Clusters of Characterized Proteins

Clustering the characterized proteins for leuC (citramalate isomerase large subunit) in L-isoleucine biosynthesis

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Definition of leuC

• Curated proteins matching citramalate isomerase large subunit
• Curated proteins matching 3-isopropylmalate dehydratase large subunit
• Curated proteins matching 3-isopropylmalate dehydratase%LeuC
• HMM TIGR00170
• HMM TIGR02083
• HMM TIGR02086
• Ignore hits to Q0QLE2 when looking for 'other' hits (2,3-dimethylmalate dehydratase large subunit; EC 4.2.1.85)
• Ignore hits to items matching EC 4.2.1.33 when looking for 'other' hits
• Ignore hits to items matching EC 4.2.1.35 when looking for 'other' hits
• UniProt sequence LEUC_DESVH: RecName: Full=3-isopropylmalate dehydratase large subunit {ECO:0000255|HAMAP-Rule:MF_01027}; EC=4.2.1.33 {ECO:0000255|HAMAP-Rule:MF_01027}; AltName: Full=Alpha-IPM isomerase {ECO:0000255|HAMAP-Rule:MF_01027}; Short=IPMI {ECO:0000255|HAMAP-Rule:MF_01027}; AltName: Full=Isopropylmalate isomerase {ECO:0000255|HAMAP-Rule:MF_01027};
• Ignore hits to CH_122621 when looking for 'other' hits (alpha isopropylmalate isomerase (Eurofung))
• Comment: In leucine synthesis, LeuCD allows the dehydration of 2-isopropylmalate and hydration to 3-isopropylmalate. Similarly, many of these enzymes allow the isomerization of citramalate to 3-methylmalate via citraconate. Citramalate isomerase is usually given as EC 4.2.1.35, as opposed to 4.2.1.33 for traditional leuCD. However, in initial testing, all of the bacteria with the citramalate pathway appeared to have "typical" leuBCD (Desulfovibrio vulgaris Hildenborough, Desulfovibrio vulgaris Miyazaki F, Bacteroides thetaiotaomicron, Magnetospirillum magneticum AMB-1, and Synechococcus elongatus PCC 7942). Ignore a 2,3-methylmalate dehydratase (Q0QLE2,Q0QLE1) which is >50% identical to leuCD from DvH (DVU2982,DVU2983) Ignore some BRENDA annotations without subunit information, and ignore CharProtDB::CH_122621 (leuCD fusion) which is not actually characterized DvH leuC (DVU2982) has similarity to both LeuC and to homoaconitase, and fitness data confirms its role in amino acid biosynthesis, so explicitly include it

Fetched 11 sequences

Running BLASTp

Found similarities, at above 30% identity and 75% coverage, for 10 of these sequences

Found 1 clusters of similar sequences. Another 1 sequences are not clustered. Download as table or as draft rules or view by organism

Cluster 1 418-569 amino acids (8/10 heteromeric)

P81291 Isopropylmalate/citramalate isomerase large subunit; (R)-2-methylmalate dehydratase; (R)-citramalate dehydratase; 3-isopropylmalate dehydratase; Alpha-isopropylmalate dehydratase; Citraconate hydratase; Isopropylmalate isomerase; IPMI; Maleate hydratase; Malease; EC 4.2.1.33; EC 4.2.1.35; EC 4.2.1.31
P81291 3-isopropylmalate dehydratase (EC 4.2.1.33); homoaconitate hydratase (EC 4.2.1.36)
PFams: Aconitase, Aconitase
Heteromeric, 424 amino acids: PaperBLAST, CDD, Compare to cluster

Q58409 Methanogen homoaconitase large subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114
Q58409 methanogen homoaconitase (EC 4.2.1.114)
MONOMER-2003 homoaconitase α subunit (EC 4.2.1.114; EC 4.2.1.36) (from HMM only)
CH_091727 homoaconitase; EC 4.2.1.-; EC 4.2.1.36
PFams: Aconitase
Heteromeric, 420 amino acids: PaperBLAST, CDD, Compare to cluster

Q94AR8 3-isopropylmalate dehydratase large subunit, chloroplastic; AtLEUC; Isopropylmalate isomerase large subunit 1; AtIIL1; EC 4.2.1.33
Q94AR8 2-(omega-methylthio)alkylmalate dehydratase (subunit 2/2) (EC 4.2.1.170); 3-isopropylmalate dehydratase (EC 4.2.1.33)
PFams: Aconitase
Heteromeric, 509 amino acids: PaperBLAST, CDD, Compare to cluster

LEUC-MONOMER 3-isopropylmalate dehydratase subunit LeuC (EC 4.2.1.33)
LEUC-MONOMER LeuC
CH_024771 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33
PFams: Aconitase
Heteromeric, 466 amino acids: PaperBLAST, CDD, Compare to cluster

P15717 3-isopropylmalate dehydratase large subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33
PFams: Aconitase
Heteromeric, 466 amino acids: PaperBLAST, CDD, Compare to cluster

P58946 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33
PFams: Aconitase
Heteromeric, 481 amino acids: PaperBLAST, CDD, Compare to cluster

Q7TXH6 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33
PFams: Aconitase
Heteromeric, 473 amino acids: PaperBLAST, CDD, Compare to cluster

Q9ZNE0 Homoaconitase large subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (from HMM only)
PFams: Aconitase
Heteromeric, 418 amino acids: PaperBLAST, CDD, Compare to cluster

LEUC_DESVH 3-isopropylmalate dehydratase large subunit {ECO:0000255|HAMAP-Rule:MF_01027}; EC=4.2.1.33 {ECO:0000255|HAMAP-Rule:MF_01027}; Alpha-IPM isomerase {ECO:0000255|HAMAP-Rule:MF_01027}; Short=IPMI {ECO:0000255|HAMAP-Rule:MF_01027}; AltName: Full=Isopropylmalate isomerase {ECO:0000255|HAMAP-Rule:MF_01027}
419 amino acids: PaperBLAST, CDD, Compare to cluster

MONOMER-18024 benzylmalate isomerase (from HMM only)
PFams: Aconitase_C, Aconitase
569 amino acids: PaperBLAST, CDD, Compare to cluster

Singletons (0/1 heteromeric)

S3E7P8 3-isopropylmalate dehydratase large subunit gloJ; L-homotyrosine biosynthesis sub-cluster protein gloJ; Pneumocandin biosynthesis cluster protein J; EC 4.2.1.33
PFams: Aconitase, Aconitase_C
880 amino acids: PaperBLAST, CDD