1LS3

Crystal Structure of the Complex between Rabbit Cytosolic Serine Hydroxymethyltransferase and TriGlu-5-formyl-tetrahydrofolate

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1ls3b_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	Serine hydroxymethyltransferase	rabbit (Oryctolagus cuniculus ) [TaxId: 9986 ],	SCOPe (2.08)
C	d1ls3c_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	Serine hydroxymethyltransferase	rabbit (Oryctolagus cuniculus ) [TaxId: 9986 ],	SCOPe (2.08)
D	d1ls3d_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	Serine hydroxymethyltransferase	rabbit (Oryctolagus cuniculus ) [TaxId: 9986 ],	SCOPe (2.08)
A	d1ls3a_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	Serine hydroxymethyltransferase	rabbit (Oryctolagus cuniculus ) [TaxId: 9986 ],	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-dependent transferases	8038953	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8038953	3000954	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLP-dependent transferases	8038953	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8038953	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)
B	Aminotran_5_N	e1ls3B3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
C	Aminotran_5_N	e1ls3C3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
D	Aminotran_5_N	e1ls3D3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
A	Aminotran_5_N	e1ls3A3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
C	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)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
D	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)
A	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, C, D	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, C, D	Serine Hydroxymethyltransferase	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding organic cyclic compound binding anion binding heterocyclic compound binding organic acid binding cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding 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 translation regulator activity mRNA regulatory element binding translation repressor activity translation regulator activity, nucleic acid binding nucleic acid binding translation repressor activity identical protein binding protein binding protein homodimerization activity protein dimerization activity transferase activity, transferring one-carbon groups glycine hydroxymethyltransferase activity transferase activity hydroxymethyl-, formyl- and related transferase activity catalytic activity RNA binding mRNA 5'-UTR binding mRNA binding zinc ion binding	protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular process cellular component organization or biogenesis nucleobase biosynthetic process purine nucleobase metabolic process purine nucleobase biosynthetic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular process cellular component organization or biogenesis nucleobase biosynthetic process purine nucleobase metabolic process purine nucleobase biosynthetic process primary metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process nucleobase metabolic process small molecule metabolic process metabolic process folic acid-containing compound metabolic process tetrahydrofolate interconversion modified amino acid metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process one-carbon metabolic process catabolic process serine family amino acid metabolic process oxoacid metabolic process amino acid metabolic process organic 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 carboxylic acid metabolic process L-amino acid catabolic 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 glycine metabolic process dicarboxylic acid metabolic process vitamin metabolic process amide metabolic process water-soluble vitamin metabolic process folic acid metabolic process response to peptide response to stimulus response to chemical response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor organic acid biosynthetic process carboxylic acid biosynthetic process glycine biosynthetic process glycine biosynthetic process from serine small molecule biosynthetic process L-amino acid biosynthetic process amino acid biosynthetic process proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process cellular response to nitrogen compound cellular response to stimulus response to tetrahydrofolate cellular response to organic cyclic compound cellular response to tetrahydrofolate response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to organic cyclic compound	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR019798	Serine hydroxymethyltransferase, pyridoxal phosphate binding site	Binding Site
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	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D	IPR049943	Serine hydroxymethyltransferase-like	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, B	serine hydroxymethyltransferase M-CSA #147	serine hydroxymethyltransferase (SHMT) is a PLP-dependent protein that catalyses the reversible interconversion of serine and glycine with tetrahydrofolate serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine and many neurotransmitters.	Defined by 6 residues: ASP:A-227 [auth A-200]THR:A-253 [auth A-226]LYS:A-256 [auth A-229]ARG:A-262 [auth A-235]TYR:B-72 [auth B-55]GLU:B-74 [auth B-57] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.1.2.1 (PDB Primary Data) Search M-CSA Motif + EC 2.1.2.1

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.