1VFS | pdb_00001vfs

Crystal structure of D-cycloserine-bound form of alanine racemase from D-cycloserine-producing Streptomyces lavendulae

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	d1vfsb1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Alanine racemase-like, C-terminal domain	Alanine racemase	(Streptomyces lavendulae ) [TaxId: 1914 ],	SCOPe (2.08)
B	d1vfsb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Alanine racemase	(Streptomyces lavendulae ) [TaxId: 1914 ],	SCOPe (2.08)
B	d1vfsb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces lavendulae ) [TaxId: 1914 ],	SCOPe (2.08)
A	d1vfsa1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Alanine racemase-like, C-terminal domain	Alanine racemase	(Streptomyces lavendulae ) [TaxId: 1914 ],	SCOPe (2.08)
A	d1vfsa2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Alanine racemase	(Streptomyces lavendulae ) [TaxId: 1914 ],	SCOPe (2.08)
A	d1vfsa3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces lavendulae ) [TaxId: 1914 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	PLP-binding barrel	8041338	3000273	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8041335	3001044	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8041335	3001044	SCOP2B (2022-06-29)
A	SCOP2 Family	Alanine racemase	8028956	4003518	SCOP2 (2022-06-29)
A	SCOP2 Family	Alanine racemase-like, N-terminal domain	8028959	4003111	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Alanine racemase C-terminal domain-like	8041335	3001044	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLP-binding barrel	8041338	3000273	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e1vfsB1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Trypsin	F:	ECOD (20:10:01)
B		e1vfsB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)
A		e1vfsA1	A: cradle loop barrel	X: RIFT-related	H: Alanine racemase-C	T: Ala_racemase_C	F:	ECOD (20:10:01)
A		e1vfsA2	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: Ala_racemase_N	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
B	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
A	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
A	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	alanine racemase	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding isomerase activity racemase and epimerase activity alanine racemase activity racemase and epimerase activity, acting on amino acids and derivatives amino-acid racemase activity catalytic activity	carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process cellular process metabolic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis macromolecule metabolic process cell wall macromolecule metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process D-alanine metabolic process carboxylic acid biosynthetic process non-proteinogenic amino acid metabolic process D-amino acid metabolic process small molecule metabolic process alanine biosynthetic process non-proteinogenic amino acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process amino acid biosynthetic process D-amino acid biosynthetic process D-alanine biosynthetic process alanine metabolic 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	IPR029066	PLP-binding barrel	Homologous Superfamily
A, B	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal	Homologous Superfamily
A, B	IPR020622	Alanine racemase, pyridoxal-phosphate attachment site	Binding Site
A, B	IPR011079	Alanine racemase, C-terminal	Domain
A, B	IPR001608	Alanine racemase, N-terminal	Domain
A, B	IPR000821	Alanine racemase	Family

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.