4IJZ | pdb_00004ijz

Crystal structure of diaminopimelate epimerase from Escherichia coli

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4ijza1	Alpha and beta proteins (a+b)	Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	Diaminopimelate epimerase	Diaminopimelate epimerase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4ijzb1	Alpha and beta proteins (a+b)	Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	Diaminopimelate epimerase	Diaminopimelate epimerase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4ijzb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e4ijzA1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: FtsJ	F:	ECOD (20:10:01)
B		e4ijzB1	A: Alpha-beta plaits	X: Family B DNA polymerase insertion domain	H: Family B DNA polymerase insertion domain	T: Oxidored_q6	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)
B	3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01678	Diaminopimelate epimerase (DAP_epimerase)	Diaminopimelate epimerase	Diaminopimelate epimerase contains two domains of the same alpha/beta fold, both contained in this family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Diaminopimelate epimerase	isomerase activity racemase and epimerase activity diaminopimelate epimerase activity racemase and epimerase activity, acting on amino acids and derivatives amino-acid racemase activity catalytic activity enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding protein binding binding protein homodimerization activity isomerase activity racemase and epimerase activity diaminopimelate epimerase activity racemase and epimerase activity, acting on amino acids and derivatives amino-acid racemase activity catalytic activity enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	lysine metabolic process oxoacid metabolic process L-lysine biosynthetic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process L-lysine biosynthetic process via diaminopimelate small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process lysine metabolic process oxoacid metabolic process L-lysine biosynthetic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process L-lysine biosynthetic process via diaminopimelate small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001653	Diaminopimelate epimerase, DapF	Family
A, B	IPR018510	Diaminopimelate epimerase, active site	Active Site

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.