6YME

Crystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the PLP-internal aldimine state

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6ymea1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	(Aphanothece halophytica ) [TaxId: 72020 ],	SCOPe (2.08)
A	d6ymea2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aphanothece halophytica ) [TaxId: 72020 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	GABA-aminotransferase-like	8094934	4000675	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLP-dependent transferases	8094935	3000954	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)
A	PF00464	e6ymeA2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: PF00464	ECOD (1.6)
A	PF00464	e6ymeA1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: PF00464	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00464	Serine hydroxymethyltransferase (SHMT)	Serine hydroxymethyltransferase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Serine hydroxymethyltransferase	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding organic cyclic compound binding anion binding heterocyclic compound binding organic acid binding serine binding amino acid binding carboxylic acid binding glycine hydroxymethyltransferase activity hydroxymethyl-, formyl- and related transferase activity zinc ion binding	organonitrogen compound metabolic process oxoacid metabolic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process organic acid metabolic process vitamin metabolic process cellular modified amino acid metabolic process folic acid-containing compound metabolic process small molecule metabolic process metabolic process cellular process amide metabolic process water-soluble vitamin metabolic process organonitrogen compound metabolic process oxoacid metabolic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process organic acid metabolic process vitamin metabolic process cellular modified amino acid metabolic process folic acid-containing compound metabolic process small molecule metabolic process metabolic process cellular process amide metabolic process water-soluble vitamin metabolic process pteridine-containing compound metabolic process folic acid metabolic process methylation tetrahydrofolate interconversion tetrahydrofolate metabolic process one-carbon metabolic process catabolic process serine family amino acid metabolic process amino acid metabolic process organic acid catabolic process L-serine catabolic process alpha-amino acid metabolic process cellular catabolic process carboxylic acid catabolic process amino acid catabolic process organonitrogen compound catabolic process L-amino acid catabolic process primary metabolic process L-serine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process serine family amino acid catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process cellular biosynthetic process organonitrogen compound biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process glycine metabolic process glycine biosynthetic process glycine biosynthetic process from serine small molecule biosynthetic process L-amino acid biosynthetic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A	IPR039429	Serine hydroxymethyltransferase-like domain	Domain
A	IPR001085	Serine hydroxymethyltransferase	Family
A	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A	IPR049943	Serine hydroxymethyltransferase-like	Family
A	IPR019798	Serine hydroxymethyltransferase, pyridoxal phosphate binding site	Binding Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

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 R01GM133198.