PaperBLAST
PaperBLAST Hits for SwissProt::Q52011 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; HOPDA hydrolase; 2,6-dioxo-6-phenylhexa-3-enoate hydrolase; EC 3.7.1.8 (Pseudomonas furukawaii) (286 a.a., MTALTESSTS...)
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>SwissProt::Q52011 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; HOPDA hydrolase; 2,6-dioxo-6-phenylhexa-3-enoate hydrolase; EC 3.7.1.8 (Pseudomonas furukawaii)
MTALTESSTSKFVKINEKGFSDFNIHYNEAGNGETVIMLHGGGPGAGGWSNYYRNVGPFV
DAGYRVILKDSPGFNKSDAVVMDEQRGLVNARAVKGLMDALGIDRAHLVGNSMGGATALN
FAIEYPERIGKLILMGPGGPGPSMFAPMPMEGIKLLFKLYAEPSYENLKQMIQVFLYDQS
LITEELLQGRWEAIQRQPEHLKNFLISAQKAPLSTWDVTARLGEIKAKTFITWGRDDRFV
PLDHGLKLLWNIDDARLHVFSKCGHWAQWEHADEFNRLAIDFLRQA
Running BLASTp...
Found 250 similar proteins in the literature:
BPHD_PSEFK / Q52011 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; HOPDA hydrolase; 2,6-dioxo-6-phenylhexa-3-enoate hydrolase; EC 3.7.1.8 from Pseudomonas furukawaii (see paper)
bphD / BAA12881.1 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid hydrolase from Pseudomonas oleovorans (see paper)
100% identity, 100% coverage
- function: Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo- 6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2- hydroxy-2,4-pentadienoic acid (HPD).
catalytic activity: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = 2-oxopent-4-enoate + benzoate + H(+) (RHEA:17161)
subunit: Homodimer.
BPHD_PARXL / P47229 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; HOPDA hydrolase; 2,6-dioxo-6-phenylhexa-3-enoate hydrolase; EC 3.7.1.8 from Paraburkholderia xenovorans (strain LB400) (see 2 papers)
P47229 2,6-dioxo-6-phenylhexa-3-enoate hydrolase (EC 3.7.1.8) from Paraburkholderia xenovorans (see 2 papers)
BphD / CAA46911.1 2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate hydrolase from Pseudomonas sp (see paper)
WP_011494293 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Paraburkholderia xenovorans LB400
97% identity, 100% coverage
- function: Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo- 6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2- hydroxy-2,4-pentadienoic acid (HPD).
catalytic activity: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = 2-oxopent-4-enoate + benzoate + H(+) (RHEA:17161)
subunit: Homodimer. - The lid domain of the MCP hydrolase DxnB2 contributes to the reactivity toward recalcitrant PCB metabolites.
Ruzzini, Biochemistry 2013 - GeneRIF: Data indicate that the chlorine substituent is accommodated by a hydrophobic pocket that is larger than the homologous site in BphDLB400 from Burkholderia xenovorans LB400.
- Evidence for a gem-diol reaction intermediate in bacterial C-C hydrolase enzymes BphD and MhpC from 13C NMR spectroscopy.
Li, Biochemistry 2006 (PubMed)- GeneRIF: Site-directed single mutants of BphD in which catalytic residues His-265 and Ser-112 were replaced with Ala possessed 10(4)-fold reduced k(cat) values, and in each case, the C-C cleavage step was rate-limiting.
- Catalytic role for arginine 188 in the C-C hydrolase catalytic mechanism for Escherichia coli MhpC and Burkholderia xenovorans LB400 BphD.
Li, Biochemistry 2006 (PubMed)- GeneRIF: replacements with Gln and Lys for Arg-190 of BphD led to 400- and 700-fold decreases, respectively, in k(cat)
2og1A / P47229 Crystal structure of bphd, a c-c hydrolase from burkholderia xenovorans lb400 (see paper)
97% identity, 100% coverage
BPHD_PSEPU / Q52036 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; HOPDA hydrolase; 2,6-dioxo-6-phenylhexa-3-enoate hydrolase; EC 3.7.1.8 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see paper)
96% identity, 100% coverage
- function: Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo- 6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2- hydroxy-2,4-pentadienoic acid (HPD).
catalytic activity: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = 2-oxopent-4-enoate + benzoate + H(+) (RHEA:17161)
subunit: Homodimer. - Metabolic perceptrons for neural computing in biological systems
Pandi, Nature communications 2019 - “...sp.) identifier: UniProtKB - P17297 bphD (2-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC: 3.7.1.8), Pseudomonas putida) identifier: UniProtKB - Q52036 Benzamide transforming enzyme (Amidase (EC: 3.5.1.4), Rhodococcus erythropolis) identifier: UniProtKB - B4XEY3 Sequence and source of all the genes and parts are available in Supplementary Table 5 and the plasmids...”
B5SU85 2,6-dioxo-6-phenylhexa-3-enoate hydrolase (EC 3.7.1.8) from Dyella ginsengisoli (see paper)
89% identity, 100% coverage
Q2VLB9 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Burkholderia cepacia
81% identity, 99% coverage
BPHD_PSES1 / P17548 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; HOPDA hydrolase; 2,6-dioxo-6-phenylhexa-3-enoate hydrolase; EC 3.7.1.8 from Pseudomonas sp. (strain KKS102) (see paper)
79% identity, 99% coverage
- function: Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo- 6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2- hydroxy-2,4-pentadienoic acid (HPD).
catalytic activity: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = 2-oxopent-4-enoate + benzoate + H(+) (RHEA:17161)
subunit: Homodimer.
MHPC_COMTE / Q8KZP5 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase; 2-hydroxy-6-ketonona-2,4-diene-1,9-dioic acid 5,6-hydrolase; 2-hydroxy-6-oxonona-2,4,7-triene-1,9-dioic acid 5,6-hydrolase; 2-hydroxy-6-oxonona-2,4-diene-1,9-dioic acid 5,6-hydrolase; EC 3.7.1.14 from Comamonas testosteroni (Pseudomonas testosteroni) (see paper)
78% identity, 99% coverage
- function: Catalyzes the cleavage of the C5-C6 bond of 2-hydroxy-6- oxononadienedioate, and probably also 2-hydroxy-6-oxononatrienedioate, a dienol ring fission product of the bacterial meta-cleavage pathway for degradation of phenylpropionic acid.
catalytic activity: (2Z,4E)-2-hydroxy-6-oxonona-2,4-dienedioate + H2O = (2Z)-2- hydroxypenta-2,4-dienoate + H(+) + succinate (RHEA:34187)
catalytic activity: (2Z,4E,7E)-2-hydroxy-6-oxonona-2,4,7-trienedioate + H2O = (2Z)-2-hydroxypenta-2,4-dienoate + fumarate + H(+) (RHEA:34191)
subunit: Homodimer.
G5B91_07370 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Pseudomonas nitroreducens
62% identity, 100% coverage
hbpD / O06648 2-hydroxy-6-oxo-6-phenyl-2,4-hexadienoate hydrolase [multifunctional] (EC 3.7.1.8) from Pseudomonas nitroreducens (see 2 papers)
62% identity, 100% coverage
AGH13449.1 hybrid C-C meta-cleavage hydrolase-carboxylesterase from Cycloclasticus zancles (see paper)
62% identity, 100% coverage
b0349 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase from Escherichia coli str. K-12 substr. MG1655
51% identity, 95% coverage
- Bioinformatic prediction reveals posttranscriptional regulation of the chromosomal replication initiator gene dnaA by the attenuator sRNA rnTrpL in Escherichia coli
Li, RNA biology 2021 (secret) - Cloning, screening and characterization of enantioselective ester hydrolases from Escherichia coli K-12
Tang, World journal of microbiology & biotechnology 2011 - Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions
Mariño-Ramírez, Journal of bacteriology 2004 - “...b1517 b1512 b2463 b1620 b4037 b4346 b4119 b3929 b3939 b0349 b0783 b4351 b0091 b2733 b2286 b1393 b1396 b0134 b3019 b2564 b4100 b1020 b3724 b0951 b4201 b0467...”
- Definition of the Escherichia coli MC4100 genome by use of a DNA array
Peters, Journal of bacteriology 2003 - “...yagF cynR, lacA, lacI, lacZ, mhpB, yagG, yeiQ, b0271, b0349 cynS, cynT, yagC, yagE, yagT, ykfD,a b0331, b0333 eaeH b0323, b0324, b0325, b0350a yagA, yagB, yagJ,...”
- Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
Sabina, Journal of bacteriology 2003 - “...pin rplD b2667 rplC rplY rpmC rpsJ trmD b2797 b2796 b0349 b0699 b1759 b3983 b0218 b3984 b3184 b0574 b1445 b1035 b4162 b3986 b3316 b3985 b3313 b3314 b0719 b3317...”
- Sequence analysis of Tn10 insertion sites in a collection of Escherichia coli strains used for genetic mapping and strain construction
Nichols, Journal of bacteriology 1998 - “.... , . , thrA carB leuO yadC yafC proA lacI b0349 b0374 tsx b0441 gsk purK b0604 ybeG asnB nadA ig,e b0786-b0787 potI ig, ycaD-b0899 b0940 yccE yceG b1160 fadR...”
MhpC / b0349 2-hydroxy-6-ketonona-2,4-dienedioate hydrolase (EC 3.7.1.14) from Escherichia coli K-12 substr. MG1655 (see 2 papers)
mhpC / P77044 2-hydroxy-6-ketonona-2,4-dienedioate hydrolase (EC 3.7.1.14) from Escherichia coli (strain K12) (see 10 papers)
MHPC_ECOLI / P77044 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase; 2-hydroxy-6-ketonona-2,4-diene-1,9-dioic acid 5,6-hydrolase; 2-hydroxy-6-oxonona-2,4,7-triene-1,9-dioic acid 5,6-hydrolase; 2-hydroxy-6-oxonona-2,4-diene-1,9-dioic acid 5,6-hydrolase; EC 3.7.1.14 from Escherichia coli (strain K12) (see 4 papers)
P77044 2-hydroxy-6-oxonona-2,4-dienedioate hydrolase (EC 3.7.1.14) from Escherichia coli (see 4 papers)
NP_414883 2-hydroxy-6-ketonona-2,4-dienedioate hydrolase from Escherichia coli str. K-12 substr. MG1655
51% identity, 97% coverage
- function: Catalyzes the cleavage of the C5-C6 bond of 2-hydroxy-6- oxononadienedioate and 2-hydroxy-6-oxononatrienedioate, a dienol ring fission product of the bacterial meta-cleavage pathway for degradation of phenylpropionic acid. MhpC shows some selectivity for the carboxylate of the side chain.
catalytic activity: (2Z,4E)-2-hydroxy-6-oxonona-2,4-dienedioate + H2O = (2Z)-2- hydroxypenta-2,4-dienoate + H(+) + succinate (RHEA:34187)
catalytic activity: (2Z,4E,7E)-2-hydroxy-6-oxonona-2,4,7-trienedioate + H2O = (2Z)-2-hydroxypenta-2,4-dienoate + fumarate + H(+) (RHEA:34191)
subunit: Homodimer. - Evidence for a gem-diol reaction intermediate in bacterial C-C hydrolase enzymes BphD and MhpC from 13C NMR spectroscopy.
Li, Biochemistry 2006 (PubMed)- GeneRIF: A new line-broadened signal was observed upon incubation of the (13)C-labeled substrate with an H114A MhpC mutant, which is able to accept the 6-phenyl-containing substrate, on a shorter time scale.
- Catalytic role for arginine 188 in the C-C hydrolase catalytic mechanism for Escherichia coli MhpC and Burkholderia xenovorans LB400 BphD.
Li, Biochemistry 2006 (PubMed)- GeneRIF: Replacement of Arg-188 in MhpC with Gln and Lys led to 200- and 40-fold decreases, respectively, in k(cat).
- Catalytic mechanism of C-C hydrolase MhpC from Escherichia coli: kinetic analysis of His263 and Ser110 site-directed mutants.
Li, Journal of molecular biology 2005 (PubMed)- GeneRIF: A catalytic mechanism is proposed involving stabilisation of reactive intermediates and activation of a nucleophilic water molecule by Ser110
- The structure of the C-C bond hydrolase MhpC provides insights into its catalytic mechanism.
Dunn, Journal of molecular biology 2005 (PubMed)
cbzF / AAX50133.1 CbzF from Pseudomonas putida (see paper)
56% identity, 87% coverage
MSMEG_6037 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase from Mycobacterium smegmatis str. MC2 155
43% identity, 96% coverage
- Pathogen roid rage: cholesterol utilization by Mycobacterium tuberculosis
Wipperman, Critical reviews in biochemistry and molecular biology 2014 - “...Rv3567c MSMEG_6035 hsaB 3-hydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione 4-hydroxylase reductase component KstR1 Rv3568c MSMEG_6036 hsaC 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione 4,5-dioxygenase KstR1 Rv3569c MSMEG_6037 hsaD 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase Essential KstR1 Rv3570c MSMEG_6038 hsaA 3-hydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione 4-monooxygenase component Essential KstR1 Rv3571 MSMEG_6039 kshB 3-ketosteroid 9-hydroxylase reductase component Induced KstR1 Rv3572 MSMEG_6040 conserved hypothetical protein ? KstR1 Rv3573c...”
hsaD / Q9KWQ6 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase monomer (EC 3.7.1.17) from Rhodococcus jostii (strain RHA1) (see paper)
HSAD_RHOJR / Q9KWQ6 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase; Meta-cleavage product hydrolase; MCP hydrolase; EC 3.7.1.17 from Rhodococcus jostii (strain RHA1) (see 2 papers)
RHA1_ro04540 4,9-DSHA hydrolase from Rhodococcus sp. RHA1
RHA1_RS22130 4,5:9,10-diseco-3-hydroxy-5,9, 17-trioxoandrosta-1(10),2-diene-4-oate hydrolase from Rhodococcus jostii RHA1
44% identity, 96% coverage
- function: Catalyzes the hydrolysis of a carbon-carbon bond in 4,5: 9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate (4,9- DSHA) to yield 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oate (DOHNAA) and 2-hydroxy-hexa-2,4-dienoate (HHD). Also involved in biphenyl and polychlorinated biphenyls (PCBs) degradation.
catalytic activity: (1E,2Z)-3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta- 1(10),2-dien-4-oate + H2O = (2Z,4Z)-2-hydroxyhexa-2,4-dienoate + 3- [(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate + H(+) (RHEA:32035)
subunit: Homodimer. - Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...(RHA1_RS22125) HsaC TesB CtCNB1_1275 RHA1_ro05803 RHA1_ro04541 Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105) HsaG TesF...”
- Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105) HsaG TesF CtCNB1_1352 RHA1_ro05800 RHA1_ro04534 Rv3535c Propanol dehydrogenase...”
hsaD / P9WNH5 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase monomer (EC 3.7.1.17) from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 3 papers)
HSAD_MYCTU / P9WNH5 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase; 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; HOPDA hydrolase; Meta-cleavage product hydrolase; MCP hydrolase; EC 3.7.1.17; EC 3.7.1.8 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 4 papers)
P9WNH5 2,6-dioxo-6-phenylhexa-3-enoate hydrolase (EC 3.7.1.8) from Mycobacterium tuberculosis (see paper)
Mb3600c 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD from Mycobacterium bovis AF2122/97
Rv3569c 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD from Mycobacterium tuberculosis H37Rv
44% identity, 97% coverage
- function: Catalyzes the hydrolysis of a carbon-carbon bond in 4,5: 9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate (4,9- DSHA) to yield 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oate (DOHNAA) and 2-hydroxy-hexa-2,4-dienoate (HHD). Is also able to catalyze the hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) and the synthetic analog 8-(2-chlorophenyl)-2-hydroxy-5- methyl-6-oxoocta-2,4-dienoic acid (HOPODA).
catalytic activity: (1E,2Z)-3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta- 1(10),2-dien-4-oate + H2O = (2Z,4Z)-2-hydroxyhexa-2,4-dienoate + 3- [(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate + H(+) (RHEA:32035)
catalytic activity: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = 2-oxopent-4-enoate + benzoate + H(+) (RHEA:17161)
subunit: Homodimer. - Structure of HsaD, a steroid-degrading hydrolase, from Mycobacterium tuberculosis
Lack, Acta crystallographica. Section F, Structural biology and crystallization communications 2008 - “...and Rv3566c . The corresponding genes in M. bovis BCG have accession numbers Mb3601c , Mb3600c , Mb3599c , Mb3598c , Mb3597c and Mb3596c . Figure 2 Sequence alignment of the HsaD protein from M. tuberculosis with BphDs from B. xenovorans (PDB code 2og1 ) and...”
- Characterization of the putative operon containing arylamine N-acetyltransferase (nat) in Mycobacterium bovis BCG
Anderton, Molecular microbiology 2006 (PubMed)- “...operon. Two genes in the operon, Mb3599c and Mb3600c, are predicted to encode homologues of enzymes annotated as a 2,3-dihydroxybiphenyl 1,2-dioxygenase (bphC5)...”
- “...A2, A3, A4, A5 and A6 correspond to Mb3601c, Mb3600c, Mb3599c, Mb3568c, Mb3567c and Mb3566c respectively, using either cDNA (+) and mock cDNA produced without...”
- Direct capture, inhibition and crystal structure of HsaD (Rv3569c) from M. tuberculosis
Barelier, The FEBS journal 2023 (PubMed)- “...many of them involved in lipid or steroid metabolisms. One of the captured enzymes, HsaD (Rv3569c), is required for the survival of M. tb within macrophages and is thus a potential therapeutic target. This prompted us to further explore and validate, through a combination of biochemical...”
- The Prospect of Repurposing Immunomodulatory Drugs for Adjunctive Chemotherapy against Tuberculosis: A Critical Review
Lee, Antibiotics (Basel, Switzerland) 2021 - “...in vitro whole-cell screens but are critical in vivo, such as mycobacterial HsaD. The hsaD (Rv3569c) gene is found to be essential for mycobacterial cholesterol metabolism within macrophages, and its hypomorphs have been used to identify and develop novel chemical leads in antibiotic discovery [ 91...”
- Comprehensive Comparative Analysis of Cholesterol Catabolic Genes/Proteins in Mycobacterial Species
van, International journal of molecular sciences 2019 - “...probable acyl-CoA dehydrogenase fadE32 Rv3563 a,b,c probable acyl-CoA dehydrogenase hsaC Rv3568c a,c,d 3,4-DHSA dioxygenase hsaD Rv3569c b,c,d 4,9-DHSA hydrolase hsaA Rv3570c b,c,d 3-hydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione hydroxylase (3-HSA hydroxylase, reductase) kshB Rv3571 a,c,d ketosteroid-9-hydroxylase, reductase mce4F Rv3494c c,d Mce4 transport system mce4D Rv3496c c,d Mce4 transport system mce4B Rv3498c...”
- More than cholesterol catabolism: regulatory vulnerabilities in Mycobacterium tuberculosis
Bonds, Current opinion in chemical biology 2018 - “...Cholesterol CD Ring Degradation Acyl-CoA dehydrogenase (-subunit) Rv3568c HsaC Cholesterol AB Ring Degradation 3,4-DHSA dioxygenase Rv3569c HsaD Cholesterol AB Ring Degradation 4,9-DHSA hydrolase RV3570c HsaA Cholesterol AB Ring Degradation 3-hydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione hydroxylase 1 Red circle: acetylation; yellow star: succinylation; SS : disulfide formation. Highlights Cholesterol is important...”
- Cyclipostins and Cyclophostin analogs as promising compounds in the fight against tuberculosis
Nguyen, Scientific reports 2017 - “...32.1 Lipase/esterase LM 43 Mycolic acid synthase UmaA Rv0469 33.1 Methyltransferase LM 34 Hydrolase hsaD Rv3569c 32.1 Macrophages and growth on cholesterol Hydrolase IM/R 53 , 54 7 Monoglyceride lipase Rv0183 30.2 Lipase/esterase IM/R 39 , 40 Thioesterase tesA Rv2928 29.1 in vitro Lipase/esterase LM 48...”
- “...and Ag85C (Rv0129c), the thioesterase TesA (Rv2928), the carboxylesterase CaeA (Rv2224c) and the hydrolase HsaD (Rv3569c); the latter two proteins being annotated as essential enzymes 44 . Ag85A and Ag85C express both a mycolyl transferase activity. They catalyze the transfer of mycolic acids from trehalose monomycolate...”
- Cholesterol metabolism: a potential therapeutic target in Mycobacteria
Abuhammad, British journal of pharmacology 2017 - “...facilitate the optimization of these inhibitors. HsaD HsaD (Rv3569c) was identified as a meta-cleavage product (MCP) hydrolase. It catalyses the hydrolysis of a...”
- Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...HsaC TesB CtCNB1_1275 RHA1_ro05803 RHA1_ro04541 Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105) HsaG TesF CtCNB1_1352...”
- Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery
Rebollo-Lopez, PloS one 2015 - “...Significant links between compound families and targets. Compound FamID Target Pathway Essentiality Prediction TCMDC-143652 1 Rv3569c Degradation of aromatic compounds (mtu01220) Steroid degradation (mtu00984) Non TCMDC-143653 1 Rv3569c Degradation of aromatic compounds (mtu01220) Steroid degradation (mtu00984) Non TCMDC-143657 1 Rv3569c Degradation of aromatic compounds (mtu01220) Steroid...”
- “...mtu00984 (Steroid degradation). Specifically, the link found by compounds TCMDC-143652, TCMDC-143653, TCMDC-143657, and TCMDC-143650 targeting Rv3569c (4,9-DHSA Hydrolase) involved both pathways. Family 3 is significantly associated with two different KEGG pathways, mtu00480 (Glutathione metabolism) and mtu003410 (Base excision repair). Specifically, compounds TCMDC-143687 and TCMDC-143666 are predicted...”
- More
5jz9A / P9WNH5 Crystal structure of hsad bound to 3,5-dichloro-4- hydroxybenzenesulphonic acid (see paper)
44% identity, 98% coverage
- Ligand: 3,5-dichloro-4-hydroxybenzene-1-sulfonic acid (5jz9A)
bphD / BAA25612.1 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Rhodococcus erythropolis (see paper)
43% identity, 92% coverage
bpdF / AAB17100.1 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Rhodococcus sp. M5 (see paper)
45% identity, 88% coverage
BHE75_04572 alpha/beta fold hydrolase from Sphingomonas haloaromaticamans
40% identity, 98% coverage
KR76_14475 4,5:9,10-diseco-3-hydroxy-5,9, 17-trioxoandrosta-1(10),2-diene-4-oate hydrolase from Pimelobacter simplex
38% identity, 96% coverage
A0QWD3 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_2900 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Mycobacterium smegmatis str. MC2 155
MSMEG_2900, MSMEI_2827 alpha/beta fold hydrolase from Mycolicibacterium smegmatis MC2 155
38% identity, 91% coverage
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...Uncharacterized N -acetyltransferase MSMEG_3513 (EC 2.3.1.) 0.05 0.04 A0QV52 MSMEG_2450, MSMEI_2388 Adenosylmethionine-8-amino-7-oxononanoate transaminase 0.03 0.02 A0QWD3 MSMEG_2900, MSMEI_2827 2-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC 3.7.1.) 0.03 0.02 0.27 0.24 A0QZ01 lipT , MSMEG_3848, MSMEI_3758 Carboxylic ester hydrolase (EC 3.1.1.) 0.02 0.02 A0QZ33 MSMEG_3880, MSMEI_3790 Nitrilase/cyanide hydratase 0.13 0.07 A0QTM5...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...N -acetyltransferase MSMEG_3513 (EC 2.3.1.) 0.05 0.04 A0QV52 MSMEG_2450, MSMEI_2388 Adenosylmethionine-8-amino-7-oxononanoate transaminase 0.03 0.02 A0QWD3 MSMEG_2900, MSMEI_2827 2-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC 3.7.1.) 0.03 0.02 0.27 0.24 A0QZ01 lipT , MSMEG_3848, MSMEI_3758 Carboxylic ester hydrolase (EC 3.1.1.) 0.02 0.02 A0QZ33 MSMEG_3880, MSMEI_3790 Nitrilase/cyanide hydratase 0.13 0.07 A0QTM5 pcaD...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...-acetyltransferase MSMEG_3513 (EC 2.3.1.) 0.05 0.04 A0QV52 MSMEG_2450, MSMEI_2388 Adenosylmethionine-8-amino-7-oxononanoate transaminase 0.03 0.02 A0QWD3 MSMEG_2900, MSMEI_2827 2-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC 3.7.1.) 0.03 0.02 0.27 0.24 A0QZ01 lipT , MSMEG_3848, MSMEI_3758 Carboxylic ester hydrolase (EC 3.1.1.) 0.02 0.02 A0QZ33 MSMEG_3880, MSMEI_3790 Nitrilase/cyanide hydratase 0.13 0.07 A0QTM5 pcaD ,...”
MAB_3810 Putative hydrolase, alpha/beta fold from Mycobacterium abscessus ATCC 19977
38% identity, 92% coverage
- The unusual convergence of steroid catabolic pathways in Mycobacterium abscessus
Crowe, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...two candidates, each encoding proteins with 40% amino acid sequence identity to HsaD Mtb : Mab_3810 and Mab_4366c. The former, identified henceforth as hsaD , occurs in a predicted single gene operon, 1.8 Mb from the hsaACB operon. Interestingly, a mycobacterial KstR-binding site as defined by...”
- “...plasmids for HsaD Mtb were described previously ( 7 ). The hsaD Mab gene ( mab_3810 ) was amplified from M. abscessus ATCC 19977 (ASM6918v1) genomic DNA using oligonucleotides MabhsaD_NdeI_F and MabhsaD_HindIII_R ( SI Appendix , Table S4 ). The amplicon was digested with NdeI and...”
MAV_2517 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase from Mycobacterium avium 104
38% identity, 96% coverage
RHA1_RS28300 alpha/beta fold hydrolase from Rhodococcus jostii RHA1
RHA1_ro05797 alpha/beta-fold C-C bond hydrolase from Rhodococcus sp. RHA1
38% identity, 89% coverage
- Degradation of Bile Acids by Soil and Water Bacteria
Feller, Microorganisms 2021 - “...-steroid dioxygenase C211_RS11215 CTCNB1_RS06510 (TesB) RHA1_RS28330 (HsaC3) Nov2c350 4,5,9,10-di seco -steroid hydroxylase C211_RS11155 CTCNB1_RS06910 (TesD) RHA1_RS28300 (HsaD3) Nov2c348 C/D-ring (HIP) side-chain degradation CoA-ligase C211_RS11045 (StdA3 *) CTCNB1_RS06940 (ScdA) RHA1_RS22410 ** (FadD3) Nov2c359 ACAD C211_RS11065 (Scd3A) CTCNB1_RS06570 (ScdC1) RHA1_RS22390 ** Nov2c367 C211_RS11070 (Scd3B) CTCNB1_RS06575 (ScdC2) RHA1_RS22415 **...”
- Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...RHA1_ro04541 Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105) HsaG TesF CtCNB1_1352 RHA1_ro05800 RHA1_ro04534 Rv3535c Propanol...”
- Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...(RHA1_RS28325) (RHA1_RS22125) HsaC TesB CtCNB1_1275 RHA1_ro05803 RHA1_ro04541 Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105) HsaG...”
Q73ZZ9 AB hydrolase-1 domain-containing protein from Mycolicibacterium paratuberculosis (strain ATCC BAA-968 / K-10)
36% identity, 85% coverage
CTCNB1_RS06910 alpha/beta fold hydrolase from Comamonas thiooxydans
CtCNB1_1354 alpha/beta hydrolase fold protein from Comamonas testosteroni CNB-2
36% identity, 96% coverage
- Degradation of Bile Acids by Soil and Water Bacteria
Feller, Microorganisms 2021 - “...9,10- seco -steroid dioxygenase C211_RS11215 CTCNB1_RS06510 (TesB) RHA1_RS28330 (HsaC3) Nov2c350 4,5,9,10-di seco -steroid hydroxylase C211_RS11155 CTCNB1_RS06910 (TesD) RHA1_RS28300 (HsaD3) Nov2c348 C/D-ring (HIP) side-chain degradation CoA-ligase C211_RS11045 (StdA3 *) CTCNB1_RS06940 (ScdA) RHA1_RS22410 ** (FadD3) Nov2c359 ACAD C211_RS11065 (Scd3A) CTCNB1_RS06570 (ScdC1) RHA1_RS22390 ** Nov2c367 C211_RS11070 (Scd3B) CTCNB1_RS06575 (ScdC2)...”
- Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...RHA1_ro05803 RHA1_ro04541 Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105) HsaG TesF CtCNB1_1352 RHA1_ro05800 RHA1_ro04534 Rv3535c...”
- Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Bergstrand, mBio 2016 - “...(CTCNB1_RS06920) (RHA1_RS28325) (RHA1_RS22125) HsaC TesB CtCNB1_1275 RHA1_ro05803 RHA1_ro04541 Rv3568c 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione-4,5-dioxygenase (CTCNB1_RS06510) (RHA1_RS28330) (RHA1_RS22135) HsaD TesD CtCNB1_1354 RHA1_ro05797 RHA1_ro04540 Rv3569c 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (CTCNB1_RS06910) (RHA1_RS28300) (RHA1_RS22130) HsaE TesE CtCNB1_1353 RHA1_ro05799 RHA1_ro04533 Rv3536c 2-Hydroxyhexa-2,4-dienoate hydratase (CTCNB1_RS06905) (RHA1_RS28310) (RHA1_RS22095) HsaF TesG CtCNB1_1351 RHA1_ro05801 RHA1_ro04535 Rv3534c 4-Hydroxy-2-oxohexanoate aldolase (CTCNB1_RS06905) (RHA1_RS28320) (RHA1_RS22105)...”
F1721_00695 alpha/beta fold hydrolase from Saccharopolyspora hirsuta
35% identity, 90% coverage
P96965 2-hydroxymuconate-6-semialdehyde hydrolase (EC 3.7.1.9) from Pseudomonas fluorescens (see 2 papers)
cumD / BAA12150.1 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase from Pseudomonas fluorescens (see paper)
37% identity, 91% coverage
tesD / Q83VZ6 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (EC 3.7.1.17) from Comamonas testosteroni (see 3 papers)
36% identity, 96% coverage
1iunB / P96965 Meta-cleavage product hydrolase from pseudomonas fluorescens ip01 (cumd) s103a mutant hexagonal (see paper)
37% identity, 91% coverage
- Ligand: acetate ion (1iunB)
KR76_27085 alpha/beta fold hydrolase from Pimelobacter simplex
36% identity, 90% coverage
bphD / BAM76235.1 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Janibacter sp. TYM3221 (see paper)
36% identity, 98% coverage
MAB_4366c Putative hydrolase, alpha/beta fold from Mycobacterium abscessus ATCC 19977
36% identity, 87% coverage
- The unusual convergence of steroid catabolic pathways in Mycobacterium abscessus
Crowe, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...each encoding proteins with 40% amino acid sequence identity to HsaD Mtb : Mab_3810 and Mab_4366c. The former, identified henceforth as hsaD , occurs in a predicted single gene operon, 1.8 Mb from the hsaACB operon. Interestingly, a mycobacterial KstR-binding site as defined by Kendall etal....”
- “...hsaD start codon, with 15 nucleotides of the 18-nucleotide sequence being conserved. For its part, mab_4366c occurs within a putative six-gene operon predicted to encode enzymes involved in the degradation of an aromatic compound ( SI Appendix , Table S1 ). Similarly organized genes in R....”
Alide2_0281, Alide_0336 alpha/beta fold hydrolase from Alicycliphilus denitrificans K601
37% identity, 92% coverage
- Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601(T.)
Oosterkamp, PloS one 2013 - “...to 2-oxopent-4-enoate. The enzyme catalyzing this conversion is a 2-hydroxymuconic semialdehyde hydrolase (Alide_0336 in BC; Alide2_0281 in K601 T ). Methyl-catechol and catechol are converted to 2-oxopent-4-enoate using the oxalocrotonate branch of the meta-cleavage pathway, which proceeds via a dehydrogenase, tautomerase and decarboxylase (Alide_0335+0340+0342 in BC;...”
- “...of 2-hydroxymuconic semialdehyde to 2-oxopent-4-enoate. The enzyme catalyzing this conversion is a 2-hydroxymuconic semialdehyde hydrolase (Alide_0336 in BC; Alide2_0281 in K601 T ). Methyl-catechol and catechol are converted to 2-oxopent-4-enoate using the oxalocrotonate branch of the meta-cleavage pathway, which proceeds via a dehydrogenase, tautomerase and decarboxylase...”
KZ686_10070 alpha/beta fold hydrolase from Cupriavidus cauae
Q1LNT5 2-hydroxymuconic semialdehyde hydrolase (HMSH)-alpha/beta hydrolase superfamily (Belongs to CMGI-2) from Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)
37% identity, 91% coverage
G3KFX4 2-hydroxymuconate-6-semialdehyde hydrolase (EC 3.7.1.9) from Pseudomonas sp. (see paper)
38% identity, 92% coverage
todF / P23133 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase (EC 3.7.1.25) from Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1) (see paper)
TODF_PSEP1 / P23133 2-hydroxy-6-oxo-2,4-heptadienoate hydrolase; HOHH; EC 3.7.1.25 from Pseudomonas putida (strain ATCC 700007 / DSM 6899 / JCM 31910 / BCRC 17059 / LMG 24140 / F1) (see 2 papers)
36% identity, 91% coverage
Q8KRR8 2-hydroxymuconic semialdehyde hydrolase from Pseudomonas fluorescens
36% identity, 88% coverage
P19076 2-hydroxymuconate semialdehyde hydrolase from Pseudomonas sp. (strain CF600)
35% identity, 92% coverage
BHE75_04577 alpha/beta fold hydrolase from Sphingomonas haloaromaticamans
34% identity, 90% coverage
NSU_pLA1124 alpha/beta fold hydrolase from Novosphingobium pentaromativorans US6-1
34% identity, 90% coverage
IM701_21000 alpha/beta fold hydrolase from Novosphingobium sp. ES2-1
33% identity, 92% coverage
cmpF / CAB06612.1 2-hydroxymuconic semialdehyde hydrolase from Sphingomonas sp (see 2 papers)
33% identity, 90% coverage
nahN / BAE92169.1 2-hydroxymuconic semialdehyde hydrolase NahN from Pseudomonas putida (see 2 papers)
35% identity, 88% coverage
bphD / Q75WN8 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC 3.7.1.8) from Rhodococcus jostii (strain RHA1) (see 2 papers)
etbD / BAA18939.1 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase from Rhodococcus sp (see 2 papers)
33% identity, 97% coverage
AGH13447.1 hybrid C-C meta-cleavage hydrolase-carboxylesterase from Cycloclasticus zancles (see paper)
33% identity, 90% coverage
SGRAN_1584 alpha/beta fold hydrolase from Sphingopyxis granuli
31% identity, 92% coverage
plu2202 No description from Photorhabdus luminescens subsp. laumondii TTO1
34% identity, 85% coverage
- Cinnamic acid, an autoinducer of its own biosynthesis, is processed via Hca enzymes in Photorhabdus luminescens
Chalabaev, Applied and environmental microbiology 2008 - “...MhpC, and MhpD homologs in P. luminescens are Plu2208, Plu2202, and Plu2201, respectively, with amino acid identities of 41% (e-value of 5e-73), 28% (e-value of...”
- “...Dotted arrows indicate homology between plu2201 and mhpD, plu2202 and mhpC, and plu2208 and mhpB. For hca genes, genes with similar shadings encode subunits...”
xylF / P23106 2-hydroxymuconic semialdehyde hydrolase (EC 3.7.1.9) from Pseudomonas putida (see paper)
XYLF_PSEPU / P23106 2-hydroxymuconate semialdehyde hydrolase; HMSH; 2-hydroxymuconic semialdehyde hydrolase; EC 3.7.1.9 from Pseudomonas putida (Arthrobacter siderocapsulatus)
32% identity, 92% coverage
- function: Catalyzes the conversion of 2-hydroxymuconate semialdehyde to 2-hydroxypent-2,4-dienoate.
catalytic activity: (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + H2O = 2-oxopent-4- enoate + formate + H(+) (RHEA:14549)
hppC / AAB81313.1 2-hydroxy-6-ketonona-2,4-dienoate hydrolase from Rhodococcus globerulus (see paper)
32% identity, 90% coverage
AGH13448.1 hybrid C-C meta-cleavage hydrolase-carboxylesterase from Cycloclasticus zancles (see paper)
32% identity, 85% coverage
BHE75_04587 alpha/beta fold hydrolase from Sphingomonas haloaromaticamans
30% identity, 93% coverage
EstN1 / K0IAM1 pimeloyl-[acyl-carrier protein] methyl ester esterase (EC 3.1.1.85) from Nitrososphaera gargensis (strain Ga9.2) (see paper)
31% identity, 92% coverage
Ngar_c14400 alpha/beta fold hydrolase from Candidatus Nitrososphaera gargensis Ga9.2
31% identity, 92% coverage
- The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli ΔbioH-complementing esterase EstN1
Chow, Scientific reports 2018 - “...possible candidates that could serve as bioC analogues ( bioC1-4 ). The ORFs Ngar_c21820, Ngar_c24650, Ngar_c14400 ( i . e . estN1 ), Ngar_c30910 ( i . e . estN2 ), Ngar_c32780 and Ngar_c35080, which could possibly encode a BioH analogue, were amplified with specific primers,...”
- “...in E . coli Rosetta-gami 2 (DE3) and enzyme purification As mentioned above, thegene estN1 (Ngar_c14400) encoding an active esterasewas cloned into the pET21a expression vector (Table S1). The plasmid was transformed into E . coli BL21 [DE3; F ompT hsdS g (r g m g...”
Swit_3055 alpha/beta hydrolase fold from Sphingomonas wittichii RW1
28% identity, 97% coverage
- Proteomic profiling of the dioxin-degrading bacterium Sphingomonas wittichii RW1
Colquhoun, Journal of biomedicine & biotechnology 2012 - “...[ 21 ]. The one identified in the present study is the product of the Swit_3055 locus, a gene also known as DxnB2 [ 21 ]. Its identification in this study corroborates previous findings [ 21 ]. Unlike the dioxin dioxygenase, this gene is found on...”
- “...148555586 Swit_2674 Adenosylhomocysteinase 1.97 0.062 418 148553385 Swit_0461 Elongation factor Ts 2.10 0.05 934 115279619 Swit_3055 Meta -cleavage pathway hydrolase 2.54 0.055 603 148555952 Swit_3046 Glyoxalase/bleomycin resistance protein/ dioxygenase 3.88 0.031 a Arbitrary identifier for spot location (see Figure 2 ). b NCBI gi number. c...”
- Genome-Wide Analysis of Salicylate and Dibenzofuran Metabolism in Sphingomonas Wittichii RW1
Coronado, Frontiers in microbiology 2012 - “...were characterized (Happe et al., 1993 ), and two hydrolases, DxnB and DxnB2 (Swit_4895 and Swit_3055), were described (Bnz et al., 1993 ; Seah et al., 2007 ). Several of the genes for the above-mentioned enzymes were cloned and characterized, such as fdx1 (Swit_5088, Armengaud and...”
AXG94_01195 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Pseudomonas corrugata
32% identity, 71% coverage
4lxhA Crystal structure of the s105a mutant of a carbon-carbon bond hydrolase, dxnb2 from sphingomonas wittichii rw1, in complex with 3- cl hopda (see paper)
28% identity, 97% coverage
- Ligand: (2z,4e)-3-chloro-2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (4lxhA)
Ngar_c35080 alpha/beta fold hydrolase from Candidatus Nitrososphaera gargensis Ga9.2
26% identity, 92% coverage
- The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli ΔbioH-complementing esterase EstN1
Chow, Scientific reports 2018 - “.... e . estN1 ), Ngar_c30910 ( i . e . estN2 ), Ngar_c32780 and Ngar_c35080, which could possibly encode a BioH analogue, were amplified with specific primers, cloned into pDrive (PCR Cloning Kit, Qiagen, Hilden, Germany) and transformed into competent E . coli DH5 cells....”
- “...BioH-activities. According to a conserved domain search, three of the candidate enzymes (Ngar_c21820, Ngar_c24650 and Ngar_c35080) showed domains for being members of the /-hydrolase superfamily (e-values between 1.9e 44 and 2.1e 17 ), while three others even showed possible pimeloyl-ACP methyl ester carboxylesterase domains [Ngar_c14400 (...”
NTE_01571 alpha/beta fold hydrolase from Candidatus Nitrososphaera evergladensis SR1
29% identity, 95% coverage
TTE0552 predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) from Thermoanaerobacter tengcongensis MB4
28% identity, 93% coverage
- Carboxylic ester hydrolases from hyperthermophiles
Levisson, Extremophiles : life under extreme conditions 2009 - “...210 GISGN Thermoanaerobacter tengcongensis TTE0035 AAM23348 Hypothetical protein 237 GDSIS TTE0419 AAM23703 Lysophospholipase 314 GHSFG TTE0552 AAM23828 Predicted hydrolase 279 GVSMG TTE0556 AAM23832 Predicted hydrolase 298 GWSMG TTE1809 AAM25001 Alpha/beta hydrolase 258 GLSMG TTE2321 AAM25462 Alpha/beta hydrolase 414 CHSMG TTE2547 AAM25672 Alpha/beta hydrolase 285 AHSFG Thermococcus...”
flnE / BAC75995.1 meta cleavage compound hydrolase from Terrabacter sp. DBF63 (see paper)
Q83ZF0 2-hydroxy-6-oxo-6-(2'-carboxyphenyl)-hexa-2,4-dienoate hydrolase from Terrabacter sp. (strain DBF63)
28% identity, 83% coverage
ELZ14_17090 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Pseudomonas brassicacearum
31% identity, 71% coverage
A0U95_29285 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Pseudomonas brassicacearum
31% identity, 71% coverage
WP_042686824 alpha/beta fold hydrolase from Candidatus Nitrosotenuis chungbukensis
26% identity, 91% coverage
YP_001188192 alpha/beta hydrolase fold from Pseudomonas mendocina ymp
27% identity, 91% coverage
- Novel lipolytic enzymes identified from metagenomic library of deep-sea sediment
Jeon, Evidence-based complementary and alternative medicine : eCAM 2011 - “...acyl hydrolase from Moritella marina ; YP_001530963, an / hydrolase fold from Desulfococcus oleovorans Hxd3; YP_001188192, an / hydrolase fold from Pseudomonas mendocina ymp (YP_001188192). (c) EstD2 family including EM3L2: ZP_01915829, a hypothetical protein from Limnobacter sp. MED105; ADN26553, an EstD2 from uncultured bacterium; ZP_00952831, a...”
6eb3B Structural and enzymatic characterization of an esterase from a metagenomic library
30% identity, 92% coverage
- Ligand: 2-hydroxypropane-1,3-diyl dibutanoate (6eb3B)
Q84II3 2-hydroxy-6-oxo-6-(2-aminophenyl)hexa-2,4-dienoate hydrolase (EC 3.7.1.13) from Janthinobacterium sp. J3 (see paper)
28% identity, 97% coverage
carC / Q9AQM4 2-hydroxy-6-oxo-6-(2'-aminophenyl)-hexa-2,4dienoate hydrolase monomer (EC 3.7.1.13) from Pseudomonas resinovorans (see paper)
CARC_PSERE / Q9AQM4 2-hydroxy-6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoic acid hydrolase; HOPDA; EC 3.7.1.13 from Pseudomonas resinovorans (see 3 papers)
Q9AQM4 2-hydroxy-6-oxo-6-(2-aminophenyl)hexa-2,4-dienoate hydrolase (EC 3.7.1.13) from Pseudomonas resinovorans (see paper)
carC / BAC41548.1 meta cleavage compound hydrolase from Pseudomonas resinovorans (see 9 papers)
28% identity, 97% coverage
- function: Involved in the degradation of carbazole, a toxic N- heterocyclic aromatic compound containing dibenzopyrrole system. Catalyzes the hydrolytic cleavage of a carbon-carbon bond of 2-hydroxy- 6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoic acid (HOPDA) to yield anthranilate. CarC is specific for 2-hydroxy-6-oxo-6-phenylhexa-2,4- dienoic acid (6-phenyl-HODA), and has little activity toward 2-hydroxy- 6-oxohepta-2,4-dienoic acid and 2-hydroxymuconic semialdehyde. The effect of the presence of an amino group or hydroxyl group at the 2'- position of phenyl moiety of 6-phenyl-HODA on the enzyme activity is found to be small.
catalytic activity: (2E,4E)-6-(2-aminophenyl)-2-hydroxy-6-oxohexa-2,4-dienoate + H2O = (2E)-2-hydroxypenta-2,4-dienoate + anthranilate + H(+) (RHEA:27870)
subunit: Homodimer. - SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.
Dana, Nucleic acids research 2019 - “...O93523 3.5.4.45 Melamine deaminase Q9EYU0 98% 4v1x 4v1y 3.8.1.8 Atrazine chlorohydrolase P72156 3.7.1.13 2-hydroxy-6-oxo-6-(2-aminophenyl)hexa-2,4-dienoate hydrolase Q9AQM4 98% 1j1i 3.7.1.8 2,6-dioxo-6-phenylhexa-3-enoate hydrolase Q84II3 4.1.2.9 Phosphoketolase Q9AEM9 95% 3ahc 3ahd 3ahe 3ahf 3ahg 3ahh 3ahi 3ahj 4.1.2.22 Fructose-6-phosphate phosphoketolase D6PAH1 4.2.3.32 Levopimaradiene synthase H8ZM70 99% 3s9v 4.2.3.18 4.2.3.132...”
Swit_4895 alpha/beta hydrolase fold from Sphingomonas wittichii RW1
28% identity, 91% coverage
- Genome-Wide Analysis of Salicylate and Dibenzofuran Metabolism in Sphingomonas Wittichii RW1
Coronado, Frontiers in microbiology 2012 - “...gene (Swit_4902) were characterized (Happe et al., 1993 ), and two hydrolases, DxnB and DxnB2 (Swit_4895 and Swit_3055), were described (Bnz et al., 1993 ; Seah et al., 2007 ). Several of the genes for the above-mentioned enzymes were cloned and characterized, such as fdx1 (Swit_5088,...”
- “...containing protein, and Swit_1861 for a putative dioxygenase). Transposon insertions in the previously identified genes Swit_4895 ( dnxB ) and Swit_4897 ( dxnA1 ) were 10-fold or more underrepresented in the DBF-grown library but not completely absent (Table S2 in Supplementary Material). None of the other...”
cmtE / Q51980 HOMODA hydrolase from Pseudomonas putida (see 2 papers)
cmtE / AAB62292.1 HOMODA hydrolase from Pseudomonas putida (see 3 papers)
30% identity, 94% coverage
bioH / BAB39459.1 BioH from Kurthia sp. 538-KA26 (see paper)
29% identity, 91% coverage
CC2395 acetoin dehydrogenase E2 component, putative from Caulobacter crescentus CB15
28% identity, 92% coverage
- The metabolic enzyme CTP synthase forms cytoskeletal filaments
Ingerson-Mahar, Nature cell biology 2010 - “...cell periphery is marked with a gfp fusion (green) to the periplasmic protein encoded by CC2395. (g) ECT filaments in creS cells (ZG17). Arrows point to filaments ends. (hi) Co-localization of Caulobacter mCherry-CtpS (red) and CreS-tc (green) in both Caulobacter (h, ZG218) and upon heterologous co-expression...”
PA4152 probable hydrolase from Pseudomonas aeruginosa PAO1
29% identity, 71% coverage
JV35_11985 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Pectobacterium betavasculorum
26% identity, 75% coverage
PA14_10240 putative hydrolase from Pseudomonas aeruginosa UCBPP-PA14
CIA_04250 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Pseudomonas aeruginosa PA14
29% identity, 71% coverage
- Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype
Thöming, NPJ biofilms and microbiomes 2020 - “...exaD 3.0 PA14_06680 PA0512 nirH 3.2 PA14_10200 PA4156 2.8 PA14_38920 4.1 PA14_06690 PA0513 nirG 2.9 PA14_10240 PA4152 acoC 2.8 PA14_38970 PA1976 2.9 PA14_06700 PA0514 nirL 3.3 PA14_10250 PA4151 acoB 3.0 PA14_38990 PA1975 3.1 PA14_06710 PA0515 nirD 3.3 PA14_10260 PA4150 acoA 3.1 PA14_39000 PA1974 4.9 PA14_06720 PA0516...”
- The novel type II toxin-antitoxin PacTA modulates Pseudomonas aeruginosa iron homeostasis by obstructing the DNA-binding activity of Fur
Song, Nucleic acids research 2022 - “...dehydratase PrpD, succinate dehydrogenase SdhD, 3-hydroxybutyrate dehydrogenase BdhA, amino acid dehydrogenase CIA_03490, 2,3-butanediol catabolism dehydrogenase CIA_04250, Glycolate oxidase subunit GlcF, formiminoglutamate deiminase HutF, aspartate aminotransferase IlvE, nucleotide hydrolases dgt2, 3-butanediol catabolism dehydrogenase CIA_04250. Furthermore, the proteins involved in transport process were also reduced, including peptide transporter...”
PP0553, PP_0553 acetoin dehydrogenase, dihydrolipoamide acetyltransferase component from Pseudomonas putida KT2440
30% identity, 71% coverage
- UEG Week 2024 Poster Presentations
, United European gastroenterology journal 2024 - UEG Week 2023 Poster Presentations
, United European gastroenterology journal 2023 - Dehydrogenation Mechanism of Three Stereoisomers of Butane-2,3-Diol in Pseudomonas putida KT2440
Liu, Frontiers in bioengineering and biotechnology 2021 - “...PAO1 ( Liu et al., 2018 ). Comparative genomics analysis indicated that PP0555, PP0554, and PP0553 exhibit strikingly high homology to AcoA, AcoB, and AcoC in AC dehydrogenase enzyme system (AoDH ES) of P. aeruginosa PAO1. R , R -BDH and (2 S ,3 S )-2,3-BDO...”
- “...with 2gL 1 mixed 2,3-BDO as the sole carbon source. Since pp0555 , pp0554 , pp0553 and pp0552 were located adjacent to acoX ( pp0556 ) and acoR ( pp0557 ) gene homologues of AC utilization operons in other bacteria, we hypothesized that these genes may...”
- Light Response of Pseudomonas putida KT2440 Mediated by Class II LitR, a Photosensor Homolog
Sumi, Journal of bacteriology 2020 (secret) - Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol
Beckers, Microbial cell factories 2016 - “...Pyruvate dehydrogenase 1.16 1.86 1.03 0.33 acoB PP0554 Pyruvate dehydrogenase 1.5 1.88 1.04 0.66 acoC PP0553 Pyruvate dehydrogenase 1.57 1.81 0.96 0.72 PP0545 Aldehyde dehydrogenase 0.2 0.11 0.91 1.01 acsA PP4487 Acetyl-CoA synthetase 0.13 0.23 0.15 3.56 accC - 2 PP5347 Pyruvate carboxylase 0.22 0.27 0.12...”
- Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida
Borrero-de, Microbial cell factories 2014 - “...Pyruvate metabolism acoA PP0555 Pyruvate dehydrogenase 12.4 5.3 acoB PP0554 Pyruvate dehydrogenase 1.5 1.0 acoC PP0553 Pyruvate dehydrogenase 0.7 0.7 PP0545 Aldehyde dehydrogenase 0.1 -1.0 acsA PP4487 Acetyl-CoA synthetase 0.8 1.4 accC-2 PP5347 Pyruvate carboxylase 0.5 0.2 ppsA PP2082 Phosphoenolpyruvate synthase 0.5 0.4 ppc PP1505 Phosphoenolpyruvate...”
- “...Pyruvate metabolism acoA PP0555 Pyruvate dehydrogenase 1.3 -2.7 acoB PP0554 Pyruvate dehydrogenase 0.7 -0.8 acoC PP0553 Pyruvate dehydrogenase 0.5 -1.2 PP0545 Aldehyde dehydrogenase 0.5 -0.9 acsA PP4487 Acetyl-CoA synthetase -0.3 -0.6 accC-2 PP5347 Pyruvate carboxylase 0.8 2.3 ppsA PP2082 Phosphoenolpyruvate synthase 0.2 -0.1 ppc PP1505 Phosphoenolpyruvate...”
- The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach
Poblete-Castro, Microbial cell factories 2012 - “...-6.7 -8.3 PP0556 Acetoin catabolism protein -3.7 -4.6 PP0554 Acetoin dehydrogenase beta subunit -4.6 -4.2 PP0553 Acetoin dehydrogenase dihydrolipoamide -5.3 -4.0 PP0557 Acetoin catabolism regulatory protein -3.4 -3.6 PP2149 Glyceraldehyde 3-phospate dehydrogenase 1.5 -3.7 PP4715 Triosephosphate isomerase 1.9 -3.3 PP4737 D-lactate dehydrogenase putative -2.6* -3.1 PP0545...”
- “...-4.0 7 -8.3 0 Acetoin dehydrogenase -sub PP0554 AcoB -5.6 23 -4.2 0 Acetoin dehydrogenase PP0553 AcoC -3.7 10 -4.0 0 Nitrogen metabolism Nitrogen regulatory protein P-II PP5234 GlnK only in CN 6 10.4 0 Protein synthesis Elongation factor Tu PP0452 TUF-2 only in CN 16...”
- Transcriptome dynamics of Pseudomonas putida KT2440 under water stress
Gülez, Applied and environmental microbiology 2012 - “...PP_4034 PP_0103 PP_0104 PP_0105 PP_0106 PP_0490 PP_0552 PP_0553 PP_0554 PP_0555 PP_0556 PP_0557 PP_0596 PP_0989 PP_0999 PP_1000 PP_1001 PP_1157 PP_2351 PP_2422...”
PA0829 probable hydrolase from Pseudomonas aeruginosa PAO1
26% identity, 88% coverage
- Recent advances in therapeutic targets identification and development of treatment strategies towards Pseudomonas aeruginosa infections
Sanya, BMC microbiology 2023 - “...also positively monitors the expression of genes in a second putative operon, comprising genes PA0807 PA0829 , to facilitate the survival of P. aeruginosa cells in the host [ 48 ]. On the other hand, P. aeruginosa contains some rhamnolipids (glycolipids molecules) forming micelles that transport...”
- Control of a programmed cell death pathway in Pseudomonas aeruginosa by an antiterminator
Peña, Nature communications 2021 - “...regulates the expression of all of the genes on the positive strand between PA0807 and PA0829 (i.e. PA0807 ( ampDh3 ), PA0808 , PA0815 , PA0817 , PA0819 , PA0820 , PA0828 , and PA0829 ) (Fig. 1a, b ), a finding we confirmed using quantitative...”
- “...(Supplementary Table 1 ). These findings suggest that AlpA exerts its regulatory effects on PA0807 PA0829 directly. AlpA did not detectably associate with the alpB promoter region as assessed by ChIP-Seq (Supplementary Table 1 ). AlpR binding to the alpB promoter region during our ChIP-Seq studies...”
WP_095844694 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Gibbsiella quercinecans
27% identity, 69% coverage
acoC / AAA21950.1 FMP from Cupriavidus necator (see paper)
27% identity, 68% coverage
O73957 carboxylesterase (EC 3.1.1.1) from Sulfolobus acidocaldarius (see paper)
26% identity, 84% coverage
ABHD6_MOUSE / Q8R2Y0 Monoacylglycerol lipase ABHD6; 2-arachidonoylglycerol hydrolase; Abhydrolase domain-containing protein 6; EC 3.1.1.23 from Mus musculus (Mouse) (see 4 papers)
25% identity, 78% coverage
- function: Lipase that preferentially hydrolysis medium-chain saturated monoacylglycerols including 2-arachidonoylglycerol (PubMed:18096503, PubMed:20657592). Through 2-arachidonoylglycerol degradation may regulate endocannabinoid signaling pathways (PubMed:18096503, PubMed:20657592). Also has a lysophosphatidyl lipase activity with a preference for lysophosphatidylglycerol among other lysophospholipids (PubMed:24095738). Also able to degrade bis(monoacylglycero)phosphate (BMP) and constitutes the major enzyme for BMP catabolism (PubMed:26491015). BMP, also known as lysobisphosphatidic acid, is enriched in late endosomes and lysosomes and plays a key role in the formation of intraluminal vesicles and in lipid sorting (PubMed:26491015).
catalytic activity: Hydrolyzes glycerol monoesters of long-chain fatty acids.
catalytic activity: 2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-glycerol + H2O = (5Z,8Z,11Z,14Z)-eicosatetraenoate + glycerol + H(+) (RHEA:26132)
catalytic activity: 1-octanoylglycerol + H2O = glycerol + H(+) + octanoate (RHEA:44328)
catalytic activity: 1-decanoylglycerol + H2O = decanoate + glycerol + H(+) (RHEA:44320)
catalytic activity: 1-dodecanoylglycerol + H2O = dodecanoate + glycerol + H(+) (RHEA:44316)
catalytic activity: 1-tetradecanoylglycerol + H2O = glycerol + H(+) + tetradecanoate (RHEA:44312)
catalytic activity: 2-hexadecanoylglycerol + H2O = glycerol + H(+) + hexadecanoate (RHEA:39963)
catalytic activity: 2-(9Z-octadecenoyl)-glycerol + H2O = (9Z)-octadecenoate + glycerol + H(+) (RHEA:38491)
catalytic activity: 1-(9Z-octadecenoyl)-glycerol + H2O = (9Z)-octadecenoate + glycerol + H(+) (RHEA:38487)
catalytic activity: 2-(9Z,12Z-octadecadienoyl)-glycerol + H2O = (9Z,12Z)- octadecadienoate + glycerol + H(+) (RHEA:44732)
catalytic activity: 1-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-glycerol + H2O = (5Z,8Z,11Z,14Z)-eicosatetraenoate + glycerol + H(+) (RHEA:44728)
catalytic activity: 1-(9Z,12Z-octadecadienoyl)-glycerol + H2O = (9Z,12Z)- octadecadienoate + glycerol + H(+) (RHEA:48428)
catalytic activity: 3-(9Z-octadecenoyl)-sn-glycero-1-phospho-(3'-(9Z- octadecenoyl)-1'-sn-glycerol) + H2O = (9Z)-octadecenoate + 3-(9Z- octadecenoyl)-sn-glycero-1-phospho-(1'-sn-glycerol) + H(+) (RHEA:55712)
catalytic activity: (S,S)-2-(9Z-octadecenoyl)-sn-glycero-1-phospho-(2'-(9Z- octadecenoyl)-1'-sn-glycerol) + H2O = (9Z)-octadecenoate + (S,S)-2- (9Z-octadecenoyl)-sn-glycero-1-phospho-(1'-sn-glycerol) + H(+) (RHEA:55716)
catalytic activity: (R,R)-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-(2'-(9Z- octadecenoyl)-3'-sn-glycerol) + H2O = (9Z)-octadecenoate + (R,R)-2- (9Z-octadecenoyl)-sn-glycero-3-phospho-(3'-sn-glycerol) + H(+) (RHEA:55804)
disruption phenotype: Abhd6 partial knockdown inducing a stronger depletion in liver, kidney and white adipose tissues protects mice against hight-fat diet-induced metabolic disorder and obesity. De novo lipogenesis in liver is reduced and associated with a reduced expression of lipogenic genes. Accumulation of phospholipids and lysophospholipds in the liver is also observed. - Predicting cancer-relevant proteins using an improved molecular similarity ensemble approach.
Zhou, Oncotarget 2016 - “...0.0253 (23) [ 69 ] Q27757 Luciferin 4-monooxygenase Firefly 0.0239 (20) 0.0153 (14) 0.0241 (20) Q8R2Y0 Monoacylglycerol lipase ABHD6 Mouse 0.0245 (21) 0.0272 (29) - [ 70 ] P49286 Melatonin receptor type 1B Human 0.0247 (22) 0.0245 (24) 0.0247 (22) [ 53 ] P35968 Vascular endothelial...”
Pden_4983 alpha/beta hydrolase fold from Paracoccus denitrificans PD1222
27% identity, 72% coverage
YP_003372868 alpha/beta hydrolase fold protein from Pirellula staleyi DSM 6068
25% identity, 88% coverage
A1S_0954 putative hydrolase from Acinetobacter baumannii ATCC 17978
37% identity, 38% coverage
Q5XI64 Monoacylglycerol lipase ABHD6 from Rattus norvegicus
NP_001007681 monoacylglycerol lipase ABHD6 from Rattus norvegicus
25% identity, 78% coverage
ABHD6_HUMAN / Q9BV23 Monoacylglycerol lipase ABHD6; 2-arachidonoylglycerol hydrolase; Abhydrolase domain-containing protein 6; EC 3.1.1.23 from Homo sapiens (Human) (see 2 papers)
NP_001307055 monoacylglycerol lipase ABHD6 from Homo sapiens
25% identity, 78% coverage
- function: Lipase that preferentially hydrolysis medium-chain saturated monoacylglycerols including 2-arachidonoylglycerol (PubMed:22969151). Through 2-arachidonoylglycerol degradation may regulate endocannabinoid signaling pathways (By similarity). Also has a lysophosphatidyl lipase activity with a preference for lysophosphatidylglycerol among other lysophospholipids (By similarity). Also able to degrade bis(monoacylglycero)phosphate (BMP) and constitutes the major enzyme for BMP catabolism (PubMed:26491015). BMP, also known as lysobisphosphatidic acid, is enriched in late endosomes and lysosomes and plays a key role in the formation of intraluminal vesicles and in lipid sorting (PubMed:26491015).
catalytic activity: Hydrolyzes glycerol monoesters of long-chain fatty acids.
catalytic activity: 1-octanoylglycerol + H2O = glycerol + H(+) + octanoate (RHEA:44328)
catalytic activity: 1-decanoylglycerol + H2O = decanoate + glycerol + H(+) (RHEA:44320)
catalytic activity: 1-dodecanoylglycerol + H2O = dodecanoate + glycerol + H(+) (RHEA:44316)
catalytic activity: 1-tetradecanoylglycerol + H2O = glycerol + H(+) + tetradecanoate (RHEA:44312)
catalytic activity: 2-hexadecanoylglycerol + H2O = glycerol + H(+) + hexadecanoate (RHEA:39963)
catalytic activity: 2-(9Z-octadecenoyl)-glycerol + H2O = (9Z)-octadecenoate + glycerol + H(+) (RHEA:38491)
catalytic activity: 1-(9Z-octadecenoyl)-glycerol + H2O = (9Z)-octadecenoate + glycerol + H(+) (RHEA:38487)
catalytic activity: 2-(9Z,12Z-octadecadienoyl)-glycerol + H2O = (9Z,12Z)- octadecadienoate + glycerol + H(+) (RHEA:44732)
catalytic activity: 2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-glycerol + H2O = (5Z,8Z,11Z,14Z)-eicosatetraenoate + glycerol + H(+) (RHEA:26132)
catalytic activity: 1-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-glycerol + H2O = (5Z,8Z,11Z,14Z)-eicosatetraenoate + glycerol + H(+) (RHEA:44728)
catalytic activity: 1-(9Z,12Z-octadecadienoyl)-glycerol + H2O = (9Z,12Z)- octadecadienoate + glycerol + H(+) (RHEA:48428)
catalytic activity: 3-(9Z-octadecenoyl)-sn-glycero-1-phospho-(3'-(9Z- octadecenoyl)-1'-sn-glycerol) + H2O = (9Z)-octadecenoate + 3-(9Z- octadecenoyl)-sn-glycero-1-phospho-(1'-sn-glycerol) + H(+) (RHEA:55712)
catalytic activity: (S,S)-2-(9Z-octadecenoyl)-sn-glycero-1-phospho-(2'-(9Z- octadecenoyl)-1'-sn-glycerol) + H2O = (9Z)-octadecenoate + (S,S)-2- (9Z-octadecenoyl)-sn-glycero-1-phospho-(1'-sn-glycerol) + H(+) (RHEA:55716)
catalytic activity: (R,R)-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-(2'-(9Z- octadecenoyl)-3'-sn-glycerol) + H2O = (9Z)-octadecenoate + (R,R)-2- (9Z-octadecenoyl)-sn-glycero-3-phospho-(3'-sn-glycerol) + H(+) (RHEA:55804) - ABHD6 suppresses colorectal cancer progression via AKT signaling pathway.
Xiong, Molecular carcinogenesis 2024 (PubMed)- GeneRIF: ABHD6 suppresses colorectal cancer progression via AKT signaling pathway.
- Enhanced monoacylglycerol lipolysis by ABHD6 promotes NSCLC pathogenesis.
Tang, EBioMedicine 2020 - GeneRIF: Enhanced monoacylglycerol lipolysis by ABHD6 promotes NSCLC pathogenesis.
- Cutting Edge: Dysregulated Endocannabinoid-Rheostat for Plasmacytoid Dendritic Cell Activation in a Systemic Lupus Endophenotype.
Rahaman, Journal of immunology (Baltimore, Md. : 1950) 2019 (PubMed)- GeneRIF: We discovered a regulatory role of ABHD6 in human plasmacytoid dendritic cells (pDCs) through modulating the local abundance of its substrate, the endocannabinoid 2-arachidonyl glycerol (2-AG), and elucidated a hitherto unknown cannabinoid receptor 2-mediated regulatory role of 2-AG on IFN-alpha induction by pDCs.
- Metabolic disease and ABHD6 alter the circulating bis(monoacylglycerol)phosphate profile in mice and humans.
Grabner, Journal of lipid research 2019 - GeneRIF: It demonstrate that ABHD6 affect Bis(monoacylglycerol)phosphate (BMP) metabolism in mice and humans.
- Monoacylglycerol signalling and ABHD6 in health and disease.
Poursharifi, Diabetes, obesity & metabolism 2017 (PubMed)- GeneRIF: Data suggest that ABHD6 plays important role in regulation of signaling via monoacylglycerols (MAGs) in both central and peripheral tissues; alterations in MAG signaling are involved in type 2 diabetes, obesity, and metabolic syndrome. [REVIEW]
- α/β-Hydrolase domain-containing 6 (ABHD6) negatively regulates the surface delivery and synaptic function of AMPA receptors.
Wei, Proceedings of the National Academy of Sciences of the United States of America 2016 - GeneRIF: The hydrolase activity of ABHD6 was not required for the effects of ABHD6 on AMPAR function in either neurons or transfected HEK293T cells. Thus, these findings reveal a novel and unexpected mechanism governing AMPAR trafficking at synapses through ABHD6.
- PXK locus in systemic lupus erythematosus: fine mapping and functional analysis reveals novel susceptibility gene ABHD6.
Oparina, Annals of the rheumatic diseases 2015 (PubMed)- GeneRIF: Results confirm the genetic association of the locus 3p14.3 with systemic lupus erythematosus in Europeans and point to the ABHD6 and not PXK, as the major susceptibility gene in the region.
- α/β Hydrolase Domain-containing 6 (ABHD6) Degrades the Late Endosomal/Lysosomal Lipid Bis(monoacylglycero)phosphate.
Pribasnig, The Journal of biological chemistry 2015 - GeneRIF: data suggest that ABHD6 controls BMP catabolism and is therefore part of the late endosomal/lysosomal lipid-sorting machinery
- More
- Refining S-acylation: Structure, regulation, dynamics, and therapeutic implications.
Anwar, The Journal of cell biology 2023 - “...Q9UMR5 70,881 ABHD2 P08910 4,273 ABHD3 Q8WU67 1,825 ABHD4 Q8TB40 9,544 ABHD5 Q8WTS1 9,921 ABHD6 Q9BV23 21,560 ABHD10 Q9NUJ1 197,249 ABHD11 Q8NFV4 157,176 ABHD12 Q8N2K0 55,135 ABHD13 Q7L211 4,159 ABHD14A Q9Y3T7 2,545 ABHD14B Q96IU4 607,032 ABHD15 Q96EC5 3,469 ABHD16A O95870 25,149 ABHD17A Q96GS6 27,342 ABHD17B Q5VST6...”
- THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Enzymes.
Alexander, British journal of pharmacology 2017 - “...Hydrolase 6 HGNC, UniProt DAGLA , Q9Y4D2 DAGLB , Q8NCG7 MGLL , Q99685 ABHD6 , Q9BV23 EC number 3.1.1. 3.1.1. 3.1.1.23 3.1.1.23 Common abreviation DAGL DAGL MAGL ABHD6 Endogenous substrates diacylglycerol diacylglycerol 2oleoyl glycerol = 2arachidonoylglycerol anandamide [ 181 ] 1arachidonoylglycerol > 2arachidonoylglycerol > 1oleoylglycerol >...”
- The Concise Guide to PHARMACOLOGY 2015/16: Enzymes.
Alexander, British journal of pharmacology 2015 - “...been reported to be hydrolysed by multiple enzyme activities from neural preparations, including ABHD6 ( Q9BV23 ) [ 41 ], ABHD12 ( 8N2K0 ) [ 41 ], neuropathy target esterase ( PNPLA6 , Q8IY17 [ 316 ]) and carboxylesterase 1 ( CES1 , P23141 [ 533...”
- A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs.
Dingerdissen, Biology direct 2014 - “...P18900 Q9UQB9 P38991 Q99447 P33412 P04180 P40345 O14734 P41903 P30793 P51601 Q9Y3Q0 P47161 P14550 P14065 Q9BV23 P53750 O43175 P40054 P08243 P49090 P56937 Q12452 P22830 P16622 Q86V88 P40081 Q16769 P43599 O95336 P38858 Q8IXB1 P40564 Q15386 P53119 Q969P6 P04786 Q9Y3B8 P54964 Q9Y2H1 P53894 Q9Y2Z4 P48527 P00813 P53909 Q9UI42...”
- Highly predictive ligand-based pharmacophore and homology models of ABHD6.
Bowman, Chemical biology & drug design 2013 - “...sequence for human ABHD6 was taken from the SWISSPROT protein sequence database (primary accession number Q9BV23). Initial analysis of the ABHD6 sequence indicates that first ~9 residues are extracellular, the next ~30 residues are involved in a transmembrane helix, and the remaining ~290 residues are intracellular....”
- “...5 a non-selective ABHD6 inhibitor. Figure 2 Modeling alignment for the sequences of human ABHD6 (Q9BV23) and BphD from Burkholderia xenovorans LB400 (PDB ID: 2OG1). Aligned query and template residues that are identical are highlighted in black; conserved residues (according to the BLOSUM62 scoring matrix), in...”
AT3G10840 hydrolase, alpha/beta fold family protein from Arabidopsis thaliana
25% identity, 54% coverage
- A binary interaction map between turnip mosaic virus and Arabidopsis thaliana proteomes
Martínez, Communications biology 2023 - “...P3 and 6K2 both interact with the products of genes AT2G20920 (the chaperone DUF3353) and AT3G10840 (an /-hydrolase superfamily protein associated to chloroplast external membranes) or the SGS domain-containing protein, mentioned above, that may simultaneously form a complex with HC-Pro and NIb inside the VRC (Fig....”
- Defining the core proteome of the chloroplast envelope membranes
Simm, Frontiers in plant science 2013 - “...B 4 -Helical TM 6 I At3g02900 YCF1.2 protein A 1 -Helical TM 4 I At3g10840 Putative alpha/beta-fold-type hydrolase A,B 2 -Helical TM 4 I At3g32930 Pterin 4 alpha carbinolamine dehydratase A None 4 I At3g54390 Putative DNA-binding protein (SWI3, ADA2, N-CoR, and TFIIIB) A None...”
- “...correctly assigned to the IE membrane. The proteins encoded by AT1G33810, AT1G42960, AT2G35800, AT2G38550, AT3G02900, AT3G10840, AT3G32930, AT4G13590, AT5G03900, AT5G08540, and AT5G12470 are assigned as (inner) envelope proteins (Ferro et al., 2003 , 2010 ; Froehlich et al., 2003 ; Brutigam et al., 2008 ; Brutigam...”
FRAAL3408 putative hydrolase from Frankia alni ACN14a
29% identity, 88% coverage
- The Proteogenome of Symbiotic Frankia alni in Alnus glutinosa Nodules
Pujic, Microorganisms 2022 - “...- A 0.001 WP_050997247.1 FRAAL5736 ftsK Cell division protein FtsK 6.43 D A 0.000 WP_011604554.1 FRAAL3408 Alpha/beta hydrolase 6.37 R f 0.001 WP_041938863.1 FRAAL1156 sucC Succinyl-CoA synthetase subunit beta SucC 6.14 C A 0.012 WP_011605559.1 FRAAL4438 Sugar-phosphate dehydrogenase 6.08 C A 0.002 WP_041939760.1 FRAAL5796 smc Chromosome...”
Q9HZF5 Probable hydrolytic enzyme from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA3053 probable hydrolytic enzyme from Pseudomonas aeruginosa PAO1
31% identity, 44% coverage
1mu0A / P96084 Crystal structure of the tricorn interacting factor f1 complex with pck (see paper)
pip / GB|AAC44636.1 prolyl aminopeptidase; EC 3.4.11.5 from Thermoplasma acidophilum (see 3 papers)
P96084 Proline iminopeptidase from Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)
26% identity, 84% coverage
- Ligand: (2r,3s)-3-amino-1-chloro-4-phenyl-butan-2-ol (1mu0A)
- Proteolytic systems of archaea: slicing, dicing, and mincing in the extreme
Maupin-Furlow, Emerging topics in life sciences 2018 - “...1mtz, 1mu0, 1xqv, 1xqw, xqx, 1xqy, 1xrl, 1xrm, xrn, 1xro, 1xrp, 1xrq, 1xrr Ta F1 (P96084) [ 182 184 ] (proline iminopeptidase) Tricorn interacting factor F2/F3 [M01, EC:3.4.11.-] Intracellular 1z5h Ta F2 (O93654) [ 185 , 186 ]; Ta F3 (O93655) [ 187 ] Tetrahedral amino-peptidase...”
TTE2547 predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) from Thermoanaerobacter tengcongensis MB4
27% identity, 97% coverage
- Carboxylic ester hydrolases from hyperthermophiles
Levisson, Extremophiles : life under extreme conditions 2009 - “...hydrolase 298 GWSMG TTE1809 AAM25001 Alpha/beta hydrolase 258 GLSMG TTE2321 AAM25462 Alpha/beta hydrolase 414 CHSMG TTE2547 AAM25672 Alpha/beta hydrolase 285 AHSFG Thermococcus kodakaraensis TK0522 BAD84711 Carbohydrate esterase 449 GSSLG Thermotoga maritima TM1022 AAD36099 Esterase 253 GLSMG TM1160 AAD36236 Esterase 306 GLSAG TM1350 AAD36421 Lipase, putative 259...”
F1SGJ4 Abhydrolase domain containing 6, acylglycerol lipase from Sus scrofa
25% identity, 80% coverage
SSO2262 Conserved hypothetical protein from Sulfolobus solfataricus P2
36% identity, 44% coverage
- Carboxylic ester hydrolases from hyperthermophiles
Levisson, Extremophiles : life under extreme conditions 2009 - “...GHSLG PAB2176 CAB49187 Hypothetical esterase 286 GFSMG Sulfolobus solfataricus SSO0102 AAK40458 Esterase, tropinesterase 231 GHSIG SSO2262 AAK42427 Hypothetical protein 197 GASMG SSO2518 AAK42649 Esterase, putative 353 GESFG SSO2521 AAK42652 Lipase 311 GDSAG SSO2979 AAK43083 Hypothetical protein 320 GHSSG SSO3052 AAK43152 Hypothetical protein 210 GISGN Thermoanaerobacter tengcongensis...”
MXAN_0220 hydrolase, alpha/beta fold family from Myxococcus xanthus DK 1622
39% identity, 27% coverage
SMc04033 PUTATIVE PROLINE IMINOPEPTIDASE PROTEIN from Sinorhizobium meliloti 1021
26% identity, 86% coverage
NP_001001804 epoxide hydrolase 4 isoform 1 from Mus musculus
Q6IE26 Epoxide hydrolase 4 from Mus musculus
25% identity, 77% coverage
slr0314 bromoperoxidase from Synechocystis sp. PCC 6803
25% identity, 95% coverage
- Deep Proteogenomics of a Photosynthetic Cyanobacterium
Spät, Journal of proteome research 2023 - “...genes encoding hidden proteins, one with six genes ( ssr0511 , slr0311 , slr0313 , slr0314 , slr0316 , ssr0515 ), of which only one ( slr0316 ) was previously detected at the transcriptome level (TU3202). Interestingly, a significant proportion of the hidden proteins are encoded...”
RSP_1258 putative hydrolase from Rhodobacter sphaeroides 2.4.1
25% identity, 80% coverage
- Convergence of the transcriptional responses to heat shock and singlet oxygen stresses
Dufour, PLoS genetics 2012 - “...Detoxification RSP_1057, RSP_2389, RSP_2693, RSP_3263 Toxin production and resistance RSP_2803 Central intermediary metabolism Other RSP_0897, RSP_1258, RSP_1397, RSP_3072 Phosphorus compounds RSP_0782 Protein synthesis/fate Amino acid biosynthesis RSP_0398 Degradation of proteins, peptides, and glycopeptides RSP_0686, RSP_1490 Protein folding and stabilization RSP_1219 tRNA and rRNA base modification RSP_2971...”
WP_030890495 alpha/beta fold hydrolase from Streptomyces varsoviensis
27% identity, 92% coverage
C7JDV2 Esterase/lipase from Acetobacter pasteurianus (strain NBRC 105184 / IFO 3283-01)
24% identity, 73% coverage
APA386B_2085 acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit from Acetobacter pasteurianus 386B
24% identity, 73% coverage
NP_775838 epoxide hydrolase 4 from Homo sapiens
Q8IUS5 Epoxide hydrolase 4 from Homo sapiens
24% identity, 77% coverage
CBL13_02626 alpha/beta fold hydrolase from Pseudomonas putida
25% identity, 92% coverage
oleB / Q8EG65 3-alkyl-4-acyloxetan-2-one decarboxylase (EC 4.1.1.114) from Shewanella oneidensis (strain MR-1) (see paper)
OLEB_SHEON / Q8EG65 Cis-3-alkyl-4-alkyloxetan-2-one decarboxylase; EC 4.1.1.114 from Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1) (see paper)
SO1743, SO_1743 hydrolase, alpha/beta hydrolase fold family from Shewanella oneidensis MR-1
24% identity, 79% coverage
- function: Involved in olefin biosynthesis (PubMed:20418444). Catalyzes the elimination of carbon dioxide from beta-lactones to form the final olefin product (By similarity). The S.oneidensis oleABCD genes produce 3,6,9,12,15,19,22,25,28-hentriacontanonaene, which may aid the cells in adapting to a sudden drop in temperature (PubMed:20418444).
catalytic activity: a cis-3-alkyl-4-alkyloxetan-2-one = a cis-alkene + CO2 (RHEA:18345)
disruption phenotype: Deletion of the entire oleABCD gene cluster leads to the complete absence of nonpolar extractable products. The oleABCD deletion strain shows a significantly longer lag phase than the wild- type strain when shifted to a lower temperature. - A universal TagModule collection for parallel genetic analysis of microorganisms
Oh, Nucleic acids research 2010 - “...25 LB + salt mutants suggests the importance of fatty acid biosynthesis (SO1599, SO1602, SO1742, SO1743 and SO1744), transporters (SO4693, ftsX , ftsE ), and uncharacterized proteins (including two independent mutants in SO4008) in the response and adaptation of S. oneidensis MR-1 to high salinity. Interestingly,...”
- Structure, function, and insights into the biosynthesis of a head-to-head hydrocarbon in Shewanella oneidensis strain MR-1
Sukovich, Applied and environmental microbiology 2010 - “...24373311, and 24373312, respectively; locus tags SO_1742, SO_1743, SO_1744, and SO1745, respectively). For creation of the oleC knockout strain, primers oleCUF,...”
PP4540 hydrolase, alpha/beta fold family from Pseudomonas putida KT2440
25% identity, 92% coverage
estRB8 / CAE54381.1 carboxylesterase, partial from Oleispira antarctica (see paper)
estRB8 / CAE54384.1 carboxylesterase from Oleispira antarctica (see paper)
24% identity, 79% coverage
Q3B8N9 Biphenyl hydrolase-like (Serine hydrolase) from Rattus norvegicus
27% identity, 90% coverage
5h3hB Esterase (eaest) from exiguobacterium antarcticum (see paper)
25% identity, 92% coverage
- Ligand: ethaneperoxoic acid (5h3hB)
O66382 Esterase2 from Acetobacter pasteurianus
24% identity, 66% coverage
MXAN_1644 putative epoxide hydrolase from Myxococcus xanthus DK 1622
26% identity, 87% coverage
- Biotransformation of polyunsaturated fatty acids to bioactive hepoxilins and trioxilins by microbial enzymes
An, Nature communications 2018 - “...comparison with the sequences of human corresponding genes. The genes of MXAN_1744 , MXAN_1745 , MXAN_1644 , MXAN_5137 , MXAN_5217 , MXAN_0683 , MXAN_2304 and MXAN_3623 in M . xanthus were predicted to be the genes encoding LOX, LOX, EH, EH, COX, twothromboxane A (TXA) synthases...”
- “...The putative LOX enzymes expressed from MXAN_1745 and MXAN_1744 , and the putative EH from MXAN_1644 were purified from crude cell extracts as single soluble proteins using His-Trap affinity chromatography (Supplementary Fig. 4 ). The substrate specificity and products of these purified enzymes are summarized in...”
WP_014479220 epoxide hydrolase EphM from Bacillus subtilis
25% identity, 94% coverage
- Enhancement of Soluble Expression and Biochemical Characterization of Two Epoxide Hydrolases from Bacillus
Wu, Iranian journal of biotechnology 2019 - “...were found to encode EHs. These two EHs were assigned as BsuEH (GenBank accession no. WP_014479220) and BpuEH (GenBank accession no. WP_008342154). Based on the coding sequences of BpuEH and BsuEH , primers were designed to amplify these genes ( Table 1 ). The PCR reaction...”
- “...1. Multiple sequence alignment of epoxide hydrolases (EHs) from Bacillus subtilis (BsuEH, GenBank accession no. WP_014479220), B. pumilus (BpuEH, GenBank accession no. WP_008342154), B. cereus (BceEH, GenBank Accession no. KXY30655), and B. megaterium (BmeEH, GenBank Accession no. ADV36302). Solid triangles indicate putative active site residues (Asp-Asp-His);...”
wcw_1298 alpha/beta fold hydrolase from Waddlia chondrophila WSU 86-1044
26% identity, 90% coverage
BCAL1048 putative hydrolase from Burkholderia cenocepacia J2315
35% identity, 27% coverage
WP_024569139 alpha/beta fold hydrolase from Cupriavidus metallidurans
26% identity, 82% coverage
pydB / Q5IH18 4-formamido-2-oxobut-3-enoate deformylase from Rhizobium sp. TAL1145 (see 2 papers)
25% identity, 87% coverage
all2068 unknown protein from Nostoc sp. PCC 7120
25% identity, 85% coverage
- The composition of the global and feature specific cyanobacterial core-genomes
Simm, Frontiers in microbiology 2015 - “...all1862 Putative peptidase 22,2 9,6 Fis1 0/0 None all2008 Serine proteinase 1,2 1,2 6/198 None all2068 Alpha/beta hydrolase fold protein 1,3 1,0 59/482 None all2357 Phosphonate ABC transport ATP-binding component 4,9 3,3 Nos2 485/497 None all2358 Periplasmic phosphonate binding protein 6,3 2,9 0/148 None alr2463 Aminoglycoside...”
RSPO_c00415 alpha/beta fold hydrolase from Ralstonia solanacearum Po82
24% identity, 69% coverage
- A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum
Castillo, BMC evolutionary biology 2019 - “...precursor transmembrane protein IIB/chromosome RSPO_c00179 gcl 1 0.0240** 2.1552** 1.5475** Tartronate-semialdehyde synthase (glyoxylate carboligase) IIB/chromosome RSPO_c00415 RSPO_c00416 1 0.0352** 2.0846** 1.4063** b-ketoadipate enol-lactone hydrolase protein and 3-ketoacyl-(acyl-carrier-protein) reductase IIB/chromosome RSPO_c00497 secY 1 0.0282** 1.9898** 1.5826** Preprotein translocase (membrane subunit) IIB/chromosome RSPO_c00765 phcB 1 0.0240** 2.1264** 1.5475**...”
NWF34_11730 alpha/beta fold hydrolase from Gordonia sp. GONU
23% identity, 89% coverage
DR0791, DR_0791 chloride peroxidase, putative from Deinococcus radiodurans R1
26% identity, 85% coverage
NP_001087143 epoxide hydrolase 2, cytoplasmic L homeolog from Xenopus laevis
Q6DCH2 Ephx2-prov protein from Xenopus laevis
26% identity, 46% coverage
DR2549 epoxide hydrolase-related protein from Deinococcus radiodurans R1
34% identity, 46% coverage
A1YV97 Lipase (Fragment) from Fervidobacterium changbaicum
27% identity, 90% coverage
- Role of the NC-loop in catalytic activity and stability in lipase from Fervidobacterium changbaicum
Li, PloS one 2012 - “...Server ( http://www.sbg.bio.ic.ac.uk/phyre/ ) was used to derive the 3D structure of FClip1 (UniProt accession: A1YV97). The aryl esterase PFE from Pseudomonas fluorescens (PDB code: 1VA4) [42] was chosen as the template. Structural qualities of the generated models were evaluated using Protein Structure Validation Software [43]...”
- “...repesented by the accession numbers were the same as in figure 1 . Although FClip1 (A1YV97) belongs to the lipase family, it situates at the root of the lipases branch and is near the perhydrolases branch. It might be an evolutionary intermediate between lipases and perhydrolases...”
BPHL_HUMAN / Q86WA6 Valacyclovir hydrolase; VACVase; Valacyclovirase; Biphenyl hydrolase-like protein; Biphenyl hydrolase-related protein; Bph-rp; Breast epithelial mucin-associated antigen; MCNAA; EC 3.1.-.- from Homo sapiens (Human) (see 2 papers)
27% identity, 97% coverage
BC4345 Lipase from Bacillus cereus ATCC 14579
25% identity, 89% coverage
SSO3115 Tricorn protease interacting factor F1 from Sulfolobus solfataricus P2
25% identity, 84% coverage
- Activity-based protein profiling as a robust method for enzyme identification and screening in extremophilic Archaea
Zweerink, Nature communications 2017 - “...and ApeH-2, SSO2141, MW 64.3kDa), a serine aminopeptidase (SSO2518, MW 40.5kDa), a proline iminopeptidase (Pip, SSO3115, MW 36.0kDa), and 2 amidases (SSO2122, MW 55.7kDa and GatA-1, SSO0765, MW 44.1kDa). In total, we robustly identified 10 serine hydrolases out of the 18 predicted hydrolases (56%). This number...”
- Proteolysis in hyperthermophilic microorganisms
Ward, Archaea (Vancouver, B.C.) 2002 - “...from the sequence to suggest otherwise. Peptidases SSO3115 SSO2154 SSO2675 SSO0010 SSO0363 SSO0433 SSO0434 SSO1355 SSO1952 SSO3105 SSO1465 SSO1607 SSO1864...”
NCU02904 alpha/beta hydrolase fold protein from Neurospora crassa OR74A
27% identity, 69% coverage
- Discovering functions of unannotated genes from a transcriptome survey of wild fungal isolates
Ellison, mBio 2014 - “...right, are NCU01066, NCU01816, NCU02333, NCU03076, NCU03257, NCU05387, NCU07675, NCU08356, NCU10007, NCU00721, NCU00130, NCU01140, NCU01449, NCU02904, NCU03151, NCU04039, NCU04197, NCU04460, NCU04963, NCU08746, NCU10021, and NCU07363. PP4 controls expression of nitrogen metabolite repression and carbon catabolite repression targets. The NMR target genes differentially expressed between the Louisiana...”
LPC_0888 biotin biosynthesis protein BioH from Legionella pneumophila str. Corby
25% identity, 91% coverage
- The opportunistic pathogen Pseudomonas aeruginosa exploits bacterial biotin synthesis pathway to benefit its infectivity
Shi, PLoS pathogens 2023 - “...5 orthologs consisted of three BioH-like enzymes (i.e., V . cholerae vc2718, Xanthomonas Xcc0385, plus Lpc_0888 of Legionella pneumophila ), and two BioHC fusion proteins, namely i) CJA_0428 (502 aa) of Cellvibrio japonicus , and ii) Sde_3137 (558 aa) of Saccharophagus degradans ). The structure of...”
- “...plant pathogen Xanthomonas campestris for Xcc_0385, iv) the intracellular pathogen Legionella pneumophila str. Corby for LPC_0888, and v) the opportunistic pathogen Vibrio cholerae N16961 for vc2718. (TIF) Click here for additional data file. S2 Fig The monomeric BioH (PA0502) is active in demethylating pimeloyl-ACP methyl ester....”
NP_001289706 valacyclovir hydrolase isoform 2 from Homo sapiens
26% identity, 98% coverage
MAB_3034 Probable hydrolase from Mycobacterium abscessus ATCC 19977
MAB_3034 alpha/beta fold hydrolase from Mycobacteroides abscessus ATCC 19977
21% identity, 78% coverage
- Genetic diversification of persistent Mycobacterium abscessus within cystic fibrosis patients
Lewin, Virulence 2021 - “...protein 4014-1 MAB_3029 HIFIHNKG_02972 ideR Iron-dependent repressor [K] 6516-20, 7716-4 Iron acquisition [ 48 ] MAB_3034 HIFIHNKG_02977 Alpha/beta hydrolase fold family hydrolase [I] 6516-20, 7716-4 MAB_3036c HIFIHNKG_02979 nrdR Transcriptional repressor NrdR [K] 4014-3 MAB_3404c HIFIHNKG_03344 nrdF Ribonucleoside-diphosphate reductase subunit beta [F] 7416-1, 10317-1 No homolog HIFIHNKG_03363...”
MSMEG_4707 non-heme bromoperoxidase BPO-A2 from Mycobacterium smegmatis str. MC2 155
27% identity, 90% coverage
2ocgA / Q86WA6 Crystal structure of human valacyclovir hydrolase (see paper)
27% identity, 97% coverage
- Ligand: manganese (ii) ion (2ocgA)
AF2336 carboxylesterase (est-3) from Archaeoglobus fulgidus DSM 4304
26% identity, 89% coverage
blr5346 blr5346 from Bradyrhizobium japonicum USDA 110
26% identity, 69% coverage
IYO_RS05655 pyrimidine utilization protein D from Pseudomonas syringae pv. actinidiae ICMP 18884
24% identity, 91% coverage
GSU3157 hydrolase, alpha/beta fold family from Geobacter sulfurreducens PCA
25% identity, 91% coverage
HVO_2702 predicted hydrolase or acyltransferase (alpha/beta hydrolase superfamily) from Haloferax volcanii DS2
27% identity, 91% coverage
BCE_2449 hydrolase, alpha/beta fold family from Bacillus cereus ATCC 10987
35% identity, 39% coverage
ZP_01697334 alpha/beta hydrolase fold from Bacillus coagulans 36D1
24% identity, 91% coverage
- Novel lipolytic enzymes identified from metagenomic library of deep-sea sediment
Jeon, Evidence-based complementary and alternative medicine : eCAM 2011 - “...marina (49% identity), LpqC (ZP_01463024) from Stigmatella aurantiaca DW4/3-1 (39% identity), / hydrolase fold protein (ZP_01697334) from Bacillus coagulans 36D1 (33% identity), and lipase (ACJ13070) from uncultured bacterium (58% identity), respectively. To see how the ORFs were related to known esterases/lipases, the phylogenetic relationship was analyzed...”
- “...including EM3L1 and EM3L6: YP_003395264, an / hydrolase fold protein from Conexibacter woesei DSM 14684; ZP_01697334, an / hydrolase fold from Bacillus coagulans 36D1; NP_767479, a hypothetical protein bll0839 from Bradyrhizobium japonicum USDA 110; ZP_06812025, an / hydrolase fold protein from Geobacillus thermoglucosidasius C56-YS93. (b) Family...”
Spro_0990 alpha/beta hydrolase fold from Serratia proteamaculans 568
25% identity, 79% coverage
ZP_01897865 putative haloalkane dehalogenase from Moritella sp. PE36
24% identity, 88% coverage
lnmJ / Q8GGP2 leinamycin polyketide synthase LnmJ from Streptomyces atroolivaceus (see 5 papers)
Q8GGP2 Polyketide synthase from Streptomyces atroolivaceus
27% identity, 3% coverage
NE2298 possible BioH, catalyzes some early step in biotin biosynthesis from Nitrosomonas europaea ATCC 19718
26% identity, 85% coverage
XP_001492725 bifunctional epoxide hydrolase 2 from Equus caballus
24% identity, 47% coverage
Bphyt_6134 alpha/beta hydrolase fold from Burkholderia phytofirmans PsJN
27% identity, 91% coverage
VIN14_02820 proline iminopeptidase-family hydrolase from Lacticaseibacillus casei
25% identity, 77% coverage
H16_A3742 alpha/beta fold hydrolase from Cupriavidus necator H16
H16_A3742 Lipase from Ralstonia eutropha H16
24% identity, 82% coverage
GRMZM2G032910 uncharacterized protein LOC100192768 from Zea mays
33% identity, 43% coverage
- Proteomic Analysis of Silk Viability in Maize Inbred Lines and Their Corresponding Hybrids
Ma, PloS one 2015 - “...- LZ-D 12 gi|413933924 epoxide hydrolase 2 isoform 1 [Zea mays] 35469.8/5.09 118 100 7 GRMZM2G032910 5:2463857424636922 5.20E-49 Nucleotide metabolism 225 Y/N + LZ-D 10 gi|414589043 pyrimidine-specific ribonucleoside hydrolase rihB 34329.6/5.36 254 100 5 GRMZM2G104999 2:166013604166017041 1.60E-116 266 Y/N + - XZ-D 12 gi|414589043 pyrimidine-specific ribonucleoside...”
XCV2196 putative non-heme chloroperoxidase from Xanthomonas campestris pv. vesicatoria str. 85-10
25% identity, 91% coverage
5aljA / P34913 Ligand complex structure of soluble epoxide hydrolase (see paper)
24% identity, 50% coverage
- Ligand: 2-(3-fluoro-4-methyl-anilino)-4-methyl-quinolin-5-ol (5aljA)
VOW57_04040 proline iminopeptidase-family hydrolase from Lacticaseibacillus paracasei
24% identity, 80% coverage
O06734 AB hydrolase superfamily protein YisY from Bacillus subtilis (strain 168)
27% identity, 89% coverage
Q6Q2C2 Bifunctional epoxide hydrolase 2 from Sus scrofa
24% identity, 47% coverage
- Label-Free Quantitative Analysis of Pig Liver Proteome after Hepatitis E Virus Infection
Martino, Viruses 2024 - “...GLMS glutamine-fructose-6-phosphate aminotransferase 1 13 58.72 0.0000 2.19 P37111 ACY1 aminoacylase-1 12 86.53 0.0009 2.34 Q6Q2C2 EPHX2 bifunctional epoxide hydrolase 2 12 54.89 0.0174 1.66 A0A286ZRS0 GSS glutathione synthetase 11 44.56 0.0071 1.91 P28839 LAP3 xaa-Pro dipeptidase 11 48.18 0.0023 2.64 A0A4X1TBE8 GSTM3 glutathione S-transferase 11...”
- Evaluating nursery pig responses to in-feed sub-therapeutic antibiotics
Helm, PloS one 2019 - “...ribosomal protein L32 Q6QAT0 0.301 0.004 Apolipoprotein A-I P18648 0.318 0.038 Bifunctional epoxide hydrolase 2 Q6Q2C2 0.437 0.046 Cystathionine gamma-lyase Q19QT7 0.341 0.029 Cytochrome c oxidase subunit 5B, mitochondrial Q5S3G4 0.389 0.023 Dihydropteridine reductase Q8MJ30 0.308 0.022 Elongation factor 1-beta P29412 0.303 0.039 Elongation factor 1-gamma...”
SMa1166 Putative hydrolase protein from Sinorhizobium meliloti 1021
26% identity, 75% coverage
BC_4774 alpha/beta fold hydrolase from Bacillus cereus ATCC 14579
BC4774 Non-heme chloroperoxidase from Bacillus cereus ATCC 14579
26% identity, 95% coverage
- Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach
Stelder, Journal of proteome research 2018 - “...b BC_2889 N-acetylmuramoyl- l -alanine amidase BC_2823 N-acetylmuramoyl- l -alanine amidase BC_1494 Nonheme chloroperoxidase a BC_4774 Oligopeptide-binding protein oppA a BC_3586 Oligopeptide-binding protein oppA BC_3585 Oligopeptide-binding protein oppA BC_3584 Oligopeptide-binding protein oppA a BC_2026 Protein translocase subunit YajC a BC_4410 Putative hydrolase a BC_3133 Putative stage...”
- Biofilm formation displays intrinsic offensive and defensive features of Bacillus cereus
Caro-Astorga, NPJ biofilms and microbiomes 2020 - “...devoted to scavenging diverse ROS: catalase (BC3008), superoxide dismutases ( BC1468, BC4907 ), chloroperoxidase ( BC4774 ), alkylhydroperoxidase ( BC2830 ,), and glyoxalases ( BC5092*, BC3178, BC0824 ). Additionally, iTRAQ analysis showed higher amounts of glutathione peroxidase ( BC2114 ), glyoxalases ( BC5092, BC3532 ), superoxide...”
6i8wB / Q9KJG6 Crystal structure of a membrane phospholipase a, a novel bacterial virulence factor (see paper)
22% identity, 82% coverage
- Ligand: undecanoic acid (6i8wB)
Q9KJG6 triacylglycerol lipase (EC 3.1.1.3) from Pseudomonas aeruginosa (see paper)
PA2949 probable lipase from Pseudomonas aeruginosa PAO1
22% identity, 80% coverage
- Mining bacterial genomes for novel arylesterase activity
Wang, Microbial biotechnology 2010 - “...purified carboxylic ester hydrolases. Property PaEST1 PpEST1 PpEST2 PpEST3 RpEST1 RpEST2 RpEST3 SavEST1 UniProt ID Q9KJG6 Q88QX0 Q88CC8 Q88GS3 Q6NCW9 Q6N0W4 Q6N4A9 Q82QJ4 MW a 34.8 26.3 30 31.1 32.4 26.2 27.2 28.5 pI a 6.1 5.0 4.9 5.1 5.3 5.3 5.6 5.4 pH optimum 79...”
- Molecular Mechanisms Underlying Medium-Chain Free Fatty Acid-Regulated Activity of the Phospholipase PlaF from Pseudomonas aeruginosa
Gentile, JACS Au 2024 - “...procedures. 6 For obtaining PlaF variants of the lid-like domain, site-directed mutagenesis of plaF ( pa2949 ) was carried out using the Quik-Change PCR method with the Phusion DNA polymerase and the pET_pa2949 plasmid. 74 Similarly, mutants located in the T3 tunnel were generated through site-directed...”
- “...Gohlke H. ; Batra-Safferling R. ; Jaeger K. E. ; Kovacic F. Pseudomonas aeruginosa esterase PA2949, a bacterial homolog of the human membrane esterase ABHD6: expression, purification and crystallization . Acta Crystallogr. F Struct. Biol. 2019 , 75 ( 4 ), 270 7 . 10.1107/S2053230X19002152 ....”
- Structural, mechanistic, and physiological insights into phospholipase A-mediated membrane phospholipid degradation in Pseudomonas aeruginosa
Bleffert, eLife 2022 - “...P. aeruginosa PAO1 (WT) cells transformed ( Choi et al., 2006 ) with plasmid pBBR- pa2949 ( Kovacic et al., 2016 ), here abbreviated as p- plaF , were grown overnight at 37C in lysogeny broth (LB) medium supplemented with tetracycline (100 g/ml) ( Bleffert et...”
- “...F Granzin J Gohlke H Batra-Safferling R Jaeger KE Kovacic F 2019 Pseudomonas aeruginosa esterase PA2949, a bacterial homolog of the human membrane esterase ABHD6: expression, purification and crystallization Acta Crystallographica. Section F, Structural Biology Communications 75 270 277 10.1107/S2053230X19002152 30950828 Bleves S Lazdunski A Filloux...”
- Pseudomonas aeruginosa esterase PA2949, a bacterial homolog of the human membrane esterase ABHD6: expression, purification and crystallization
Bleffert, Acta crystallographica. Section F, Structural biology communications 2019 - “...2053-230X International Union of Crystallography 6450514 aq5005 10.1107/S2053230X19002152 ACSFEN S2053230X19002152 Research Communications Pseudomonas aeruginosa esterase PA2949, a bacterial homolog of the human membrane esterase ABHD6: expression, purification and crystallization Pseudomonas aeruginosa esterase PA294 Bleffert Florian a Granzin Joachim b Gohlke Holger b c d Batra-Safferling Renu...”
- “...of this article is available from Crystallography Journals Online. Homologous expression of the membrane-bound esterase PA2949 from Pseudomonas aeruginosa PA01 and the purification of detergent-solubilized enzyme resulted in stable PA2949 protein that crystallized. The crystals obtained were used for X-ray analysis and diffracted to a resolution...”
- Disruption of microbial community composition and identification of plant growth promoting microorganisms after exposure of soil to rapeseed-derived glucosinolates
Siebers, PloS one 2018 - “...as the amount of enzyme releasing 1.0 mol min -1 of lauric acid. Phospholipase A PA2949 from Pseudomonas aeruginosa was used as control [ 35 ]. Protease activity was determined by degradation of fluorescein-tagged casein using the Thermo fluorescent protease assay kit (Thermo Scientific) with 25...”
- “..., Wilhelm S , Granzin J , Batra-Safferling R , et al A membrane-bound esterase PA2949 from Pseudomonas aeruginosa is expressed and purified from Escherichia coli . FEBS Open Bio . 2016 ; 6 ( 5 ): 484 93 . doi: 10.1002/2211-5463.12061 27419054 36 Grosser K...”
- Additive Effects of Quorum Sensing Anti-Activators on Pseudomonas aeruginosa Virulence Traits and Transcriptome
Asfahl, Frontiers in microbiology 2017 - “...) 1.5 NC NC NC PA2939 probable aminopeptidase ( pepB ) 2.7 4.1 9.1 11.5 PA2949 probable lipase 1.4 NC NC NC PA3326 clpP2 ClpP2 2.5 7.2 7.3 7.0 PA3327 probable non-ribosomal peptide synthetase 3.3 16.1 8.1 3.5 PA3328 probable FAD-dependent monooxygenase 4.5 21.9 12.4 5.4...”
- A membrane-bound esterase PA2949 from Pseudomonas aeruginosa is expressed and purified from Escherichia coli
Kovacic, FEBS open bio 2016 - “...Wiley and Sons Inc. Hoboken 4856427 10.1002/2211-5463.12061 FEB412061 Research Article Research Articles A membranebound esterase PA2949 from Pseudomonasaeruginosa is expressed and purified from Escherichiacoli F. Kovacic etal . Kovacic Filip 1 Bleffert Florian 1 Caliskan Muttalip 1 Wilhelm Susanne 1 Granzin Joachim 2 BatraSafferling Renu 2...”
- “...a precursor of captopril, a drug used for treatment of hypertension. We show here that PA2949 from P.aeruginosa PA01, a homologue of EstA, can efficiently be expressed in an enzymatically active form in E.coli . The enzyme is membraneassociated as demonstrated by cell fractionation studies. PA2949...”
- Sequence- and activity-based screening of microbial genomes for novel dehalogenases
Chan, Microbial biotechnology 2010 - “...activity pNPpalmitate PalmitoylCoA pNPP+Mg 2+ pNPP+cations ABH PA5513 High 0.76 3.2 1.0 1.2 Thioesterase ABH PA2949 Low 2.6 2.2 0.92 0.92 Esterase ABH PP4164 High 0.83 2.8 0.90 0.95 Thioesterase ABH PP2567 High 0.88 2.4 0.95 0.99 Thioesterase ABH PP2083 High 0.74 2.1 0.92 0.96 Thioesterase...”
- In vivo evidence of Pseudomonas aeruginosa nutrient acquisition and pathogenesis in the lungs of cystic fibrosis patients
Son, Infection and immunity 2007 - “...Phospholipases and lipases PA0843 PA0844 PA2862 PA2863 PA2949 PA4813 Gene VOL. 75, 2007 P. AERUGINOSA NUTRIENT ACQUISITION AND PATHOGENESIS 5321 material)....”
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Q45QT1 soluble epoxide hydrolase (EC 3.3.2.10) from Gallus gallus (see paper)
25% identity, 46% coverage
CDSM653_00572 alpha/beta hydrolase from Caldanaerobacter subterraneus subsp. pacificus DSM 12653
34% identity, 38% coverage
P29715 bromide peroxidase (EC 1.11.1.18) from Kitasatospora aureofaciens (see 2 papers)
bpoA2 / GI|150457 non-heme bromoperoxidase BPO-A2; EC 1.11.1.- from Streptomyces aureofaciens (see 4 papers)
23% identity, 96% coverage
rrnAC0572 3-oxoadipate enol-lactone hydrolase from Haloarcula marismortui ATCC 43049
29% identity, 76% coverage
- Genome information management and integrated data analysis with HaloLex
Pfeiffer, Archives of microbiology 2008 - “...HQ2751A rrnAC0546 1,791 1,833 Shortened HQ1573A, OE1495R, NP1746A rrnAC0568 699 435 Extended HQ1615A, rrnAC3127, NP1996A rrnAC0572 804 855 Shortened HQ3669A, rrnAC2557, NP0792A, OE3115F rrnAC0589 657 846 Shortened rrnAC2321, OE8048F rrnAC0617 1,335 1,413 Shortened NP0212A, HQ2634A, OE8010R rrnAC0619 1,272 963 Extended HQ3141A, OE4634F, NP0578A rrnAC0620 1,566 1,431...”
cpoT / GB|AAB86626.1 non-heme chloroperoxidase from Streptomyces aureofaciens (see paper)
23% identity, 96% coverage
HYES_HUMAN / P34913 Bifunctional epoxide hydrolase 2; EC 3.3.2.10; EC 3.1.3.76 from Homo sapiens (Human) (see 12 papers)
P34913 2-lysophosphatidate phosphatase (EC 3.1.3.106); soluble epoxide hydrolase (EC 3.3.2.10) from Homo sapiens (see 47 papers)
NP_001970 bifunctional epoxide hydrolase 2 isoform 1 from Homo sapiens
24% identity, 47% coverage
- function: Bifunctional enzyme (PubMed:12574510). The C-terminal domain has epoxide hydrolase activity and acts on epoxides (alkene oxides, oxiranes) and arene oxides (PubMed:12574510, PubMed:12869654, PubMed:22798687). Plays a role in xenobiotic metabolism by degrading potentially toxic epoxides (By similarity). Also determines steady- state levels of physiological mediators (PubMed:12574510, PubMed:12869654, PubMed:21217101, PubMed:22798687).
function: Bifunctional enzyme (PubMed:12574510). The N-terminal domain has lipid phosphatase activity, with the highest activity towards threo-9,10-phosphonooxy-hydroxy-octadecanoic acid, followed by erythro- 9,10-phosphonooxy-hydroxy-octadecanoic acid, 12-phosphonooxy-octadec- 9Z-enoic acid and 12-phosphonooxy-octadec-9E-enoic acid (PubMed:12574510). Has phosphatase activity toward lyso- glycerophospholipids with also some lower activity toward lysolipids of sphingolipid and isoprenoid phosphates (PubMed:22217705, PubMed:22387545).
catalytic activity: an epoxide + H2O = an ethanediol (RHEA:19037)
catalytic activity: (9S,10S)-10-hydroxy-9-(phosphooxy)octadecanoate + H2O = (9S,10S)-9,10-dihydroxyoctadecanoate + phosphate (RHEA:16537)
catalytic activity: 12-phosphooxy-(9Z)-octadecenoate + H2O = 12-hydroxy-(9Z)- octadecenoate + phosphate (RHEA:45272)
catalytic activity: 12-phosphooxy-(9E)-octadecenoate + H2O = 12-hydroxy-(9E)- octadecenoate + phosphate (RHEA:45276)
catalytic activity: 12-(phosphooxy)octadecanoate + H2O = 12-hydroxyoctadecanoate + phosphate (RHEA:45280)
catalytic activity: 8,9-epoxy-(5Z,11Z,14Z)-eicosatrienoate + H2O = 8,9-dihydroxy- (5Z,11Z,14Z)-eicosatrienoate (RHEA:44048)
catalytic activity: 11,12-epoxy-(5Z,8Z,14Z)-eicosatrienoate + H2O = 11,12- dihydroxy-(5Z,8Z,14Z)-eicosatrienoate (RHEA:44044)
catalytic activity: 14,15-epoxy-(5Z,8Z,11Z)-eicosatrienoate + H2O = 14,15- dihydroxy-(5Z,8Z,11Z)-eicosatrienoate (RHEA:44040)
catalytic activity: 9,10-epoxy-(12Z)-octadecenoate + H2O = 9,10-dihydroxy-(12Z)- octadecenoate (RHEA:44032)
catalytic activity: 8-hydroxy-(11S,12S)-epoxy-(5Z,9E,14Z)-eicosatrienoate + H2O = (8,11R,12S)-trihydroxy-(5Z,9E,14Z)-eicosatrienoate (RHEA:50896)
catalytic activity: 10-hydroxy-(11S,12S)-epoxy- (5Z,8Z,14Z)-eicosatrienoate + H2O = (10,11S,12R)-trihydroxy-(5Z,8Z,14Z)-eicosatrienoate (RHEA:50900)
catalytic activity: 1-tetradecanoyl-sn-glycerol 3-phosphate + H2O = 1- tetradecanoyl-sn-glycerol + phosphate (RHEA:53592)
catalytic activity: 1-octadecanoyl-sn-glycero-3-phosphate + H2O = 1-octadecanoyl- sn-glycerol + phosphate (RHEA:53596)
catalytic activity: 1-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphate + H2O = 1-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycerol + phosphate (RHEA:53600)
catalytic activity: 1-hexadecanoyl-sn-glycero-3-phosphate + H2O = 1-hexadecanoyl- sn-glycerol + phosphate (RHEA:53604)
catalytic activity: 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O = 1-(9Z- octadecenoyl)-sn-glycerol + phosphate (RHEA:39835)
catalytic activity: (8S,9R)-epoxy-(5Z,11Z,14Z)-eicosatrienoate + H2O = (8S,9S)- dihydroxy-(5Z,11Z,14Z)-eicosatrienoate (RHEA:53972)
catalytic activity: (11S,12R)-epoxy-(5Z,8Z,14Z)-eicosatrienoate + H2O = (11R,12R)- dihydroxy-(5Z,8Z,14Z)-eicosatrienoate (RHEA:53980)
catalytic activity: (11S,12R)-epoxy-(5Z,8Z,14Z)-eicosatrienoate + H2O = (11S,12S)- dihydroxy-(5Z,8Z,14Z)-eicosatrienoate (RHEA:53984)
catalytic activity: (14S,15R)-epoxy-(5Z,8Z,11Z)-eicosatrienoate + H2O = (14R,15R)- dihydroxy-(5Z,8Z,11Z)-eicosatrienoate (RHEA:53992)
catalytic activity: (14S,15R)-epoxy-(5Z,8Z,11Z)-eicosatrienoate + H2O = (14S,15S)- dihydroxy-(5Z,8Z,11Z)-eicosatrienoate (RHEA:53996)
catalytic activity: (11R,12S)-epoxy-(5Z,8Z,14Z)-eicosatrienoate + H2O = (11S,12S)- dihydroxy-(5Z,8Z,14Z)-eicosatrienoate (RHEA:54004)
catalytic activity: (11R,12S)-epoxy-(5Z,8Z,14Z)-eicosatrienoate + H2O = (11R,12R)- dihydroxy-(5Z,8Z,14Z)-eicosatrienoate (RHEA:54000)
catalytic activity: (8S,9R)-epoxy-(5Z,11Z,14Z)-eicosatrienoate + H2O = (8R,9R)- dihydroxy-(5Z,11Z,14Z)-eicosatrienoate (RHEA:54016)
catalytic activity: (14R,15S)-epoxy-(5Z,8Z,11Z)-eicosatrienoate + H2O = (14R,15R)- dihydroxy-(5Z,8Z,11Z)-eicosatrienoate (RHEA:53976)
cofactor: Mg(2+)
subunit: Homodimer. - Targeting the soluble epoxide hydrolase pathway as a novel therapeutic approach for the treatment of pain.
Turnbull, Current opinion in pharmacology 2024 (PubMed)- GeneRIF: Targeting the soluble epoxide hydrolase pathway as a novel therapeutic approach for the treatment of pain.
- Wide-spread enhancer effect of SNP rs2279590 on regulating epoxide hydrolase-2 and protein tyrosine kinase 2-beta gene expression.
Padhy, Gene 2023 (PubMed)- GeneRIF: Wide-spread enhancer effect of SNP rs2279590 on regulating epoxide hydrolase-2 and protein tyrosine kinase 2-beta gene expression.
- Targeting soluble epoxide hydrolase promotes osteogenic-angiogenic coupling via activating SLIT3/HIF-1α signalling pathway.
Gao, Cell proliferation 2023 - GeneRIF: Targeting soluble epoxide hydrolase promotes osteogenic-angiogenic coupling via activating SLIT3/HIF-1alpha signalling pathway.
- Role of soluble epoxide hydrolase in the abnormal activation of fibroblast-like synoviocytes from patients with rheumatoid arthritis.
Pu, Clinical immunology (Orlando, Fla.) 2023 - GeneRIF: Role of soluble epoxide hydrolase in the abnormal activation of fibroblast-like synoviocytes from patients with rheumatoid arthritis.
- A hypothesis-driven study to comprehensively investigate the association between genetic polymorphisms in EPHX2 gene and cardiovascular diseases: Findings from the UK Biobank.
Zhu, Gene 2022 (PubMed)- GeneRIF: A hypothesis-driven study to comprehensively investigate the association between genetic polymorphisms in EPHX2 gene and cardiovascular diseases: Findings from the UK Biobank.
- No impact of soluble epoxide hydrolase rs4149243, rs2234914 and rs751142 genetic variants on the development of type II diabetes and its hypertensive complication among Jordanian patients.
Khamees, International journal of clinical practice 2021 (PubMed)- GeneRIF: No impact of soluble epoxide hydrolase rs4149243, rs2234914 and rs751142 genetic variants on the development of type II diabetes and its hypertensive complication among Jordanian patients.
- Preservation of epoxyeicosatrienoic acid bioavailability prevents renal allograft dysfunction and cardiovascular alterations in kidney transplant recipients.
Duflot, Scientific reports 2021 - GeneRIF: Preservation of epoxyeicosatrienoic acid bioavailability prevents renal allograft dysfunction and cardiovascular alterations in kidney transplant recipients.
- Association of rs11780592 Polymorphism in the Human Soluble Epoxide Hydrolase Gene (EPHX2) with Oxidized LDL and Mortality in Patients with Diabetic Chronic Kidney Disease.
Roumeliotis, Oxidative medicine and cellular longevity 2021 - GeneRIF: Association of rs11780592 Polymorphism in the Human Soluble Epoxide Hydrolase Gene (EPHX2) with Oxidized LDL and Mortality in Patients with Diabetic Chronic Kidney Disease.
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- Combined High-Throughput Proteomics and Random Forest Machine-Learning Approach Differentiates and Classifies Metabolic, Immune, Signaling and ECM Intra-Tumor Heterogeneity of Colorectal Cancer
Contini, Cells 2024 - “...SULT2 ) CE-2 0.0006 S<H 9.2 0.0004 D<H 10.9 0.0004 0.03 WB [ 72 ] P34913 (EPHX2 ) CEH 0.0002 S<H 4.8 0.00001 D<H >100 0.00001 IHC, qPCR, WB [ 73 ] P10645 ( CHGA ) CgA, pro-protein 0.0001 S<H 8.7 0.00001 D<H 18.2 0.00001 0.03...”
- Assessing structure and disorder prediction tools for de novo emerged proteins in the age of machine learning
Aubel, F1000Research 2023 - “...393 aa Cytochrome P450 Sulfurisphaera tokodaii Q972I2 367 aa Bifunctional epoxide hydrolase H. sapiens (Human) P34913 555 aa Interferon gamma Paralichthys olivaceus (Bastard halibut) B3IXK1 198 aa Myoglobin Physeter macrocephalus (Sperm whale) P02185 154 aa Disorder predictions Disorder predictions were performed locally using IUPred3 [ Erds...”
- Host macrocyclic acylcarnitines mediate symbiotic interactions between frogs and their skin microbiome.
Brunetti, iScience 2023 - “...oxygenation and epoxide opening arachidonate 5-lipoxygenase P09917 78.3 A0A1L8FJT5 84.9 0.5 0.5 epoxide hydrolase 2 P34913 56.4 Q6DCH2 73.0 10.0 13.0 Acc. n, accession number; v1, variant 1; v2, variant 2; tpm, transcripts per million. Figure2 Putative biosynthetic pathway for skin macrocyclic acylcarnitines Enzymes in green...”
- The mechanism of Renshen-Fuzi herb pair for treating heart failure-Integrating a cardiovascular pharmacological assessment with serum metabolomics
Chen, Frontiers in pharmacology 2022 - “...) that most compounds of RS-FZ mainly acted on CYP2D6 (P10635; degree = 33), EPHX2 (P34913; degree = 31), MAOB (P27338; degree = 25), and ENPP2 (Q13822; degree = 16) directly regulated the three specific metabolites, 11,12-Epoxyeicosatrienoic acid (C14770), 5-Hydroxykynurenamine (C05638) and Nicotinic acid mononucleotide (C01185)....”
- “...HF. No. UniProt ID Protein name Gene name 1 P10635 Cytochrome P450 2D6 CYP2D6 2 P34913 Soluble epoxide hydrolase 2 EPHX2 3 P27338 Monoamine oxidase-B MAOB 4 Q13822 Ectonucleotide Pyrophosphatase/Phosphodiesterase 2 ENPP2 To continue to explore the significance of the biological mechanism of the critical target...”
- Network pharmacology combined with GEO database identifying the mechanisms and molecular targets of Polygoni Cuspidati Rhizoma on Peri-implants
Shan, Scientific reports 2022 - “...N-acetylglucosaminyltransferase subunit A FLT3 P36888 Receptor-type tyrosine-protein kinase FLT3 RORA P35398 Nuclear receptor ROR-alpha EPHX2 P34913 Bifunctional epoxide hydrolase 2 GABRA3 P34903 Gamma-aminobutyric acid receptor subunit alpha-3 CCR1 P32246 CC chemokine receptor type 1 SLC6A4 P31645 Sodium-dependent serotonin transporter WEE1 P30291 Wee1-like protein kinase CCND2 P30279...”
- Mechanism of Sanhua Decoction in the Treatment of Ischemic Stroke Based on Network Pharmacology Methods and Experimental Verification
YingHuang,, BioMed research international 2022 - “...Cytochrome P450 3A4 P08684 DLG4 Disks large homolog 4 P78352 EPHX2 Bifunctional epoxide hydrolase 2 P34913 ESR1 Estrogen receptor P03372 ESR2 Estrogen receptor beta Q92731 F3 Tissue factor P13726 FABP4 Fatty acid-binding protein P15090 FOS Proto-oncogene c-Fos P01100 GAMT Guanidinoacetate N-methyltransferase Q14353 HMGCR 3-Hydroxy-3-methylglutaryl-coenzyme A reductase...”
- Integrated omics analysis revealed the Tinospora cordifolia intervention modulated multiple signaling pathways in hypertriglyceridemia patients-a pilot clinical trial
Shirolkar, Journal of diabetes and metabolic disorders 2022 - “...A0A024RAQ1 Q9NYF0 Q9NR30 Q68D51 Q9NRB8 Q9NZN4 Q9H709 P34913 P22087 P09038 Q9C0D6 Q6ZMJ9 Q4G0E1 Q8NCI6 Q9P1P4 P42262 P30050 Q8NH61 Q15751 Q9P0W2 A0A075B6R2...”
- Exploring the mechanism of Alisma orientale for the treatment of pregnancy induced hypertension and potential hepato-nephrotoxicity by using network pharmacology, network toxicology, molecular docking and molecular dynamics simulation
Liao, Frontiers in pharmacology 2022 - “...ELANE P08246 Treat/Toxic 88 Beta-secretase 1 BACE1 P56817 Toxic 11 Bifunctional epoxide hydrolase 2 EPHX2 P34913 Treat/Toxic 89 Tyrosine-protein kinase BTK BTK Q06187 Toxic 12 Estrogen receptor ESR1 P03372 Treat/Toxic 90 Cyclin-A2 CCNA2 P20248 Toxic 13 Estrogen receptor beta ESR2 Q92731 Treat/Toxic 91 Cyclin-dependent kinase 6...”
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O31243 microsomal epoxide hydrolase (EC 3.3.2.9) from Agrobacterium tumefaciens (see paper)
31% identity, 45% coverage
4haiA / P34913 Crystal structure of human soluble epoxide hydrolase complexed with n- cycloheptyl-1-(mesitylsulfonyl)piperidine-4-carboxamide. (see paper)
24% identity, 47% coverage
- Ligands: magnesium ion; n-cycloheptyl-1-[(2,4,6-trimethylphenyl)sulfonyl]piperidine-4-carboxamide (4haiA)
Pcar_0351 putative hydrolase/acyltransferase from Pelobacter carbinolicus str. DSM 2380
32% identity, 42% coverage
- The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features
Aklujkar, BMC genomics 2012 - “...genes changes expression during growth on acetoin. Other gene products of the cluster (Pcar_0333, Pcar_0349, Pcar_0351) are predicted to act on acyl-CoA substrates (Additional file 3 : Table S2), which is surprising because there is not a single acyl-CoA dehydrogenase, enoyl-CoA hydratase, or thiolase gene in...”
- “...( S )-isomer, which 3-hydroxyacyl-CoA dehydrogenase (Pcar_0349) can oxidize. A hydrolase/acyltransferase encoded in the cluster (Pcar_0351) might split 3-oxobutanoyl-CoA into acetate plus acetyl-CoA. Metabolism of glycerol and 1,3-propanediol P . carbinolicus was initially described as unable to degrade glycerol [ 1 ], but some strains in...”
- Genome-wide gene expression patterns and growth requirements suggest that Pelobacter carbinolicus reduces Fe(III) indirectly via sulfide production
Haveman, Applied and environmental microbiology 2008 - “...acetoin, a cluster of 22 genes (Pcar_0329 to Pcar_0351) encoding proteins involved in acetoin and 2,3-butanediol oxidation, was upregulated 2.1-to 4.5 fold (see...”
FQ085_11270 alpha/beta fold hydrolase from Planococcus sp. ANT_H30
27% identity, 91% coverage
ZMO0053 alpha/beta hydrolase fold protein from Zymomonas mobilis subsp. mobilis ZM4
35% identity, 39% coverage
- The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4
Seo, Nature biotechnology 2005 - “...protein ZMO0049 hypothetical protein ZMO0050 transcriptional regulator, LysR family ZMO0051 hypothetical protein ZMO0052 cyanate permease ZMO0053 beta-ketoadipate enol-lactone hydrolase, putative ZMO0054 transcriptional regulator, MarR family ZMO0055 permeases, predicted ZMO1299 capsular polysaccharide biosynthesis protein, bcbG ZMO1300 capsular polysaccharide biosynthesis protein, bcbE ZMO1301 conserved hypothetical protein ZMO1302 lipoate-protein...”
BA1019 hydrolase, alpha/beta fold family from Bacillus anthracis str. Ames
GBAA1019 hydrolase, alpha/beta fold family from Bacillus anthracis str. 'Ames Ancestor'
24% identity, 87% coverage
AT5G21950 hydrolase, alpha/beta fold family protein from Arabidopsis thaliana
25% identity, 85% coverage
A0QTM5 3-oxoadipate enol-lactonase from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_1897 3-oxoadipate enol-lactonase from Mycobacterium smegmatis str. MC2 155
MSMEG_1897, MSMEI_1857 3-oxoadipate enol-lactonase from Mycolicibacterium smegmatis MC2 155
25% identity, 66% coverage
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...MSMEI_1436 30S ribosomal protein S5 0.075 12.333 A0R1B5 MSMEG_4692, MSMEI_4575 Uncharacterized protein MSMEG_4692/MSMEI_4575 0.082 4.500 A0QTM5 pcaD , MSMEG_1897, MSMEI_1857 3-Oxoadipate enol-lactonase (EC 3.1.1.24) 0.102 4.500 A0QU11 MSMEG_2037, MSMEI_1991 Bac_luciferase domain-containing protein 0.030 3.000 A0QS62 rplJ , MSMEG_1364, MSMEI_1325 50S ribosomal protein L10 0.078 8.500 A0QX20...”
- “...MSMEI_3758 Carboxylic ester hydrolase (EC 3.1.1.) 0.02 0.02 A0QZ33 MSMEG_3880, MSMEI_3790 Nitrilase/cyanide hydratase 0.13 0.07 A0QTM5 pcaD , MSMEG_1897, MSMEI_1857 3-Oxoadipate enol-lactonase (EC 3.1.1.24) 0.1 0.05 A0R617 pks13 , MSMEG_6392, MSMEI_6224 Polyketide synthase 0.16 0.14 A0QTE1 accA3 , MSMEG_1807, MSMEI_1762 Acetyl/propionyl-coenzyme A carboxylase alpha chain 0.13...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...protein S5 0.075 12.333 A0R1B5 MSMEG_4692, MSMEI_4575 Uncharacterized protein MSMEG_4692/MSMEI_4575 0.082 4.500 A0QTM5 pcaD , MSMEG_1897, MSMEI_1857 3-Oxoadipate enol-lactonase (EC 3.1.1.24) 0.102 4.500 A0QU11 MSMEG_2037, MSMEI_1991 Bac_luciferase domain-containing protein 0.030 3.000 A0QS62 rplJ , MSMEG_1364, MSMEI_1325 50S ribosomal protein L10 0.078 8.500 A0QX20 acnA , can...”
- “...hydrolase (EC 3.1.1.) 0.02 0.02 A0QZ33 MSMEG_3880, MSMEI_3790 Nitrilase/cyanide hydratase 0.13 0.07 A0QTM5 pcaD , MSMEG_1897, MSMEI_1857 3-Oxoadipate enol-lactonase (EC 3.1.1.24) 0.1 0.05 A0R617 pks13 , MSMEG_6392, MSMEI_6224 Polyketide synthase 0.16 0.14 A0QTE1 accA3 , MSMEG_1807, MSMEI_1762 Acetyl/propionyl-coenzyme A carboxylase alpha chain 0.13 0.17 A0QV28 glnB...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...S5 0.075 12.333 A0R1B5 MSMEG_4692, MSMEI_4575 Uncharacterized protein MSMEG_4692/MSMEI_4575 0.082 4.500 A0QTM5 pcaD , MSMEG_1897, MSMEI_1857 3-Oxoadipate enol-lactonase (EC 3.1.1.24) 0.102 4.500 A0QU11 MSMEG_2037, MSMEI_1991 Bac_luciferase domain-containing protein 0.030 3.000 A0QS62 rplJ , MSMEG_1364, MSMEI_1325 50S ribosomal protein L10 0.078 8.500 A0QX20 acnA , can ,...”
- “...(EC 3.1.1.) 0.02 0.02 A0QZ33 MSMEG_3880, MSMEI_3790 Nitrilase/cyanide hydratase 0.13 0.07 A0QTM5 pcaD , MSMEG_1897, MSMEI_1857 3-Oxoadipate enol-lactonase (EC 3.1.1.24) 0.1 0.05 A0R617 pks13 , MSMEG_6392, MSMEI_6224 Polyketide synthase 0.16 0.14 A0QTE1 accA3 , MSMEG_1807, MSMEI_1762 Acetyl/propionyl-coenzyme A carboxylase alpha chain 0.13 0.17 A0QV28 glnB ,...”
llmg_1737 non-heme chloride peroxidase from Lactococcus lactis subsp. cremoris MG1363
25% identity, 97% coverage
A9762_00985 alpha/beta fold hydrolase from Pandoraea sp. ISTKB
27% identity, 92% coverage
blr3321 blr3322 from Bradyrhizobium japonicum USDA 110
24% identity, 81% coverage
P24640 Lipase 3 from Moraxella sp. (strain TA144)
26% identity, 77% coverage
- Isolation and characterization of EstC, a new cold-active esterase from Streptomyces coelicolor A3(2)
Brault, PloS one 2012 - “...BAC70810, putative hydrolase from S. avermitilis MA-4680; YP_288574, putative hydrolase from Thermobifida fusca strain YX; P24640, lipase 3 from Moraxella sp.; ADB11055, lipase from Psychrobacter sp. G; AAK81864, lipase from Streptococcus sp. (N1). The conserved Gly-X aa -Ser-X aa -Gly pentapeptide and the proposed oxyanion hole...”
- “...members of group V, which comprises many cold-adapted lipases such as Moraxella sp. lipase 3 (P24640; 31% identity and 49% positive similarity) and Psychrobacter sp. G lipase (ADB11055; 31% identity and 51% positive similarity) [6] , [38] . These results were confirmed with a BLAST against...”
- Expression of a temperature-sensitive esterase in a novel chaperone-based Escherichia coli strain
Ferrer, Applied and environmental microbiology 2004 - “...triacylglycerol lipase from Moraxella sp. (accession no. P24640), 37% amino acid identity to triacylglycerol lipase from Moritella marina (accession no....”
Bcen_4419 alpha/beta hydrolase fold from Burkholderia cenocepacia AU 1054
30% identity, 41% coverage
XP_005210358 bifunctional epoxide hydrolase 2 isoform X1 from Bos taurus
23% identity, 53% coverage
LF41_2289 alpha/beta fold hydrolase from Lysobacter dokdonensis DS-58
25% identity, 91% coverage
- Genome sequence of Lysobacter dokdonensis DS-58(T), a gliding bacterium isolated from soil in Dokdo, Korea
Kwak, Standards in genomic sciences 2015 - “...genes unrelated to the secondary metabolite gene clusters. 1, hypothetical protein (LF41_2288); 2, non-heme chloroperoxidase (LF41_2289); 3, alkylhydroperoxidase (LF41_2290); 4, membrane protein-like protein (LF41_2291); 5, 23S rRNA (guanosine-2-O-)-methyltransferase (LF41_2292); 6, permease (LF41_2293); 7, ribonuclease T (LF41_2294); 8, hypothetical protein (LF41_2295); 9, DUF692 domain containing protein (LF41_2296);...”
BCG_2728 putative hydrolase from Mycobacterium bovis BCG str. Pasteur 1173P2
Rv2715 POSSIBLE HYDROLASE from Mycobacterium tuberculosis H37Rv
21% identity, 70% coverage
- Three enigmatic BioH isoenzymes are programmed in the early stage of mycobacterial biotin synthesis, an attractive anti-TB drug target
Xu, PLoS pathogens 2022 - “...), and BCG_0695c (64.6% identity with MSMEG_1352, bioH2 ). In contrast, the most similar one, BCG_2728 displayed only 14.9% identity with MSMEG_6710 ( bioH3 ). Thus, they also were genetically amenable to functional assays. To extend biochemical assays, a panel of engineering E . coli strains...”
- Biochemical characterisation of pimelate biosynthetic genes of Mycobacterium tuberculosis
Gugu, 2019 - Oxidative Phosphorylation as a Target Space for Tuberculosis: Success, Caution, and Future Directions
Cook, Microbiology spectrum 2017 - “...is easily identifiable as encoding a protein with similar function to MenH. Rv0045c, Rv1938 and Rv2715 are all potential candidates, although none encode a protein with a high degree of similarity to MenH from E. coli . The isoprenoid tail of the menaquinone must be generated...”
- “...( 87 ), suggesting other non-specific thioesterase activities can compensate. Similarly Rv0045c , Rv1938 and Rv2715 encode potential, but low probability, candidates for 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH) in M. tuberculosis , none of which are predicted to be essential. In this case it should be noted that...”
- Structural Analysis of Mycobacterium tuberculosis Homologues of the Eukaryotic Proteasome Assembly Chaperone 2 (PAC2)
Bai, Journal of bacteriology 2017 - “...eukaryotic system, we 75 asked if Rv2125 or Rv2715 might function as bacterial proteasome assembly 76 chaperones. We conducted biochemical and structural...”
- Systematic Survey of Serine Hydrolase Activity in Mycobacterium tuberculosis Defines Changes Associated with Persistence
Ortega, Cell chemical biology 2016 - “...hydrolase Rv1769 Rv1770 peptidase peptidase Rv1794 other c Rv2061c other Rv2204c other Rv2695 hydrolase hydrolase Rv2715 hydrolase hydrolase hydrolase Rv3311 poor prediction Rv3312c hydrolase hydrolase hydrolase Rv3401 hydrolase hydrolase hydrolase Rv3528c other Rv3591c hydrolase hydrolase Rv3722c other Rv3802c lipase cutinase hydrolase a PDB: 3P2M. b Phosphoserine...”
- Partial Saturation of Menaquinone in Mycobacterium tuberculosis: Function and Essentiality of a Novel Reductase, MenJ
Upadhyay, ACS central science 2015 - “...biosynthetic pathway enzyme M. tuberculosis gene ref chorismate MenF Rv3215 isochorismate MenD Rv0555 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate MenH Rv2715 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate MenC Rv0553 2-succinylbenzoic acid MenE Rv0166 ( 37 ) 2-succinylbenzoyl-CoA MenB Rv0548c ( 34 ) 1,4-dihydroxy-2-naphthoate-CoA MenI Rv1847 1,4-dihydroxy-2-naphthoate MenA Rv0534c ( 48 ) demethylmenaquinone MenG Rv0558 , Rv0560c...”
- Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the guinea pig
Kato-Maeda, Clinical and vaccine immunology : CVI 2012 - “...Rv0634c Rv1009 Rv1140 Rv1207 Rv1638 Rv1665 Rv2416c Rv2715 Rv3167c Rv3665c Rv3886c Rv0775 Rv0826 Rv0989c Rv1152 Rv1295 Rv1317c Rv1502 Rv1811 Rv2124c Rv2394...”
- Mechanism-based inactivation by aromatization of the transaminase BioA involved in biotin biosynthesis in Mycobaterium tuberculosis
Shi, Journal of the American Chemical Society 2011 - “...type II pathway along with BioC ( Mtb ortholog: Rv0089) and BioH ( Mtb ortholog: Rv2715) for synthesis of pimeloyl-ACP, which is proposed as the physiologically relevant substrate for BioF. 7 Amiclenomycin (ACM) isolated from Streptomyces lavendulae subsp. amiclenomycini and its simplified amino-alcohol analogue ACM-OH are...”
F6QS88 Epoxide hydrolase 2 from Bos taurus
23% identity, 47% coverage
- Differential protein repertoires related to sperm function identified in extracellular vesicles (EVs) in seminal plasma of distinct fertility buffalo (Bubalus bubalis) bulls
Badrhan, Frontiers in cell and developmental biology 2024 - “...-value = 3.66E-04). In cellular components number of proteins were associated with organelles like cytosol (F6QS88, Q2KHU0, F1N189, etc.; p -value = 6.73E-05), phosphopyruvate hydratase complex (A6QR19, Q3ZC09; p -value = 0.016945), myelin sheath abaxonal region (A6QLD1, P53712; p -value = 0.021137), neuromuscular junction (Q2KJA7, F1MC13,...”
- “...= 1.71E-07), acetyl-CoA carboxylase activity (E1BGH6, F1MSC3, Q9TTS3; p -value = 5.80E-05), magnesium ion binding (F6QS88, G1K192, F1MWJ3, etc.; p -value = 2.98E-04), integrin binding (F1MDH3, Q2KJA7, F1MC13, etc.; p -value = 0.001399). In KEGG pathway analysis, the proteins were found to be associated with Carbon...”
- Identification of 56 Proteins Involved in Embryo-Maternal Interactions in the Bovine Oviduct
Banliat, International journal of molecular sciences 2020 - “...1 4.1 CNDP2 Cytosolic non-specific dipeptidase Q3ZC84 53 T 1 17 EPHX2 Epoxide hydrolase 2 F6QS88 63 T 1 T 1 PYGL Glycogen phosphorylase. liver form Q0VCM4 97 T 1 T 1 LRBA LPS responsive beige-like anchor protein E1BND6 316 T 1 8.2 DCXR l -xylulose...”
BPSS0899 putative hydrolase from Burkholderia pseudomallei K96243
27% identity, 86% coverage
- Predicting toxins found in toxin-antitoxin systems with a role in host-induced Burkholderia pseudomallei persistence
Ross, Scientific reports 2020 - “...while toxins that were constitutively expressed were highly conserved. Further examination of highly conserved toxins BPSS0899, BPSS1321, and BPSL1494 showed that they were functional, and their mutation led to reduce survival within macrophages and reduced in vivo persistence-associated pathology (abscesses) during treatment, but did not affect...”
- “...in the next section and not previously investigated. Of the toxins BPSL0034, BPSL1494, BPSL2775, BPSL2851, BPSS0899, BPSS0698, BPSS0899, BPSS1321, and BPSS2196 that were tested, 75% of the over-expressed genes led to a reduction in growth, indicating their functionality (Supplemental Figure S2 ). Figure 1 Putative toxins...”
Atu2497 hydrolase from Agrobacterium tumefaciens str. C58 (Cereon)
23% identity, 78% coverage
8hgwA / Q2MHH5 Crystal structure of mehph in complex with mbp (see paper)
21% identity, 87% coverage
- Ligands: 1-butanol; phthalic acid (8hgwA)
sll1129 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase from Synechocystis sp. PCC 6803
25% identity, 84% coverage
- Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803
Zhang, BMC genomics 2008 - “...genes 1 slr1933( rfbC ), sll0398( dgt ), slr1224( malK ) 2 sll0336( accD ), sll1129( todF ), sll0535( clpX ) 4 Phycobilisome degradation protein NblA (ssl0452 and ssl0453), sll1869( cbaB ), Sulfate transport system (slr1452( sbpA ), slr1453( cysT ), slr1454( cysW ), slr1455( cysA...”
ABUW_2914 alpha/beta fold hydrolase from Acinetobacter baumannii
26% identity, 72% coverage
ZMO1466 alpha/beta hydrolase fold protein from Zymomonas mobilis subsp. mobilis ZM4
25% identity, 91% coverage
- Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses
Yang, PloS one 2013 - “...cytidine deaminase 2.8 1.60E-03 0.3 1.91E-07 1 ZMO0760 lactoylglutathione lyase 2.8 1.80E-03 0.0 7.08E-01 0 ZMO1466 alpha/beta family hydrolase 2.7 1.10E-05 0.4 1.48E-16 1 ZMO1583 DNA topoisomerase (ATP-hydrolyzing) 2.6 3.40E-03 0.1 1.74E-02 1 ZMO1370 nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase 2.6 4.80E-03 0.4 7.08E-11 1 ZMO1722 S-(hydroxymethyl)glutathione...”
TOL_0906 alpha/beta fold hydrolase from Thalassolituus oleivorans MIL-1
24% identity, 85% coverage
FN0752 Proline iminopeptidase from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
33% identity, 35% coverage
- Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
Hendrickson, MicrobiologyOpen 2014 - “...17 29 32 14 Covers FN0060, FN0061, FN0266, FN0278, FN0370, FN0477, FN0549, FN0583, FN0590, FN0733, FN0752, FN0775, FN0873, FN0887, FN0920, FN0928, FN1029, FN1063, FN1128, FN1145, FN1186, FN1205, FN1271, FN1277, FN1280, FN1281, FN1297, FN1322, FN1426, FN1449, FN1728, FN1804, FN1826, FN1906, FN1931, FN1950, FN1978, FN2014, FN2016, FN2100. Protein...”
MXAN_0201 hydrolase, alpha/beta fold family from Myxococcus xanthus DK 1622
23% identity, 81% coverage
- The lethal cargo of Myxococcus xanthus outer membrane vesicles
Berleman, Frontiers in microbiology 2014 - “...domain protein OMV ENRICHED 62 loci Unknown 38 loci Putative lipoproteins 43 loci Other functions MXAN_0201 Hydrolase, alpha/beta fold family MXAN_0533 NAD dependent epimerase/dehydratase family MXAN_0886 Metal dependent amidohydrolase MXAN_1389 Putative alkaline phosphatase MXAN_1394 Metallo-beta-lactamase family protein MXAN_1564 Alkyl hydroperoxide reductase C MXAN_1623 Peptidase, M16 (pitrilysin)...”
- “...in OMV than in the corresponding OM samples, i.e., lipoproteins (MXAN_6367 and MXAN_7333), a hydrolase (MXAN_0201) and a hypothetical protein (MXAN_5453). The other two, chaperonins GroEL1 (MXAN__4895) and GroEL2 (MXAN__4467) ranked as the first and third most abundant protein in OMV, albeit were present at ~50%...”
BC4904 Alpha/beta hydrolase fold protein from Bacillus cereus ATCC 14579
24% identity, 88% coverage
- BC4707 is a major facilitator superfamily multidrug resistance transport protein from Bacillus cereus implicated in fluoroquinolone tolerance
Simm, PloS one 2012 - “...described as a bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrase II protein, involved in riboflavin synthesis; and bc4904 , annotated as a hydrolase of the alpha/beta fold family. Furthermore, the cold shock protein CspD ( bc4859 ), was down regulated in the bc4707 mutant compared to the wild...”
- “...protein 1.51 bc4707 drug resistance transporter, EmrB/QacA family 0.32 bc4859 Cold shock protein CspD 0.61 bc4904 Hydrolase, alpha/beta fold family 1.96 BC4707 is not involved in the acid stress defense of B. cereus According to Mols et al. bc4707 is slightly up-regulated under sub-lethal acetic acid...”
YP_001537995 alpha/beta hydrolase fold from Salinispora arenicola CNS205
31% identity, 49% coverage
AORI_1492 alpha/beta fold hydrolase from Amycolatopsis keratiniphila
25% identity, 92% coverage
- Complete genome sequence and comparative genomic analyses of the vancomycin-producing Amycolatopsis orientalis
Xu, BMC genomics 2014 - “...family protein lcl|Y16952.3_cdsid_CAC48365.1 75.91 AORI_1490 vmt Methyltransferase lcl|AJ223998.1_cdsid_CAA11779.1 73.21 AORI_1491 hpgT 4-hydroxyphenylglycine aminotransferase lcl|AJ223998.1_cdsid_CAA11790.1 89.7 AORI_1492 vhp Hydrolase lcl|AJ223998.1_cdsid_CAA11784.1 85.87 AORI_1493 vcmD Non-ribosomal peptide synthetase lcl|AJ223998.1_cdsid_CAA11773.1 83.57 AORI_1494 oxyD Cytochrome P450 lcl|Y16952.3_cdsid_CAC48370.1 85.35 AORI_1495 hmaS 4-hydroxymandelate synthase lcl|AJ223998.1_cdsid_CAA11761.1 75.56 AORI_1496 hmo 4-hydroxymandelate oxidase lcl|Y16952.3_cdsid_CAC48372.1 85.24 AORI_1497...”
- “...is hydroxylated by OxyD (AORI_1494) and then release as Ht by the action of Vhp (AORI_1492). Genes of pdh/hpgT/hmaS/hmO (AORI_1476, AORI_1491, AORI_1495-1496) are responsible for Hpg synthesis from prephenate, and dpgA/B/C/D (AORI_1502-AORI_1505) are responsible for Dpg synthesis using malonyl-CoA as the starting unit. II) The modified...”
PA3509 probable hydrolase from Pseudomonas aeruginosa PAO1
31% identity, 39% coverage
MMAR_0983 lipase/esterase LipG2 from Mycobacterium marinum M
28% identity, 83% coverage
SAPIO_CDS6465 Alpha/beta hydrolase fold family protein from Scedosporium apiospermum
26% identity, 89% coverage
- Lower Funneling Pathways in Scedosporium Species
Poirier, Frontiers in microbiology 2021 - “...of catechol ( Martins et al., 2019 ). Interestingly, orthologs of these genes, SAPIO_CDS6464 and SAPIO_CDS6465, respectively, were identified in another scaffold (scaffold 103) of the S. apiospermum genome ( Figure 4B ), clustered with a MFS gene (SAPIO_CDS6466) and genes encoding for proteins involved in...”
ECA2972 alpha/beta fold hydrolase from Pectobacterium atrosepticum SCRI1043
22% identity, 62% coverage
A1JSF8 Pimeloyl-[acyl-carrier protein] methyl ester esterase from Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)
24% identity, 92% coverage
- Discovery and biosynthesis of bosamycins from Streptomyces sp. 120454
Xu, Chemical science 2020 - “...MbtH protein AJV88378 95/55 S. drozdowiczii bsmF 1136 P450AT No hit bsmG 272 Alpha/beta hydrolase A1JSF8 84/27 Yersinia enterocolitica bsmH 330 O -methyltransferase ABX71118 96/36 S. rishiriensis orf(+1) 247 ABC transporter KIX49568 99/98 S. griseus orf(+2) 298 ABC transporter KIX49569 99/95 S. griseus a The sequence...”
ZCP4_1673 alpha/beta fold hydrolase from Zymomonas mobilis subsp. mobilis str. CP4 = NRRL B-14023
25% identity, 91% coverage
thalar_03573 alpha/beta fold hydrolase from Litoreibacter arenae DSM 19593
26% identity, 63% coverage
SMa1727 putative hydrolase from Sinorhizobium meliloti 1021
23% identity, 89% coverage
- Directed construction and analysis of a Sinorhizobium meliloti pSymA deletion mutant library
Yurgel, Applied and environmental microbiology 2013 - “...transcriptional repressor of bet operon; and lipase, SMa1727. Osmoadaptation was not affected in the Rm1021::pRG1SMa1696pD2SMa1740 strain, which lacks SMa1726,...”
- The LuxR homolog ExpR, in combination with the Sin quorum sensing system, plays a central role in Sinorhizobium meliloti gene expression
Hoang, Journal of bacteriology 2004 - “...periplasmic signal peptide protein SMa0089 SMc02111 SMa1727 SMa1262 SMc00777 SMa0091 SMb21097 SMc00670 (hisV) SMc01843 SMb20836 SMc02087 (gltA) SMa0645...”
- Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid
Barnett, Proceedings of the National Academy of Sciences of the United States of America 2001 - “...of betaine synthesis, BetI (SMA1726), and a lipase (SMA1727; Fig. 1). The S. meliloti chromosome also encodes a betaine aldehyde dehydrogenase, as well as...”
PTO0988 carboxylesterase from Picrophilus torridus DSM 9790
32% identity, 40% coverage
- Carboxylic ester hydrolases from hyperthermophiles
Levisson, Extremophiles : life under extreme conditions 2009 - “...after 3h at 90C 27.5 Kim et al. ( 2008 ) Picrophilus torridus Esterase (EstA) PTO0988 p NP-C2 NR NR NR 70 6.5 Half-life of 21h at 90C 66 (3) Hess et al. ( 2008 ) Picrophilus torridus Esterase (EstB) PTO1141 p NP-C2 NR NR NR...”
PUV_07140 alpha/beta fold hydrolase from Parachlamydia acanthamoebae UV-7
25% identity, 90% coverage
PIP_HEYCO / P46541 Proline iminopeptidase; PIP; Prolyl aminopeptidase; PAP; EC 3.4.11.5 from Heyndrickxia coagulans (Weizmannia coagulans) (see 3 papers)
pip / GB|BAA01792.1 prolyl aminopeptidase; EC 3.4.11.5 from Bacillus coagulans (see paper)
24% identity, 89% coverage
- function: Releases the N-terminal proline from various substrates including at least dipeptides Pro-Pro, Pro-Gln, Pro-Trp and Pro-Tyr. Acts also on amides (Pro-beta NA) and oligopeptides including Pro-Leu- GlyNH2, Pro-Leu-Gly, Pro-Phe-Gly-Lys, Pro-Pro-Ala-OBut and Pro-Pro-Gly- (Pro-Pro-Gly)(4). Higher activity toward small peptides (up to three residues), but very low activity for longer peptides. Has no activity against p-nitrophenyl acetate, poly_L-proline, Met-Pro or amino acyl amides other than Pro-betaNA (Pyr-betaNA, Phe-betaNA, Cys-betaNA, Met- betaNA, Leu-betaNA, Ala-betaNA and Z-Gly-Pro-betaNA).
catalytic activity: Release of N-terminal proline from a peptide.
subunit: Monomer.
YP_761108 putative epoxide hydrolase from Hyphomonas neptunium ATCC 15444
33% identity, 38% coverage
A3JB27 haloalkane dehalogenase (EC 3.8.1.5) from Marinobacter sp. (see paper)
31% identity, 43% coverage
SERP0273 hydrolase, alpha/beta hydrolase fold family from Staphylococcus epidermidis RP62A
24% identity, 91% coverage
- Toxin Mediates Sepsis Caused by Methicillin-Resistant Staphylococcus epidermidis
Qin, PLoS pathogens 2017 - “...ATP-binding protein -3.46 -8.38 2.42 czrA SERP1755 CzrA family transcriptional regulator -3.30 -2.32 -1.42 - SERP0273 alpha/beta hydrolase -3.08 -1.73 -1.78 - SERP0507 CBS domain-containing protein -3.06 -1.48 -2.07 - SERP2091 hypothetical protein -2.94 -1.32 -2.22 - SE0735 -2.91 -1.12 -2.60 - SERP1476 hypothetical protein -2.91...”
CG5377 uncharacterized protein from Drosophila melanogaster
25% identity, 97% coverage
- The mRNA transportome of the BicD/Egl transport machinery
Vazquez-Pianzola, RNA biology 2017 - “...and pole cell enrichment Maternal (BDPG) mu2 1.59E-03 13.9 NA Anterior gradient (Kasravi etal., 1999) CG5377 2.00E-03 14.8 Ubiquitous-weak Ubiquitous, early degraded (BDPG) dap 2.28E-03 12.4 NA Ubiquitous. Pole plasm- pole cell enrichment (BDPG) CG33129 2.50E-03 11.9 Pole cell enrichment-weak Ubiquitous (BDPG), pole cell enrichment (Fly-Fish)...”
- “...CG8841 Ubiquitous-strong (oocyte and nc expression equal) ND mu2 Oocyte enrichment (Kasravi etal., 1999) ND CG5377 Ubiquitous-very weak ND dap Oocyte enrichment (de Nooij, J.C., et al., 2000) ND CG33129 Oocyte enrichment- Apical in follicle cell epithelia Oocyte enrichment- Apical in follicle cell epithelia RpS29 Ubiquitous-strong...”
BCAM0061 putative 3-oxoadipate enol-lactonase I from Burkholderia cenocepacia J2315
29% identity, 66% coverage
F6476_32380 poly(3-hydroxyalkanoate) depolymerase from Pseudomonas umsongensis
28% identity, 80% coverage
A6G7B1 haloalkane dehalogenase (EC 3.8.1.5) from Plesiocystis pacifica (see 2 papers)
32% identity, 40% coverage
ZP_01221858 putative haloalkane dehalogenase from Photobacterium profundum 3TCK
23% identity, 86% coverage
cg0358 hydrolase or acyltransferase from Corynebacterium glutamicum ATCC 13032
35% identity, 34% coverage
ZZ6_1149 alpha/beta fold hydrolase from Zymomonas mobilis subsp. mobilis ATCC 29191
33% identity, 39% coverage
STM0332 putative hydrolase or acyltransferase from Salmonella typhimurium LT2
27% identity, 48% coverage
MMAR_2866 epoxide hydrolase EphB from Mycobacterium marinum M
33% identity, 31% coverage
Cbei_3932 alpha/beta hydrolase fold from Clostridium beijerincki NCIMB 8052
27% identity, 88% coverage
MAP0345c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
30% identity, 43% coverage
Cbei_3997 alpha/beta hydrolase fold from Clostridium beijerincki NCIMB 8052
25% identity, 90% coverage
SEN0315 putative hydrolase or acyltransferase from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
27% identity, 48% coverage
PPTG_12738 hypothetical protein from Phytophthora nicotianae INRA-310
33% identity, 32% coverage
- A Global Survey of Carbohydrate Esterase Families 1 and 10 in Oomycetes
de, Frontiers in genetics 2020 - “...P. parasitica 1 PPTG_12733 XP_008908171.1 0.76 A. euteiches 1 Ae201684_9122.1 Ae201684_9122.1 NA P. parasitica 1 PPTG_12738 XP_008908179.1 6.95 A. euteiches 1 Ae201684_9125.1 Ae201684_9125.1 1.64 S. parasitica 1 KDO29501 XP_012199997.1 3.06 A. euteiches 1 Ae201684_9977.1 Ae201684_9977.1 0.46 S. parasitica 1 KDO23081 XP_012206193.1 2.12 A. euteiches 1 Ae201684_9978.1...”
AT4G36530 hydrolase, alpha/beta fold family protein from Arabidopsis thaliana
26% identity, 49% coverage
- Development of a Target Enrichment Probe Set for Conifer (REMcon)
Khan, Biology 2024 - “...768 60 MA_225872 AT5G14260 456 61 MA_224167 AT2G20790 900 62 MA_199851 AT3G01660 350 63 MA_196209 AT4G36530 273 64 MA_187402 AT4G31460 471 65 MA_173127 AT4G28740 548 66 MA_159115 AT2G27600 1191 67 MA_159115 AT4G27600 1056 68 MA_127668 AT3G15290 465 69 MA_123340 AT2G19870 1137 70 MA_121485 AT1G02410 749 71...”
- HSFA2 Functions in the Physiological Adaptation of Undifferentiated Plant Cells to Spaceflight
Zupanska, International journal of molecular sciences 2019 - “...AT1G78980 SRF5 STRUBBELIG-receptor family 5 2.4 X AT1G78080 WIND1 related to AP2 4 1.2 X AT4G36530 alpha/beta-Hydrolases superfamily protein 1.2 X CC endomembrane system GO:0012505 Golgi apparatus GO:0005794 At3g18260 Reticulon family protein 3.1 X At1g77510 PDIL1-2 PDI-like 1-2 protein disulfide isomerase-like 1-2 1.2 X At2g03760 ST1...”
- Catalytic and structural properties of pheophytinase, the phytol esterase involved in chlorophyll breakdown
Guyer, Journal of experimental botany 2018 - “..., 2016 ) were retrieved from TAIR ( http://www.arabidopsis.org/, last accessed 6 September 2017 ): At4g36530; At5g19850; At5g38520. Multiple sequence alignment of these proteins was generated and phylogenetic analysis (Supplementary Fig. S5B) performed with the neighbor-joining method using MEGA7 ( Kumar et al. , 2016 )....”
- Accumulation of high OPDA level correlates with reduced ROS and elevated GSH benefiting white cell survival in variegated leaves
Sun, Scientific reports 2017 - “...OPDA production in VMW. In addition, two DEGs (contig_4904 and_10685) to alpha/beta hydrolases (AT5G17780 and AT4G36530) known to be responsible for fatty acid accumulation 59 were also up-regulated ~3-fold ( Supplementary Table S3 ). These genes might facilitate the production and accumulation of fatty acids in...”
- Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana
Wan, Genome biology 2015 - “...AT4G39100, AT4G20860, AT3G23560, AT2G01830 [ 73 , 76 78 ] Redox process AT3G50440, AT4G34900, AT2G07785, AT4G36530, AT4G20860 [ 18 , 79 ] Differentially or specifically expressed during flowering AT3G23450, AT1G44890, AT5G44110, AT1G18370, AT1G05070, AT3G04620, AT5G62580, AT2G27380, AT2G45730, AT3G23560, [ 18 , 80 83 ] Response to...”
- “...AT2G27900, AT2G14080, AT2G01830 [ 78 , 88 ] Carbohydrate metabolism or energy release AT3G22210, AT1G22940, AT4G36530 [ 18 ] sn (o) RNA or other ncRNA AT3G57645 a Suggests the function of RNA itself, for example, rRNA, or the functions in its expressed proteins b The functions...”
- Integration of shot-gun proteomics and bioinformatics analysis to explore plant hormone responses
Zhang, BMC bioinformatics 2012 - “...-9.82 ATP-dependent Clp protease ATP-binding subunit ClpX, putative AT3G53520 -8.90 -11.20 NAD-dependent epimerase/dehydratase family protein AT4G36530 -10.08 -4.63 hydrolase, alpha/beta fold family protein AT5G22880 -26.74 -4.23 histone H2B, putative *IDs in bold are genes with opposite regulation Cluster analysis of zeatin and BR treated sample Besides...”
- Reduced expression of the genes encoding chloroplast-localized proteins in a cold-resistant bri1 (brassinosteroid-insensitive 1) mutant
Kim, Plant signaling & behavior 2010 (secret)
SMb20216 putative epoxide hydrolase protein from Sinorhizobium meliloti 1021
32% identity, 38% coverage
PP2804 hydrolase, alpha/beta fold family from Pseudomonas putida KT2440
26% identity, 89% coverage
Cbei_3238 alpha/beta hydrolase fold from Clostridium beijerincki NCIMB 8052
26% identity, 59% coverage
- Multiplex genome engineering in Clostridium beijerinckii NCIMB 8052 using CRISPR-Cas12a
Patinios, Scientific reports 2023 - “...knockout of five C. beijerinckii NCIMB 8052 genes ( spo0A , upp , Cbei_1291 , Cbei_3238 , Cbei_3832 ). Moreover, we achieved multiplex genome engineering by simultaneously knocking out the spo0A and upp genes in a single step with an efficiency of 18%. Finally, we showed...”
- “...study N/A C. beijerinckii NCIMB 8052, Cbei_1291 Cbei_1291 This study https://benchling.com/s/seq-51mieTUESpOi1YjGlySN?m=slm-LklOYAluMlSUJB9Vs7P8 C. beijerinckii NCIMB 8052, Cbei_3238 Cbei_3238 This study https://benchling.com/s/seq-J8n9JPZdYYAFZWkztce4?m=slm-Qe2GaA2L75nmhpdaXVGn C. beijerinckii NCIMB 8052, Cbei_3932 Cbei_3932 This study https://benchling.com/s/seq-N60RTFAV4KA28JkzX1Aj?m=slm-IDRoJQUoZQknBmZeZBhF spo0A C. beijerinckii NCIMB 8052 shows retarded growth, elimination of solvent production and increased production of acids...”
- Multiplex genome engineering in Clostridium beijerinckii NCIMB 8052 using CRISPR-Cas12a
Patinios, 2022
FGSG_01659 hypothetical protein from Fusarium graminearum PH-1
25% identity, 74% coverage
4nvrA / Q8ZRI7 2.22 angstrom resolution crystal structure of a putative acyltransferase from salmonella enterica
30% identity, 38% coverage
- Ligand: calcium ion (4nvrA)
AT4G02340 epoxide hydrolase, putative from Arabidopsis thaliana
30% identity, 34% coverage
- Integrated physiological, proteomic, and metabolomic analyses of pecan cultivar 'Pawnee' adaptation to salt stress
Jiao, Scientific reports 2022 - “...0.46 2 A0A2I4E5N6 AT4G17030 LOC108986524 TVNDGSVTGVSR 0.15 3 A0A2I4E7J1 AT2G21250 LOC108986997 TVAQIVLR 0.56 4 A0A2I4E8K1 AT4G02340 LOC108987294 ALAPDLR 0.24 5 A0A2I4EKZ7 AT4G27670 LOC108990523 DGVLYITIPK 4.05 6 A0A2I4EYA1 AT4G10960 LOC108993800 LAGDFGDNLSFHQVDIR 1.54 7 A0A2I4F2X6 AT3G23600 LOC108995000 QFEEVLTAR 0.14 8 A0A2I4F5P0 AT1G08550 LOC108995788 IQTPDGGFFTR 0.19 9 A0A2I4FFZ4 AT2G29500...”
- Transcriptome Responses of Wild Arachis to UV-C Exposure Reveal Genes Involved in General Plant Defense and Priming
Martins, Plants (Basel, Switzerland) 2022 - “...Aradu.KB9NK Leucine-rich repeat (LRR) receptor-like serine/threonine-protein kinase OG0000067 AT4G38620 Aradu.CT448; Aradu.18EWZ MYB-like transcription factor OG0000286 AT4G02340 Aradu.JJ61J Epoxide hydrolase OG0001961 AT5G48380 Aradu.8IX7E BAK1-interacting receptor-like kinase 1 OG0001992 AT3G62870 Aradu.32KIU; Aradu.9L616 60S ribosomal protein L7A (RPL7aB) OG0006245 AT2G44500 Aradu.YX17V O-fucosyltransferase family protein a Orthogroups code generated by...”
- Stimulation of adventitious root formation by the oligosaccharin OSRG at the transcriptome level
Larskaya, Plant signaling & behavior 2020 (secret) - Defining the plant peroxisomal proteome: from Arabidopsis to rice
Kaur, Frontiers in plant science 2011 - “...At4g00520 Acyl-CoA thioesterase family protein AKL LOC_Os04g47120* PKL Eubel et al. ( 2008 ) EH3 At4g02340 Epoxide hydrolase 3 ASL LOC_Os05g19150 AEM Eubel et al. ( 2008 ), Reumann et al. ( 2007 , 2009 ) LOC_Os01g15120 SKF LOC_Os03g61340 SRL LOC_Os10g35520 RQx 4 HL MCD At4g04320...”
- Different transcript patterns in response to specialist and generalist herbivores in the wild Arabidopsis relative Boechera divaricarpa
Vogel, PloS one 2007 - “...for proteins involved in cellular metabolism, e.g. acyl-CoA synthetase (At2g47240, fatty acid biosynthesis), epoxide hydrolase (At4g02340, aromatic compound metabolism), pullulanase (At5g04360, carbohydrate metabolism), and cystathione gamma lyase (At1g64660, amino acid metabolism). A complete list of the TAIR identifiers corresponding to B. divaricarpa best BLAST matches and...”
MAV_0357 haloalkane dehalogenase from Mycobacterium avium 104
29% identity, 43% coverage
- Metabolic pathways that permit Mycobacterium avium subsp. hominissuis to transition to different environments encountered within the host during infection
Abukhalid, Frontiers in cellular and infection microbiology 2023 - “...shared enzymes that could be associated with bacterial tolerance. Figure5 points to the overproduction of MAV_0357 haloalkane dehalogenase, MAV_0039 putative acyl-CoA dehydrogenase, MAV_4265 aldehyde dehydrogenase (NAD) family protein, MAV_4069 KatE catalase HPII and MAV_0927 conserved hypothetical protein. The upregulation of those proteins supports the involvement of...”
- “...growth condition (aerobic). The induction reaching 1.5-fold or higher in comparison to aerobic are presented. MAV_0357, haloalkane dehalogenase, MAV_0039, putative acyl-CoA dehydrogenase, MAV_4265, aldehyde dehydrogenase (NAD) family protein, MAV_4069 KatE catalase HPII, MAV_0927 conserved hypothetical protein. Thus far, our current understanding of TetR/AcrR is largely based...”
ABO_1197 carboxylic ester hydrolase from Alcanivorax borkumensis SK2
22% identity, 73% coverage
- Plastic-Degrading Enzymes from Marine Microorganisms and Their Potential Value in Recycling Technologies
Ruginescu, Marine drugs 2024 (no snippet) - Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase
Placido, Applied microbiology and biotechnology 2015 - “...coli BL21(DE3) Protein expression strain harbouring LIPESV12_26 This study E. coli NovaBlue Transformant strain harbouring ABO_1197 This study E. coli BL21(DE3) Protein expression strain harbouring ABO_1197 This study E. coli NovaBlue Transformant strain harbouring ABO_1251 This study E. coli BL21(DE3) Protein expression strain harbouring ABO_1251 This...”
- “...the conditions described in the Materials and methods , the other three, LIPESV12_24, LIPESV12_26, and ABO_1197, were significantly activated also in the hydrolysis of the long-chain ester p -NP-C16 and released approx. 128.0, 554.0, and 12.0mol p -NPpermg protein, respectively. Further, to study the substrate specificities...”
- Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata by using functional metagenomics
Alcaide, Applied and environmental microbiology 2015 - “...388 Le PLEe MGS-M1f MGS-M2f MGS-B1f MGS-K1f MGS-MT1f ABO_1197, ABO_1251, MGS0010, MGS0105, and MGS0109g R. exoculata enzymes 47.6 53.3 42.0 ND/NA 53.0 ND ND/NA...”
- “...obtained via genomic mining of marine bacteria (ABO_1197, ABO_1251, CCSP0084, CCSP0211, CCSP0528, and CCSP2178) or via metagenomic approaches of communities...”
SMa1809 Non-heme haloperoxidase from Sinorhizobium meliloti 1021
24% identity, 97% coverage
C2F9L5 prolyl aminopeptidase (EC 3.4.11.5) from Lacticaseibacillus paracasei subsp. paracasei (see paper)
23% identity, 82% coverage
BBD24_12800, SRX10_000249, VOW57_13235 proline iminopeptidase from Lacticaseibacillus paracasei
23% identity, 88% coverage
8pi1B / P22862 Bicyclic incypro pseudomonas fluorescens esterase (see paper)
24% identity, 92% coverage
- Ligand: n-[2-[3,5-bis[2-(2-iodanylethanoylamino)ethanoyl]-1,3,5-triazinan-1-yl]-2-oxidanylidene-ethyl]-2-iodanyl-ethanamide (8pi1B)
Q8PC98 prolyl aminopeptidase (EC 3.4.11.5) from Xanthomonas campestris pv. campestris (see paper)
34% identity, 36% coverage
Daci_1886 alpha/beta hydrolase fold from Delftia acidovorans SPH-1
21% identity, 98% coverage
- Interference of Quorum Sensing by Delftia sp. VM4 Depends on the Activity of a Novel N-Acylhomoserine Lactone-Acylase
Maisuria, PloS one 2015 - “...with different Ntn-hydrolases. Inspection of genome database of Delftia acidovorans SPH-1, revealed /-hydrolase fold homologue (Daci_1886) that was also similar to reported /-hydrolase type AHL acylase of Ochrobactrum sp. A44 [ 41 ] and other homologues. The similarity of hypo_Daci4366 to the carboxylic ester hydrolases implies...”
- “...Rhodococcus erythropolis SK121 (AbH-Rerythro, gi|229491600), Parvibaculum lavamentivorans DS-1 (AbH_Plavament, gi|154156608) and D . acidovorans SPH-1 (Daci_1886, gi| 5747443, indicated as abHf_Daci1886). White letters on a black background depict identical residues, and similar residues are depicted by black letters on a gray background and gaps are represented...”
WP_030191810 alpha/beta fold hydrolase from Streptomyces violaceorubidus
22% identity, 92% coverage
Q9HHP4 Vng6296c from Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
25% identity, 79% coverage
8agsAAA / A0A1U9WZ52 8agsAAA
23% identity, 73% coverage
EY04_01535 poly(3-hydroxyalkanoate) depolymerase from Pseudomonas chlororaphis
27% identity, 80% coverage
- Polymer-Degrading Enzymes of Pseudomonas chloroaphis PA23 Display Broad Substrate Preferences
Mohanan, International journal of molecular sciences 2023 - “...possible extracellular activity (EY04_21540, EY04_17885, and EY04_32435). Curiously, only one encodes an intracellular PHA depolymerase (EY04_01535). In our initial experiments with P. chlororaphis PA23 and Acinetobacter lwoffii , we found that hydrolysis of the ester bonds of pNP-alkanoate substrates and the ester bonds of PHA polymers...”
- “...and Homology Modeling Amino acid sequence similarity searches for LIP3 (EY04_02420), LIP4 (EY04_21540), and PhaZ (EY04_01535) of P. chlororaphis PA23 were carried out using Basic Local Alignment Search Tool (BLAST) for proteins ( http://blast.ncbi.nlm.nih.gov/Blast.cgi (accessed on 1 July 2021)). The sequences used were retrieved from the...”
- Characterization of Polymer Degrading Lipases, LIP1 and LIP2 From Pseudomonas chlororaphis PA23
Mohanan, Frontiers in bioengineering and biotechnology 2022 - “...and are extracellular lipases (EY04_21540, EY04_17885, EY04_32435), and one encodes for an intracellular PHA depolymerase (EY04_01535). In our previous study, the hydrolysis of the ester bonds of p-nitrophenyl-fatty acid substrates, and the ester bonds of PHA polymers of various subunit composition by the extracellular esterases/lipases was...”
- Polyhydroxyalkanoate (PHA) Polymer Accumulation and pha Gene Expression in Phenazine (phz⁻) and Pyrrolnitrin (prn⁻) Defective Mutants of Pseudomonas chlororaphis PA23
Sharma, Polymers 2018 - “...Expression of six pha genes of P. chlororaphis PA23 encoded by EY04_01515, EY04_01520, EY04_01525, EY04_01530, EY04_01535, and EY04_01540 was studied in the present investigation. Two Class II PHA synthase genes, phaC1 and phaC2 , are encoded in the P. chlororaphis PA23 genome. A PHA depolymerase gene,...”
WP_008342154 alpha/beta fold hydrolase from Bacillus sp. LK10
24% identity, 91% coverage
- Enhancement of Soluble Expression and Biochemical Characterization of Two Epoxide Hydrolases from Bacillus
Wu, Iranian journal of biotechnology 2019 - “...two EHs were assigned as BsuEH (GenBank accession no. WP_014479220) and BpuEH (GenBank accession no. WP_008342154). Based on the coding sequences of BpuEH and BsuEH , primers were designed to amplify these genes ( Table 1 ). The PCR reaction was set up in 50 L...”
- “...(EHs) from Bacillus subtilis (BsuEH, GenBank accession no. WP_014479220), B. pumilus (BpuEH, GenBank accession no. WP_008342154), B. cereus (BceEH, GenBank Accession no. KXY30655), and B. megaterium (BmeEH, GenBank Accession no. ADV36302). Solid triangles indicate putative active site residues (Asp-Asp-His); empty triangles indicate two Tyr residues involved...”
CEEH1_CAEEL / G5EBI4 Epoxide hydrolase 1; CEEH1; EC 3.3.2.10 from Caenorhabditis elegans (see paper)
28% identity, 34% coverage
- function: Catalyzes the hydrolysis of epoxide-containing fatty acids. Active against epoxyeicosatrienoic acids (EETs) including 8,9-epoxy- (5Z,11Z,14Z)-eicosatrienoate (8,9-EET), 11,12-epoxy-(5Z,8Z,14Z)- eicosatrienoate (11,12-EET) and 14,15-epoxy-(5Z,8Z,11Z)-eicosatrienoate (14,15-EET) and the linoleic acid metabolites 12,13-epoxy-(9Z)- octadecenoate (12,13-EpOME) and 9,10-epoxy-(12Z)-octadecenoate (9,10- EpOME). These epoxides function as lipid signaling molecules, the enzyme can deplete the supply of the epoxide signal by transforming them into diol species that are more readily eliminated through excretion.
catalytic activity: an epoxide + H2O = an ethanediol (RHEA:19037)
catalytic activity: 8,9-epoxy-(5Z,11Z,14Z)-eicosatrienoate + H2O = 8,9-dihydroxy- (5Z,11Z,14Z)-eicosatrienoate (RHEA:44048)
catalytic activity: 11,12-epoxy-(5Z,8Z,14Z)-eicosatrienoate + H2O = 11,12- dihydroxy-(5Z,8Z,14Z)-eicosatrienoate (RHEA:44044)
catalytic activity: 14,15-epoxy-(5Z,8Z,11Z)-eicosatrienoate + H2O = 14,15- dihydroxy-(5Z,8Z,11Z)-eicosatrienoate (RHEA:44040)
catalytic activity: 12,13-epoxy-(9Z)-octadecenoate + H2O = 12,13-dihydroxy-(9Z)- octadecenoate (RHEA:44036)
catalytic activity: 9,10-epoxy-(12Z)-octadecenoate + H2O = 9,10-dihydroxy-(12Z)- octadecenoate (RHEA:44032)
disruption phenotype: RNAi knockdown of both ceeh-1 and ceeh-2 results in the accumulation of 9,10-EpOME and 12,13-EpOME.
Q31KV5 2-hydroxy-6-oxohepta-24-dienoate hydrolase from Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)
28% identity, 52% coverage
PP_5004 poly(3-hydroxyalkanoate) depolymerase from Pseudomonas putida KT2440
Q88D24 Poly(3-hydroxyalkanoate) depolymerase from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
PP5004 poly(3-hydroxyalkanoate) depolymerase from Pseudomonas putida KT2440
26% identity, 80% coverage
- Synthetic Control of Metabolic States in Pseudomonas putida by Tuning Polyhydroxyalkanoate Cycle
Manoli, mBio 2022 - “...Standard molecular biology techniques were used as previously described ( 54 ). The phaZ gene (PP_5004) was inactivated by allelic exchange homologous recombination using the mobilizable plasmid pK18 mob sacB ( 55 ). PCR primer pairs ( TableS2 ) were designed to amplify approximately 800-bp regions...”
- Fed-Batch mcl- Polyhydroxyalkanoates Production in Pseudomonas putida KT2440 and ΔphaZ Mutant on Biodiesel-Derived Crude Glycerol
Borrero-de, Frontiers in bioengineering and biotechnology 2021 - “...depolymerization process is a result in part of the enzymatic action of PHA depolymerase (PhaZ, PP_5004) ( Arias et al., 2013 ). Different metabolic stimuli govern gene regulatory crosstalk, with the polymerization vs. depolymerization of PHA kinetics still unclear ( Karmann et al., 2017 ; Velzquez-Snchez...”
- Genome analysis of the metabolically versatile Pseudomonas umsongensis GO16: the genetic basis for PET monomer upcycling into polyhydroxyalkanoates
Narancic, Microbial biotechnology 2021 - “...gene phaC1 F6476_32385 Poly(3hydroxyalkanoate) synthase 1 100 82 PP_5003 phaZ1 F6476_32380 Poly(3hydroxyalkanoate) depolymerase 99 91 PP_5004 phaC2 F6476_32375 Poly(3hydroxyalkanoate) synthase 2 100 74 PP_5005 phaD F6476_32370 TetR family transcriptional regulator 99 77 PP_5006 GA2 F6476_32365 Granule associated protein 65 66 PP_5007 GA1 F6476_32360 Granule associated protein...”
- Metabolic engineering of Pseudomonas putida for increased polyhydroxyalkanoate production from lignin
Salvachúa, Microbial biotechnology 2020 - “...). To eliminate mcl PHA depolymerization, the gene encoding the PHA depolymerase ( phaZ ; PP_5004) was deleted, resulting in strain AG2102 (Table 2 ). To decrease 3hydroxyacylCoA flux towards fatty acid oxidation, two previously identified chromosomal copies of the enoylCoA hydratase/3hydroxyacylCoA dehydrogenase ( fadB )...”
- Pseudomonas putida KT2440 is naturally endowed to withstand industrial-scale stress conditions
Ankenbauer, Microbial biotechnology 2020 - “...Under carbon starvation, 3HAs are released from PHA granules by PHA depolymerase PhaZ (equals phaB (PP_5004)). Further activation via the ATPdependent ACS1 leads to hydroxyacylCoA, which fuels the fatty acid oxidation cycle (Ruth et al. , 2008 ). Each cycle yields one acetylCoA, reduces one FAD...”
- Transcriptome remodeling of Pseudomonas putida KT2440 during mcl-PHAs synthesis: effect of different carbon sources and response to nitrogen stress
Mozejko-Ciesielska, Journal of industrial microbiology & biotechnology 2018 - “...Change RNAseq RT RNAseq RT PP_5003 phaC1 PHA polymerase 3.28 4.19 Down 0.93 2.59 Up PP_5004 phaZ PHA depolymerase 2.57 3.99 Down 1.51 0.93 Up PP_5005 phaC2 PHA polymerase 2.76 3.21 Down 1.19 0.74 Up PP_5006 phaD Transcriptional regulator 2.41 3.14 Down 0.32 0.00 Up PP_5007...”
- Medium-chain-length polyhydroxyalkanoates synthesis by Pseudomonas putida KT2440 relA/spoT mutant: bioprocess characterization and transcriptome analysis
Mozejko-Ciesielska, AMB Express 2017 - “...RPKM 24h RPKM 41h Fold change phaC1 PP_5003 PHA polymerase 638.8 834.8 1.3 Up phaZ PP_5004 PHA depolymerase 128.6 161.2 1.3 UP phaC2 PP_5005 PHA polymerase 164.8 183.2 1.1 UP phaD PP_5006 Transcriptional regulator 216.6 197.5 1.1 Down phaF PP_5007 PHA granule-associated 6550.2 9404.0 1.4 Up...”
- Comparison of mcl-Poly(3-hydroxyalkanoates) synthesis by different Pseudomonas putida strains from crude glycerol: citrate accumulates at high titer under PHA-producing conditions
Poblete-Castro, BMC biotechnology 2014 - “...strains is not well understood. In a previous work, disruption of the PHA depolymerase gene (PP_5004, phaZ ) in P. putida KT2442 led to an increase in PHA synthesis using fatty acids as carbon source, but not when growing on glucose or gluconate [ 15 ],...”
- “...mutant strain in the best PHA-producing strain, P. putida KT2440. The chromosomal deletion of phaZ (PP_5004) in P. putida KT2440 was performed as described in Methods . The phaZ mutant strain was then subjected to PHA-production conditions in flask cultures in the same manner as described...”
- Comprehensive Proteomics Analysis of Polyhydroxyalkanoate (PHA) Biology in Pseudomonas putida KT2440: The Outer Membrane Lipoprotein OprL is a Newly Identified Phasin
Kelly, Molecular & cellular proteomics : MCP 2024 - “...fusing enhanced yellow fluorescent protein (eYFP) to the C-terminal of PhaI (Q88D20), PhaD (Q88D22), PhaZ (Q88D24), and PhaC1 (Q88D25). To confirm that the fusion proteins were correctly expressed, samples were analyzed by Western blot using an anti-eYFP antibody, with each fusion protein co-migrating with markers of...”
- Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol
Beckers, Microbial cell factories 2016 - “...PHA polymerase 0.11 0 0.25 0.15 phaC2 PP5005 PHA polymerase 0.27 0.29 0.48 0.46 phaZ PP5004 PHA depolymerase 0.30 0.18 0.87 0.39 phaD PP5006 Transcriptional regulator 0.19 0.24 0.50 0.07 phaG PP1408 Acyl-transferase 1.06 1.51 2.93 2.48 Glycerol metabolism oprB PP1019 Porin B transporter 0.76 0.37...”
- Comparison of mcl-Poly(3-hydroxyalkanoates) synthesis by different Pseudomonas putida strains from crude glycerol: citrate accumulates at high titer under PHA-producing conditions
Poblete-Castro, BMC biotechnology 2014 - “...for the construction of pEMG_PP5004. Approximately 600bp of the upstream and downstream regions of gene PP5004 were amplified using primers PP5004_UP_fw, PP5004_UP_rev, PP5004_DOWN_fw and PP5004_DOWN_rev (Table 4 ), Taq DNA polymerase (Qiagen, Venlo, The Netherlands) and genomic DNA from strain P. putida KT2440. Both PCR fragments...”
- “...TCTAGAGACATCCTGTTCTGGAAC PP5004_UP_rev CCCCTGTCAGGCCGCAGCTGGCACGTGACTCTTGGGTGAAGTAAAC PP5004_DOWN_fw CACCCAAGAGTCACGTGCCAGCTGCGGCCTGACAGGGGAAATGGATC PP5004_DOWN rev GGTACCGTTGAACAGCTCCTTGAC To generate a single mutant of gene PP5004, genome editing was applied [ 57 ]. Therefore, vector pEMG_PP5004 was co-integrated by a single crossover into the chromosome of P. putida KT2440 using tri-parental mating with E. coli HB101...”
- Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida
Borrero-de, Microbial cell factories 2014 - “...-0.3 0.2 phaC1 PP5003 PHA polymerase -0.2 0.7 phaC2 PP5005 PHA polymerase -0.6 -0.2 phaZ PP5004 PHA depolymerase 0.3 0.5 phaD PP5006 Transcriptional regulator -0.4 0.3 phaG PP1408 Acyl-transferase 1.5 -0.1 Transporters oprB-1 PP1019 Porin -0.7 -1.0 oprB-2 PP1445 Porin -0.5 -0.6 Glycolysis/gluconeogenesis glk PP1011 Glucokinase...”
- “...0.3 -0.4 phaC1 PP5003 PHA polymerase -0.8 -0.1 phaC2 PP5005 PHA polymerase -0.7 -0.4 phaZ PP5004 PHA depolymerase -0.4 0.0 phaD PP5006 Transcriptional regulator 0.2 0.1 phaG PP1408 Acyl-transferase 2.1 0.2 Transporters oprB-1 PP1019 Porin 0.4 -0.1 oprB-2 PP1445 Porin -0.4 -0.4 Glycolysis/gluconeogenesis glk PP1011 Glucokinase...”
- Development of a new strategy for production of medium-chain-length polyhydroxyalkanoates by recombinant Escherichia coli via inexpensive non-fatty acid feedstocks
Wang, Applied and environmental microbiology 2012 - “...MS medium Locus name Gene symbol PP5003 phaC1 PP5004 phaZ PP5005 phaC2 PP4552 phaJ1 PP0580 phaJ3 PP4817 phaJ4 PP1048 phaG a Putative identification...”
- The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach
Poblete-Castro, Microbial cell factories 2012 - “...3.1* 2.3 phaC1 PP5003 PHA polymerase 3.4* 1.0 phaC2 PP5005 PHA polymerase 1.2 1.1 phaZ PP5004 PHA depolymerase 2.1* 1.3 phaD PP5006 Transcriptional regulator 1.2 1.3 phaJ PP4552 Enoyl-CoA hydratase 1.5 1.6 phaG PP1408 Acyl-transferase 3.3* 2.2 * 0.1 > P -value > 0.05 Bold font...”
- Biosynthesis of storage compounds by Rhodococcus jostii RHA1 and global identification of genes involved in their metabolism
Hernández, BMC genomics 2008 - “...of the PHA depolymerases of R. ruber (encoded by ORF4, GGSQG) and P. putida KT2440 (Pp5004, GVSWG). Thus, R. jostii RHA1 is equipped with the necessary genes/proteins for the biosynthesis, accumulation and mobilization of PHA. Key genes for TAG metabolism The key enzymes for the biosynthesis...”
Rv3177 POSSIBLE PEROXIDASE (NON-HAEM PEROXIDASE) from Mycobacterium tuberculosis H37Rv
25% identity, 89% coverage
- Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis
Singh, 2023 - Aldehyde accumulation in Mycobacterium tuberculosis with defective proteasomal degradation results in copper sensitivity
Limón, mBio 2023 - “...or reductase 27.58 0 Rv3175 Possible amidase 2.31 1.11E-11 mesT Probable epoxide hydrolase 7.52 3.85E-80 Rv3177 Possible peroxidase 7.07 4.08E-86 Rv3178 Conserved hypothetical protein 5.48 1.41E-51 Rv0195-Rv0197 Rv0195 Possible two-component transcriptional regulatory protein (LuxR family) 2.46 2.17E-24 Rv0196 Possible transcriptional regulatory protein 15.86 2.99E-80 Rv0197 Possible...”
- Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis
Shee, eLife 2023 - “...), thiol buffering ( mshB, ino1, thiX, egtB, doxX ), antioxidant enzymes ( mymT, rv2633c, rv3177 ), Fe homeostasis ( mbtL, dppA ), sufR, redox-regulated chaperone ( rv0991c Becker et al., 2020 ), and respiration ( rv0247c, rv0248c, rv0249c, sdhA, sdhB, ctaC, ctaD, fixB ), were...”
- “...(The gradient of cyan to red colour indicates increasing log 2 fold change values). * rv3177 is 10.02 log 2 fold-change enriched. ( B ) The E MSH of Mtb mutants harboring transposon in the genes identified as part of Mtb redoxosome. The mutants were grown...”
- Analysis of the twenty-six largest outbreaks of tuberculosis in Aragon using whole-genome sequencing for surveillance purposes
Comín, Scientific reports 2022 - “...2004 isolate. In CLS_93, the isolate from 2019 had an extra IS copy located in Rv3177 , absent in the isolate from 2008. In CLS_71, the isolate from 2020 had two extra IS copies located in Rv1371 and phoT that were not present in the isolate...”
- Transcriptional Response of Mycobacterium tuberculosis to Cigarette Smoke Condensate
Willemse, Frontiers in microbiology 2021 - “...dehydrogenase/reductase Bacon et al., 2004 1.80 4.70E-03 MT3264 Rv3175 Possible amidase (aminohydrolase) 1.44 5.28E-03 MT3266 Rv3177 Putative peroxidase Reyes et al., 2012 2.78 4.78E-08 MT3301 * Rv3206c moeZ Molybdenum cofactor biosynthesis and cysteine biosynthesis Voss et al., 2011 1.16 2.66E-06 MT3318 MT3318 Conserved hypothetical 1.25 2.00E-10...”
- Biochemical characterisation of pimelate biosynthetic genes of Mycobacterium tuberculosis
Gugu, 2019 - Unraveling the role of the transcriptional regulator VirS in low pH-induced responses of Mycobacterium tuberculosis and identification of VirS inhibitors
Singh, The Journal of biological chemistry 2019 (secret) - Whole genome sequencing, analyses of drug resistance-conferring mutations, and correlation with transmission of Mycobacterium tuberculosis carrying katG-S315T in Hanoi, Vietnam
Hang, Scientific reports 2019 - “...No No mycP2, rpsL, Rv0012, Rv0219, Rv0893c, Rv1217c, Rv1443c, Rv1515c, Rv1516c, Rv2033c, Rv2277c, Rv2672, Rv2825c, Rv3177, Rv3618, yjcE 16 No No No No No Yes cysK1, espI, glmS, hsaA, lprQ, PE23, pks15, pks7, pmmB, rhlE, Rv0121c, Rv1073, Rv1639c, Rv2219, Rv3217c, Rv3254, Rv3660c, Rv3707c, thiL, vapB34 20...”
- More
BAS2061 hydrolase, alpha/beta fold family from Bacillus anthracis str. Sterne
AW20_594 alpha/beta fold hydrolase from Bacillus anthracis str. Sterne
23% identity, 83% coverage
- Beyond the spore, the exosporium sugar anthrose impacts vegetative Bacillus anthracis gene regulation in cis and trans
Norris, Scientific reports 2023 - “...KatE 1.22 AW20_944 BAS1718 Threonine dehydratase biosynthetic 1.21 AW20_1190 BAS1482 Uncharacterized protein YpbS 1.21 AW20_594 BAS2061 Hydrolase, alpha/beta fold family 1.20 AW20_2908 BAS5250 Uracil-DNA glycosylase, family 1 1.18 AW20_1379 BAS1297 Uncharacterized protein SAV1929 1.13 AW20_2124 BAS0590 Nitric oxide reductase activation protein NorD 1.09 AW20_2878 BAS5280 Glycosyl...”
- Identification of a protein subset of the anthrax spore immunome in humans immunized with the anthrax vaccine adsorbed preparation
Kudva, Infection and immunity 2005 - “...BA0513 941a 941b 1038 345 1272 BAS2700 BAS2061 BAS4188 BAS3788 BAS5123f BA2899 BA2217 BA4510 BA4077 BA5515f None/none; acetyltransferase, GNAT family None/none;...”
- Beyond the spore, the exosporium sugar anthrose impacts vegetative Bacillus anthracis gene regulation in cis and trans
Norris, Scientific reports 2023 - “...Catalase KatE 1.22 AW20_944 BAS1718 Threonine dehydratase biosynthetic 1.21 AW20_1190 BAS1482 Uncharacterized protein YpbS 1.21 AW20_594 BAS2061 Hydrolase, alpha/beta fold family 1.20 AW20_2908 BAS5250 Uracil-DNA glycosylase, family 1 1.18 AW20_1379 BAS1297 Uncharacterized protein SAV1929 1.13 AW20_2124 BAS0590 Nitric oxide reductase activation protein NorD 1.09 AW20_2878 BAS5280...”
BA2217 hydrolase, alpha/beta fold family from Bacillus anthracis str. Ames
23% identity, 82% coverage
Avin_02370 non-heme chloroperoxidase (abhydrolase_1 family) from Azotobacter vinelandii AvOP
24% identity, 91% coverage
Q2KTB5 triacylglycerol lipase (EC 3.1.1.3) from Psychrobacter sp. (see paper)
24% identity, 85% coverage
MT3266 hydrolase, alpha/beta hydrolase fold family from Mycobacterium tuberculosis CDC1551
25% identity, 85% coverage
- Transcriptional Response of Mycobacterium tuberculosis to Cigarette Smoke Condensate
Willemse, Frontiers in microbiology 2021 - “...Putative dehydrogenase/reductase Bacon et al., 2004 1.80 4.70E-03 MT3264 Rv3175 Possible amidase (aminohydrolase) 1.44 5.28E-03 MT3266 Rv3177 Putative peroxidase Reyes et al., 2012 2.78 4.78E-08 MT3301 * Rv3206c moeZ Molybdenum cofactor biosynthesis and cysteine biosynthesis Voss et al., 2011 1.16 2.66E-06 MT3318 MT3318 Conserved hypothetical 1.25...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 784,739 different protein sequences to 1,253,012 scientific articles. Searches against EuropePMC were last performed on November 25 2024.
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