2Q9J

Crystal structure of the C217S mutant of diaminopimelate epimerase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0008652	biological_process	amino acid biosynthetic process
A	0008837	molecular_function	diaminopimelate epimerase activity
A	0009085	biological_process	lysine biosynthetic process
A	0009089	biological_process	lysine biosynthetic process via diaminopimelate
A	0016853	molecular_function	isomerase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 440

Chain	Residue
A	TYR139
A	ILE140
A	ARG184
A	HOH562

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 441

Chain	Residue
A	CYS79
A	GLY8
A	PHE13
A	ASN75
A	GLY76
A	ARG78

---

Functional Information from PROSITE/UniProt

site_id	PS01326
Number of Residues	15
Details	DAP_EPIMERASE Diaminopimelate epimerase signature. NaDGSevsqCGNGaR

Chain	Residue	Details
A	ASN64-ARG78

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	Active 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"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	1
Details	Active 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"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16723397","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2GKE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GKJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16723397","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2GKJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	Site: {"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"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	Site: {"description":"Important for dimerization","evidences":[{"source":"UniProtKB","id":"P0A6K1","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	5
Details	M-CSA 334

Chain	Residue	Details
A	GLY74	hydrogen bond acceptor, proton acceptor
A	GLN163	activator, electrostatic stabiliser
A	GLY212	activator, electrostatic stabiliser
A	ALA221	hydrogen bond donor, proton donor
A	ALA224	electrostatic stabiliser, hydrogen bond donor

---