Clusters of Characterized Proteins

Clustering the characterized proteins for dapE (succinyl-diaminopimelate desuccinylase) in L-lysine biosynthesis

Or see other characterized proteins similar to dapE

Or see all steps for L-lysine biosynthesis

Or cluster curated proteins matching a keyword

Definition of dapE

• Curated proteins or TIGRFams with EC 3.5.1.18
• Predicted: UniProt sequence L0FXC2: SubName: Full=Amidohydrolase {ECO:0000313|EMBL:AGA77693.1};
• Comment: DapE is missing in several genera of Bacteroidota, and a search for conserved essential genes identified the putative aminohydrolase Echvi_1427 (L0FXC2)as a candidate. This protein is 43% identical to the dipeptidase DradM20D (PMID:26456402) and 42% identical to an carboxypeptidase/aminoacylase from Pyrococcus horikoshii (PMC92634); it also has more distant homology to N-acetyl-L,L-diaminopimelate deactylase; these are all very similar reactions. Echvi_1427 has conserved active site residues and docking N-succinyl-L,L-diaminopimelate to its predicted structure with AutoDock Vina gave predicted binding (-6.5 kcal/mol) with the amide bond near the catalytic arginine (R264).

Fetched 10 sequences

Running BLASTp

Found similarities, at above 30% identity and 75% coverage, for 9 of these sequences

Found 2 clusters of similar sequences. Another 1 sequences are not clustered. Download as table or as draft rules or view by organism

Cluster 1 375-383 amino acids (not heteromeric)

DAPE_HELPY / O25002 Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 from Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
O25002 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Helicobacter pylori
PFams: Peptidase_M20, M20_dimer
383 amino acids: PaperBLAST, CDD, Compare to cluster

P44514 N-succinyl-L,L-diaminopimelate desuccinylase subunit (EC 3.5.1.18) from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
DAPE_HAEIN / P44514 Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
P44514 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Haemophilus influenzae
PFams: Peptidase_M20, M20_dimer
377 amino acids: PaperBLAST, CDD, Compare to cluster

DAPE_VIBCH / Q9KQ52 Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Q9KQ52 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Vibrio cholerae
PFams: Peptidase_M20, M20_dimer
377 amino acids: PaperBLAST, CDD, Compare to cluster

b2472 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Escherichia coli K-12 substr. MG1655
P0AED7 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Escherichia coli (strain K12)
DAPE_ECOLI / P0AED7 Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 from Escherichia coli (strain K12)
RF|NP_416967 succinyl-diaminopimelate desuccinylase; EC 3.5.1.18 from Escherichia coli K12
PFams: Peptidase_M20, M20_dimer
375 amino acids: PaperBLAST, CDD, Compare to cluster

DAPE_SALTY / Q8ZN75 Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; Aspartyl peptidase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
PFams: Peptidase_M20, M20_dimer
375 amino acids: PaperBLAST, CDD, Compare to cluster

DAPE_NEIMB / Q9JYL2 Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 from Neisseria meningitidis serogroup B (strain MC58)
Q9JYL2 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Neisseria meningitidis
PFams: Peptidase_M20, M20_dimer
381 amino acids: PaperBLAST, CDD, Compare to cluster

Cluster 2 354-369 amino acids (not heteromeric)

P9WHS9 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Mycobacterium tuberculosis
PFams: Peptidase_M28, Peptidase_M20, M20_dimer
354 amino acids: PaperBLAST, CDD, Compare to cluster

Q59284 succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) from Corynebacterium glutamicum
PFams: Peptidase_M28, Peptidase_M20, M20_dimer
369 amino acids: PaperBLAST, CDD, Compare to cluster

DAPE_MYCS2 / A0R2G4 Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis)
PFams: Peptidase_M20, M20_dimer
355 amino acids: PaperBLAST, CDD, Compare to cluster

Singletons (0/1 heteromeric)

L0FXC2 Amidohydrolase
397 amino acids: PaperBLAST, CDD