4OT8 | pdb_00004ot8

X-ray Crystal Structure of Serine Hydroxymethyl Transferase from Burkholderia cenocepacia bound to PLP and Serine

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)
D	d4ot8d_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	(Burkholderia cenocepacia J2315 ) [TaxId: 216591 ],	SCOPe (2.08)
C	d4ot8c1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	(Burkholderia cenocepacia J2315 ) [TaxId: 216591 ],	SCOPe (2.08)
C	d4ot8c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Burkholderia cenocepacia J2315 ) [TaxId: 216591 ],	SCOPe (2.08)
B	d4ot8b_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	(Burkholderia cenocepacia J2315 ) [TaxId: 216591 ],	SCOPe (2.08)
A	d4ot8a_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	(Burkholderia cenocepacia J2315 ) [TaxId: 216591 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	PLP-dependent transferases	8075100	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8075100	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8075100	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8075100	3000954	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	PRMT_C	e4ot8D1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: PRMT_C	ECOD (v294.1)
C	PRMT_C	e4ot8C1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: PRMT_C	ECOD (v294.1)
C	Phosphodiest, Metalloenzyme	e4ot8C2	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.1)
B	PRMT_C	e4ot8B1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: PRMT_C	ECOD (v294.1)
B	Phosphodiest, Metalloenzyme	e4ot8B2	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.1)
A	PRMT_C	e4ot8A1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: PRMT_C	ECOD (v294.1)
A	Phosphodiest, Metalloenzyme	e4ot8A2	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Serine hydroxymethyltransferase	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding transferase activity, transferring one-carbon groups glycine hydroxymethyltransferase activity transferase activity hydroxymethyl-, formyl- and related transferase activity catalytic activity	folic acid-containing compound metabolic process tetrahydrofolate interconversion modified amino acid metabolic process metabolic process cellular process small molecule metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process one-carbon metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process glycine biosynthetic process from L-serine folic acid-containing compound metabolic process tetrahydrofolate interconversion modified amino acid metabolic process metabolic process cellular process small molecule metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process one-carbon metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process glycine biosynthetic process from L-serine alpha-amino acid metabolic process carboxylic acid biosynthetic process glycine metabolic process glycine biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-serine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic 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, C, D	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, C, D	IPR039429	Serine hydroxymethyltransferase-like domain	Domain
A, B, C, D	IPR001085	Serine hydroxymethyltransferase	Family
A, B, C, D	IPR049943	Serine hydroxymethyltransferase-like	Family
A, B, C, D	IPR019798	Serine hydroxymethyltransferase, pyridoxal phosphate binding site	Binding 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.