-acetyl- methionine, N-acetyl-phenylalanine, N-carbamoyl-methionine, N-formyl-D- methionine, N-formyl-D-norleucine and N-carbamoyl-D-norleucine (PubMed:25875730, Ref.1). May be a bifunctional enzyme involved in menaquinone biosynthesis and in an irreversible pathway for the conversion of D- to L-amino acids, thereby facilitating the survival and/or growth of the organism (By similarity).
catalytic activity: (1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O (RHEA:10196)
catalytic activity: N(alpha)-acetyl-D-methionine = N(alpha)-acetyl-L-methionine (RHEA:59960)
catalytic activity: N-acetyl-D-phenylalanine = N-acetyl-L-phenylalanine (RHEA:62772)
cofactor: a divalent metal cation (Shows highest activity in vitro with Co(2+), Mn(2+) and Ni(2+). {ECO:0000269|Ref.)1}
subunit: Homotetramer.
1jpmA / O34508 L-ala-d/l-glu epimerase (see paper)
21% identity, 81% coverage
- Ligand: magnesium ion (1jpmA)
BCAM0805 muconate cycloisomerase I 1 from Burkholderia cenocepacia J2315
21% identity, 67% coverage
AEEP_BACSU / O34508 L-Ala-D/L-Glu epimerase; AE epimerase; AEE; EC 5.1.1.20 from Bacillus subtilis (strain 168) (see 4 papers)
O34508 L-Ala-D/L-Glu epimerase (EC 5.1.1.20) from Bacillus subtilis (see 3 papers)
BSU12980 L-Ala-D/L-Glu epimerase from Bacillus subtilis subsp. subtilis str. 168
21% identity, 81% coverage
- function: Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of the other Ala-X dipeptides L-Ala-L- Asp, L-Ala-L-Leu, L-Ala-L-Met, and L-Ala-L-Ser. Is not able to epimerize other L-Ala-X dipeptides. Is also active with L-Ser-L-Glu and, oddly, L-Pro-L-Glu, but not with L-Glu-L-Glu, L-Lys-L-Glu, L-Lys- L-Ala, or D-Ala-D-Ala.
catalytic activity: L-alanyl-L-glutamate = L-alanyl-D-glutamate (RHEA:28394)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Homooctamer; tetramer of dimers. - Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
Pfeiffer, Genes 2021 - “...[ 282 ] 20600129 7d pathway gap EC 4.2.99.20 7d HVO_1461 menC no 29% BSU12980 O34508 [ 283 ] 11747447 Ala/Glu epimerase 7d HVO_1461 (cont.) yes 24% BSU30780 O34514 [ 284 ] 10194342 o-succinylbenzoate synthase 7d HVO_1375 menE yes 36% BSU30790 P23971 [ 285 ] 27933791...”
- Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
Pfeiffer, Genes 2021 - “...P23970 [ 282 ] 20600129 7d pathway gap EC 4.2.99.20 7d HVO_1461 menC no 29% BSU12980 O34508 [ 283 ] 11747447 Ala/Glu epimerase 7d HVO_1461 (cont.) yes 24% BSU30780 O34514 [ 284 ] 10194342 o-succinylbenzoate synthase 7d HVO_1375 menE yes 36% BSU30790 P23971 [ 285 ]...”
NSAR_BACCR / Q81IL5 N-succinyl-L-Arg/Lys racemase; N-succinyl amino acid racemase; NSAR; EC 5.1.1.- from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711) (see paper)
2p88A / Q81IL5 Crystal structure of n-succinyl arg/lys racemase from bacillus cereus atcc 14579 (see paper)
BC0371 Mandelate racemase/muconate lactonizing enzyme family protein from Bacillus cereus ATCC 14579
21% identity, 90% coverage
- function: Catalyzes efficient racemization of N-succinyl-L-Arg and N- succinyl-L-Lys, suggesting that these are physiological substrates of this enzyme. Has low activity with L-Asp-L-Lys, and even lower activity with L-Leu-L-Arg, L-Leu-L-Lys, N-succinyl-L-His and N-succinyl-L-Met (in vitro).
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Ligand: magnesium ion (2p88A)
- SigB modulates expression of novel SigB regulon members via Bc1009 in non-stressed and heat-stressed cells revealing its alternative roles in Bacillus cereus
Yeak, BMC microbiology 2023 - “...YjbD Arsenate reductase family protein -0.6 P 95 BC0353 YerQ hypothetical protein -0.6 IR 96 BC0371 BC0371 Mandelate racemase/muconate lactonizing enzyme family protein -0.6 MR 97 BC1648 BC1648 hypothetical Cytosolic Protein -0.6 S 98 BC4165 BkdR Sigma-54-dependent transcriptional activator -0.6 -1.0 KT 99 BC2940 BC2940 Histidinol-phosphate...”
- Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking
Fan, Journal of the American Chemical Society 2013 - “...20 . For example, this strategy was successfully employed, in the prediction of function for Bc0371 from Bacillus cereus as an N -succinyl arginine/lysine racemase by docking dipeptides and N -succinyl amino acids to a homology model of Bc0371 based on the X-ray structure of the...”
- The Enzyme Function Initiative
Gerlt, Biochemistry 2011 - “...muconate lactonizing enzyme (MLE) subgroup of the EN superfamily encoded by Bacillus cereus ATCC 14579 (BC0371). This prediction was accomplished by flexible receptor docking of a virtual library of dipeptides and N-succinyl amino acids to a homology model generated using the structure of the L-Ala-D/L-Glu epimerase...”
- “...(green) superimposed on experimental structure (red, with electron density contours) ( 43 ). Panel B, BC0371 (EN superfamily) in complex with substrate N-succinyl Arg, as predicted by homology modeling and docking (cyan) as well as determined by crystallography (yellow) ( 41 ). Both panels are reproduced...”
- Prediction of function in protein superfamilies
Copley, F1000 biology reports 2009 - “...[ 16 - 18 ]). An example is the identification of function of Bacillus subtilis BC0371 [ 19 ], which belongs to the muconate-lactonizing enzyme subgroup of the enolase superfamily. This enzyme clusters with the l -Ala- d/l -Glu epimerase family, but three residues typical of...”
- “...Song et al. [ 19 ] generated a homology model for the Bacillus cereus protein BC0371, which had been discovered by experimental screening of potential substrates to be an N -succinyl- l -Arg racemase (discussed in the Introduction and context section). When a set of 420...”
Q43931 Muconate cycloisomerase 1 from Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)
22% identity, 94% coverage
MENC_GEOSE / A0A0P0ZBS7 o-succinylbenzoate synthase; OSB synthase; OSBS; 4-(2'-carboxyphenyl)-4-oxybutyric acid synthase; N-acylamino acid racemase; NAAAR; N-succinylamino acid racemase; NSAAR; NSAR; o-succinylbenzoic acid synthase; EC 4.2.1.113; EC 5.1.1.- from Geobacillus stearothermophilus (Bacillus stearothermophilus) (see paper)
24% identity, 88% coverage
- function: Converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1- carboxylate (SHCHC) to 2-succinylbenzoate (OSB) (By similarity). Also acts as a N-succinylamino acid racemase (NSAR) that catalyzes the racemization of N-succinyl-D/L-phenylalanine (PubMed:25875730). Can catalyze the racemization of a broad range of N-acylamino acids, including N-acetyl-D-methionine, N-formyl-D/L-methionine, N-formyl-D/L- norleucine, N-formyl-D/L-aminobutyric acid, N-formyl-D/L-norvaline, N- formyl-D/L-homophenylalanine, N-carbamoyl-D-methionine and N-carbamoyl- D-norleucine (PubMed:25875730). May be a bifunctional enzyme involved in menaquinone biosynthesis and in an irreversible pathway for the conversion of D- to L-amino acids, thereby facilitating the survival and/or growth of the organism (By similarity).
catalytic activity: (1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O (RHEA:10196)
catalytic activity: N(alpha)-acetyl-D-methionine = N(alpha)-acetyl-L-methionine (RHEA:59960)
cofactor: a divalent metal cation (Shows highest activity in vitro with Co(2+) and Ni(2+).)
subunit: Homotetramer.
3fvdB / A3SNF7 Crystal structure of a member of enolase superfamily from roseovarius nubinhibens ism complexed with magnesium
22% identity, 89% coverage
- Ligand: magnesium ion (3fvdB)
ABD05_RS17755 muconate/chloromuconate family cycloisomerase from Burkholderia pyrrocinia
21% identity, 67% coverage
G8E09_08715 muconate/chloromuconate family cycloisomerase from Acinetobacter pittii
20% identity, 94% coverage
- Phenotypic Variation and Carbapenem Resistance Potential in OXA-499-Producing Acinetobacter pittii
Zhang, Frontiers in microbiology 2020 - “...0.0001 0.0047 G8E09_03990 BapA prefix-like domain-containing protein 2.85 0.0000 0.0000 G8E09_14955 Trehalose-phosphatase 2.82 0.0000 0.0000 G8E09_08715 Muconate cycloisomerase 2.69 0.0000 0.0000 G8E09_11610 Hypothetical protein 2.68 0.0000 0.0000 G8E09_09795 Hypothetical protein 2.66 0.0000 0.0003 G8E09_08150 SOS response-associated peptidase 2.66 0.0000 0.0000 G8E09_12315 Hypothetical protein 2.63 0.0000 0.0011...”
pRL110598 putative racemase from Rhizobium leguminosarum bv. viciae 3841
21% identity, 67% coverage
3dg6A / A0QTN8 Crystal structure of muconate lactonizing enzyme from mucobacterium smegmatis complexed with muconolactone (see paper)
20% identity, 88% coverage
- Ligands: magnesium ion; [(2s)-5-oxo-2,5-dihydrofuran-2-yl]acetic acid (3dg6A)
MSMEG_1910 muconate cycloisomerase from Mycobacterium smegmatis str. MC2 155
20% identity, 88% coverage
- Withdrawn
, Infectious disorders drug targets 2012 - “...1,4-dihydroxy-2-naphthyl-CoA synthase Metabolism 3T8A, 3T8B, 3T88, 3T89 - 0553 * M. smegmatis muconate lactonizing enzyme, MSMEG_1910 Metabolism 3DG3, 3DG6, 3DG7 - 0736 m * Anti-sigma factor, RslA Information processing 3HUG - 0757 Response regulator, PhoP Environmental stress 3R0J [ 148 ] 0805 s cAMP phosphodiesterase Metabolism...”
F8DD77 glucarate dehydratase from Halopiger xanaduensis (strain DSM 18323 / JCM 14033 / SH-6)
21% identity, 88% coverage
catB / P08310 muconate lactonizing enzyme subunit (EC 5.5.1.1) from Pseudomonas putida (see 2 papers)
CATB_PSEPU / P08310 Muconate cycloisomerase 1; Cis,cis-muconate lactonizing enzyme I; MLE; Muconate cycloisomerase I; EC 5.5.1.1 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see paper)
21% identity, 72% coverage
- function: Catalyzes a syn cycloisomerization
catalytic activity: (S)-muconolactone = cis,cis-muconate + H(+) (RHEA:30031)
cofactor: Mn(2+)
subunit: Homooctamer - A gene cluster involved in degradation of substituted salicylates via ortho cleavage in Pseudomonas sp. strain MT1 encodes enzymes specifically adapted for transformation of 4-methylcatechol and 3-methylmuconate
Cámara, Journal of bacteriology 2007 - “...SM25 CatB, AY028997; for P. putida PRS2000 CatB, P08310; for P. putida KT2440 CatB, NC_002947; for P. fluorescens PFO-1 CatB, NC_007492; for Pseudomonas sp....”
- Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci.
Ceresini, BMC evolutionary biology 2007 - “...flow with isolation by distance was found (Figure 4 ). The interior haplotypes P0062 and P08310 from Northern America contained in the one-step clade 1-1 showed significantly large (P < 0.05) D c . In addition, these internal haplotypes showed larger D c than the average...”
- “...haplotype P0061 whereas significantly large clade distance was associated with the interior haplotypes P0062 and P08310. In addition, the average interior clade distance minus the average tip clade distance was significantly large. These observations fulfilled the prediction that under restricted gene flow younger or tip clades...”
- New bacterial pathway for 4- and 5-chlorosalicylate degradation via 4-chlorocatechol and maleylacetate in Pseudomonas sp. strain MT1
Nikodem, Journal of bacteriology 2003 - “...CatB sequence of P. putida PRS2015 (accession number P08310; 10 identical amino acids), which also exhibits significant similarity (amino acids 213 to 231) to...”
MENC_GEOKA / Q5L1G9 o-succinylbenzoate synthase; OSB synthase; OSBS; 4-(2'-carboxyphenyl)-4-oxybutyric acid synthase; N-succinylamino acid racemase; NSAR; o-succinylbenzoic acid synthase; EC 4.2.1.113; EC 5.1.1.- from Geobacillus kaustophilus (strain HTA426) (see paper)
24% identity, 80% coverage
- function: Converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1- carboxylate (SHCHC) to 2-succinylbenzoate (OSB) (PubMed:16584181). Also acts as a N-succinylamino acid racemase (NSAR) that catalyzes the racemization of various N-succinylamino acids, including N-succinyl-L- valine, N-succinyl-L-alanine, N-succinyl-L-methionine, N-succinyl-L- tyrosine, N-succinyl-L-serine, N-succinyl-L-isoleucine, N-succinyl-L- phenylalanine and N-succinyl-L-leucine (PubMed:16584181). May be a bifunctional enzyme involved in menaquinone biosynthesis and in an irreversible pathway for the conversion of D- to L-amino acids, thereby facilitating the survival and/or growth of the organism (PubMed:16584181).
catalytic activity: (1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O (RHEA:10196)
cofactor: a divalent metal cation
PP3715 muconate cycloisomerase from Pseudomonas putida KT2440
PP_3715 muconate cycloisomerase family protein from Pseudomonas putida KT2440
21% identity, 72% coverage
- Microbial responses to xenobiotic compounds. Identification of genes that allow Pseudomonas putida KT2440 to cope with 2,4,6-trinitrotoluene
Fernández, Microbial biotechnology 2009 - “...AraC family 2.1 4. Metabolism PP2650 gbd 4hydroxybutyrate dehydrogenase 2.3 PP3633 argC Nacetylgammaglutamylphosphate reductase 2.1 PP3715 catB muconate cycloisomerase 2.4 M PP4250 ccoN 1cytochrome c oxidase cbb3type subunit I 2.0 M 5. Unknown/uncharacterized proteins 5.A. Membrane proteins PP1976 HlyD family secretion protein 2.0 PP2647 Major facilitator...”
- Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1
Miyakoshi, Journal of bacteriology 2007 - “...RT-PCR analysis of -ketoadipate pathway genes Gene catB (PP3715) catA2 (PP3166) pcaF (PP1377) pcaD (PP1380) pcaI (PP3951) pcaJ (PP3952) Relative quantity of...”
- A single-plasmid-based, easily curable CRISPR/Cas9 system for rapid, iterative genome editing in Pseudomonas putida KT2440
Wen, Microbial cell factories 2024 - “...conducted in this study Editing Type Gene location and function Target size Efficiency Deletions catBC PP_3715, PP_3714, Muconate cycloisomerase 1434bp 13% (2/15) yqhD PP_2492, Iron-containing alcohol dehydrogenase 500bp 59% (10/17) ech-vdh-fcs PP_3358, PP_3357, PP_3356, Enoyl-CoA-hydratase/aldolase, vanillin dehydrogenase, feruloyl-CoA-synthetase 4324bp 50% (10/20) vdh PP_3357, Vanillin dehydrogenase 1443bp...”
- Transcriptome Changes in Pseudomonas putida KT2440 during Medium-Chain-Length Polyhydroxyalkanoate Synthesis Induced by Nitrogen Limitation
Dabrowska, International journal of molecular sciences 2020 - “...family transcriptional regulator (FnrB). Another group of these significantly differentially regulated genes, PP_3289PP_3292, PP3294, PP_3713, PP_3715, and PP_3783, is believed to be regulated by another member of this family of regulators (FnrC). Interestingly, two of these genes (PP_3290, PP_3294) also code for stress proteins. Finally, two...”
- “...stress protein family 13.43 14.68 10.88 fnrC PP_3713 catB catechol 1,2-dioxygenase 19.44 4.22 5.62 nd PP_3715 syrB muconate cycloisomerase 1 32.00 19.07 4.44 nd PP_3783 nd syringomycin biosynthesis protein 2 8.42 5.00 5.81 nd PP_0807 norR DNA-binding transcriptional regulator 0.49 0.87 0.65 PP_0814 cyoC cyt. bo...”
- H-NS Family Proteins Drastically Change Their Targets in Response to the Horizontal Transfer of the Catabolic Plasmid pCAR1
Nakamura, Frontiers in microbiology 2020 - “...Up-regulated PP_3713 catA * Q Catechol 1,2-dioxygenase Up-regulated PP_3714 catC * Q Muconolactone isomerase Up-regulated PP_3715 catB * M Muconate and chloromuconate cycloisomerase Up-regulated PP_3782 PP_3782* Hypothetical protein Up-regulated PP_4403 bkdB C Branched-chain alpha-keto acid dehydrogenase subunit E2 Down-regulated PP_5033 hutU E Urocanate hydratase Down-regulated PP_5139...”
catB / AAC46430.1 muconate cycloisomerase from Acinetobacter baylyi (see 8 papers)
21% identity, 94% coverage
HYEP_ROSLO / F7ZLS5 Hydrophobic dipeptide epimerase; EC 5.1.1.- from Roseobacter litoralis (strain ATCC 49566 / DSM 6996 / JCM 21268 / NBRC 15278 / OCh 149) (see paper)
25% identity, 85% coverage
- function: Dipeptide epimerase with a preference for hydrophobic substrates. Catalyzes the epimerization of L-Ala-L-Thr, L-Ala-L-Met, L- Ala-L-His, L-Ala-L-Phe, L-Ala-L-Tyr, L-Ala-L-Trp, L-Ile-L-Ala, L-Ile-L- Ser, L-Ile-L-Met, L-Ile-L-His, L-Ile-L-Phe, L-Ile-L-Tyr, L-Ile-L-Trp, L-Phe-L-Met, L-Phe-L-His, L-Phe-L-Phe, L-Phe-L-Tyr, L-Phe-L-Trp, L-Phe- L-Ser, L-Phe-L-Thr and L-Phe-L-Lys (in vitro).
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
BMULJ_04920 mandelate racemase from Burkholderia multivorans ATCC 17616
21% identity, 67% coverage
M0JBW3 glucarate dehydratase from Haloferax denitrificans ATCC 35960
24% identity, 73% coverage
YP_070105 putative racemase from Yersinia pseudotuberculosis IP 32953
22% identity, 65% coverage
3dgbA / Q4K9X1 Crystal structure of muconate lactonizing enzyme from pseudomonas fluorescens complexed with muconolactone (see paper)
26% identity, 39% coverage
- Ligands: magnesium ion; [(2s)-5-oxo-2,5-dihydrofuran-2-yl]acetic acid (3dgbA)
CBL13_01890, T1E_1744 muconate cycloisomerase family protein from Pseudomonas putida
21% identity, 72% coverage
Q4K9X1 Muconate cycloisomerase (EC 5.5.1.1) from Pseudomonas fluorescens (see paper)
26% identity, 39% coverage
3nzgD Crystal structure of a putative racemase with mg ion
22% identity, 91% coverage
- Ligand: magnesium ion (3nzgD)
blr6118 blr6118 from Bradyrhizobium japonicum USDA 110
22% identity, 76% coverage
- Transcriptomic Characterization of Bradyrhizobium diazoefficiens Bacteroids Reveals a Post-Symbiotic, Hemibiotrophic-Like Lifestyle of the Bacteria within Senescing Soybean Nodules
Franck, International journal of molecular sciences 2018 - “...blr0925, blr1457, blr2533, blr2715, blr2809, blr3324, blr3400, blr3517, blr4155, blr4311, blr4566, blr4772, blr5162, blr5169, blr5229, blr6118, blr6544, blr6569, blr6661, blr6771, blr7060, blr7216, blr7281, blr7496, blr7595, blr7717, blr7815, blr8000, blr8060, blr8194, bsl3895, bsl7758, bsr1887, and bsr3197. Figure 8 Expressed genes representing the post-symbiotic category. The 33 genes...”
PS417_23670 Muconate cycloisomerase (EC 5.5.1.1) from Pseudomonas simiae WCS417
22% identity, 71% coverage
- mutant phenotype: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (MUCONATE-CYCLOISOMERASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
C6YXG6 Muconate cycloisomerase (EC 5.5.1.1) from Pseudomonas reinekei (see paper)
21% identity, 91% coverage
KPN_01875 L-Ala-D/L-Glu epimerase, a muconate lactonizing enzyme from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
23% identity, 72% coverage
- Deciphering the genetic network and programmed regulation of antimicrobial resistance in bacterial pathogens
Ramamurthy, Frontiers in cellular and infection microbiology 2022 - “...glsA , osmE , yjhA , yhdT , rimL , pepB , and KPN_00437, and KPN_01875 ORFs that are responsible for several DNA metabolic processes, DNA repair, and stress response ( Miryala etal., 2020 ). Of these, gyrA , parC , gyrB , parE , recA...”
- Role of SHV-11, a Class A β-Lactamase, Gene in Multidrug Resistance Among Klebsiella pneumoniae Strains and Understanding Its Mechanism by Gene Network Analysis
Miryala, Microbial drug resistance (Larchmont, N.Y.) 2020 (PubMed)- “...with its functional partner genes gyrA, parC, glsA, osmE, yjhA, yhdT, rimL, pepB, KPN_00437, and KPN_01875. We have also observed that of 51 genes, 27 genes were enriched in various Gene Ontology terms such as DNA metabolic process, DNA repair, and response to stress. The genes...”
- An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228
Liao, Journal of bacteriology 2011 - “...for these metabolic pathways are KPN_01869 to KPN_01875 and KPN_04779 to KPN_04789, respectively (8, 34). Moreover, K. pneumoniae can anaerobically...”
1f9cA / Q51958 Crystal structure of mle d178n variant (see paper)
21% identity, 76% coverage
- Ligand: manganese (ii) ion (1f9cA)
BHE75_01137 muconate/chloromuconate family cycloisomerase from Sphingomonas haloaromaticamans
22% identity, 93% coverage
NSAR_THET8 / Q5SJX8 N-succinylamino acid racemase; NSAR; N-acylamino acid racemase; NAAAR; o-succinylbenzoate synthase; OSB synthase; OSBS; EC 5.1.1.-; EC 4.2.1.113 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see 2 papers)
22% identity, 85% coverage
- function: Acts as a N-succinylamino acid racemase (NSAR) that catalyzes the racemization of N-succinyl-L-phenylglycine (PubMed:24872444). Also converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 2-succinylbenzoate (OSB) (PubMed:24872444). Catalyzes both N- succinylamino acid racemization and OSB synthesis at equivalent rates (PubMed:24872444). However, NSAR activity is probably the protein's biological function, because menaquinone biosynthesis genes are missing in this species (Probable).
catalytic activity: (1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O (RHEA:10196)
cofactor: a divalent metal cation (Binds 1 divalent metal cation per subunit.)
subunit: Homooctamer. Tetramer of dimers.
AAEP_CYTH3 / Q11T61 D-Ala-D/L-Ala epimerase; EC 5.1.1.- from Cytophaga hutchinsonii (strain ATCC 33406 / DSM 1761 / CIP 103989 / NBRC 15051 / NCIMB 9469 / D465) (see paper)
3q45A / Q11T61 Crystal structure of dipeptide epimerase from cytophaga hutchinsonii complexed with mg and dipeptide d-ala-l-val (see paper)
22% identity, 69% coverage
- function: Catalyzes the epimerization of D-Ala-D-Ala to D-Ala-L-Ala. Has broad substrate specificity and catalyzes the epimerization of a variety of dipeptides containing an N-terminal Ala followed by a hydrophobic or polar residue, such as Val, Ser and Met (in vitro).
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.) - Ligands: magnesium ion; d-alanine; valine (3q45A)
AEEP_CLOAB / Q97MK4 L-Ala-D/L-Glu epimerase; AE epimerase; AEE; EC 5.1.1.20 from Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W) (see paper)
20% identity, 81% coverage
- function: Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the epimerization of L-Ala-D-Asp.
catalytic activity: L-alanyl-L-glutamate = L-alanyl-D-glutamate (RHEA:28394)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
tfdDII / P42428 dienelactone hydrolase II subunit (EC 5.5.1.7) from Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197) (see paper)
23% identity, 89% coverage
PA4041 hypothetical protein from Pseudomonas aeruginosa PAO1
26% identity, 62% coverage
catB / AAA66202.1 muconate lactonizing enzyme from Pseudomonas putida (see paper)
20% identity, 72% coverage
PMPD1_3768 L-fuconate dehydratase from Paramixta manurensis
21% identity, 65% coverage
4kemA / D3P639 Crystal structure of a tartrate dehydratase from azospirillum, target efi-502395, with bound mg and a putative acrylate ion, ordered active site
22% identity, 60% coverage
- Ligand: magnesium ion (4kemA)
LGG_00433 enolase superfamily protein, N-acylamino acid racemase, mandelate racemase/muconate lactonizing enzyme / o-succinylbenzoate synthase from Lactobacillus rhamnosus GG
22% identity, 82% coverage
4ip4A / Q1GLV3 Crystal structure of l-fuconate dehydratase from silicibacter sp. Tm1040 liganded with mg
21% identity, 64% coverage
- Ligand: magnesium ion (4ip4A)
PA14_11580 putative racemase from Pseudomonas aeruginosa UCBPP-PA14
26% identity, 62% coverage
BCAM2284 putative mrandelate racemase/muconate lactonizing enzyme from Burkholderia cenocepacia J2315
21% identity, 69% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory