3H7F

Crystal structure of serine hydroxymethyltransferase from Mycobacterium tuberculosis

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d3h7fa1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d3h7fa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d3h7fb1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d3h7fb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	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	8075109	4000675	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLP-dependent transferases	8075110	3000954	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8075110	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)
A	PF00464	e3h7fA4	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	e3h7fA1	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)
B	PF00464	e3h7fB3	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)
B	PF00464	e3h7fB2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
B	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	Serine hydroxymethyltransferase 1	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding cation binding identical protein binding protein binding binding protein homodimerization activity protein dimerization activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding cation binding organic acid binding serine binding amino acid binding carboxylic acid binding transferase activity, transferring one-carbon groups glycine hydroxymethyltransferase activity transferase activity hydroxymethyl-, formyl- and related transferase activity catalytic activity transition metal ion binding zinc ion binding metal ion binding	symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism response to external stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction evasion of host immune response modulation by symbiont of host process response to host immune response symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism response to external stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction evasion of host immune response modulation by symbiont of host process response to host immune response response to host response to external biotic stimulus modulation of process of another organism organonitrogen compound metabolic process serine family amino acid metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process glycine metabolic process proteinogenic amino acid metabolic process organic substance metabolic process metabolic process small molecule metabolic process cellular process one-carbon metabolic process organic cyclic compound metabolic process folic acid-containing compound metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process cellular modified amino acid metabolic process dicarboxylic acid metabolic process vitamin metabolic process amide metabolic process water-soluble vitamin metabolic process folic acid metabolic process tetrahydrofolate interconversion catabolic process organic acid catabolic process L-serine catabolic process cellular catabolic process carboxylic acid catabolic process amino acid catabolic process organonitrogen compound catabolic process L-amino acid catabolic process L-serine metabolic process serine family amino acid catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process organic substance catabolic process cellular biosynthetic process organonitrogen compound biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process glycine biosynthetic process organic substance 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 cell periphery plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.