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2Q9J

Crystal structure of the C217S mutant of diaminopimelate epimerase

Functional Information from GO Data
ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0008652biological_processamino acid biosynthetic process
A0008837molecular_functiondiaminopimelate epimerase activity
A0009085biological_processlysine biosynthetic process
A0009089biological_processlysine biosynthetic process via diaminopimelate
A0016853molecular_functionisomerase activity
Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 A 440
ChainResidue
ATYR139
AILE140
AARG184
AHOH562

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 441
ChainResidue
ACYS79
AGLY8
APHE13
AASN75
AGLY76
AARG78

Functional Information from PROSITE/UniProt
site_idPS01326
Number of Residues15
DetailsDAP_EPIMERASE Diaminopimelate epimerase signature. NaDGSevsqCGNGaR
ChainResidueDetails
AASN64-ARG78

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsActive site: {"description":"Proton donor","evidences":[{"source":"PubMed","id":"16723397","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"9843410","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"journal article","publicationDate":"2000","firstPage":"6122","lastPage":"6123","volume":"122","journal":"J. Am. Chem. Soc.","title":"Identification of active site cysteine residues that function as general bases: diaminopimelate epimerase.","authors":["Koo C.W.","Sutherland A.","Vederas J.C.","Blanchard J.S."],"citationCrossReferences":[{"database":"DOI","id":"10.1021/ja001193t"}]}},{"source":"PDB","id":"1BWZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GKE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GKJ","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues1
DetailsActive site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"16723397","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"9843410","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"journal article","publicationDate":"2000","firstPage":"6122","lastPage":"6123","volume":"122","journal":"J. Am. Chem. Soc.","title":"Identification of active site cysteine residues that function as general bases: diaminopimelate epimerase.","authors":["Koo C.W.","Sutherland A.","Vederas J.C.","Blanchard J.S."],"citationCrossReferences":[{"database":"DOI","id":"10.1021/ja001193t"}]}},{"source":"PDB","id":"1BWZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GKE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GKJ","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues7
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"16723397","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2GKE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GKJ","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"16723397","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2GKJ","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues2
DetailsSite: {"description":"Could be important to modulate the pK values of the two catalytic cysteine residues","evidences":[{"source":"PubMed","id":"9843410","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1BWZ","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues1
DetailsSite: {"description":"Important for dimerization","evidences":[{"source":"UniProtKB","id":"P0A6K1","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idMCSA1
Number of Residues5
DetailsM-CSA 334
ChainResidueDetails
AGLY74hydrogen bond acceptor, proton acceptor
AGLN163activator, electrostatic stabiliser
AGLY212activator, electrostatic stabiliser
AALA221hydrogen bond donor, proton donor
AALA224electrostatic stabiliser, hydrogen bond donor

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PDB entries from 2025-10-22

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