1V5V

Crystal Structure of a Component of Glycine Cleavage System: T-protein from Pyrococcus horikoshii OT3 at 1.5 A Resolution

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1v5vb1	All beta proteins	Elongation factor/aminomethyltransferase common domain	Aminomethyltransferase beta-barrel domain	Aminomethyltransferase beta-barrel domain	Glycine cleavage system T protein, GcvT	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B	d1v5vb2	Alpha and beta proteins (a+b)	Folate-binding domain	Folate-binding domain	Aminomethyltransferase folate-binding domain	Glycine cleavage system T protein, GcvT	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
A	d1v5va1	All beta proteins	Elongation factor/aminomethyltransferase common domain	Aminomethyltransferase beta-barrel domain	Aminomethyltransferase beta-barrel domain	Glycine cleavage system T protein, GcvT	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
A	d1v5va2	Alpha and beta proteins (a+b)	Folate-binding domain	Folate-binding domain	Aminomethyltransferase folate-binding domain	Glycine cleavage system T protein, GcvT	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Aminomethyltransferase beta-barrel domain-like	8056078	3000024	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Folate-binding domain-like	8017553	3000025	SCOP2B (2022-06-29)
A	SCOP2 Family	GcvT aminomethyltransferase-like	8002408	4000062	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aminomethyltransferase beta-barrel domain-like	8056078	3000024	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Folate-binding domain-like	8017553	3000025	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	PF08669	e1v5vB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: PF08669	ECOD (1.6)
B	PF01571	e1v5vB2	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: PF01571	ECOD (1.6)
A	PF08669	e1v5vA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: PF08669	ECOD (1.6)
A	PF01571	e1v5vA4	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: PF01571	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
B	3.30.70.1400	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Aminomethyltransferase beta-barrel domains	CATH (4.3.0)
B	2.40.30.110	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
A	3.30.70.1400	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Aminomethyltransferase beta-barrel domains	CATH (4.3.0)
A	2.40.30.110	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01571	Aminomethyltransferase folate-binding domain (GCV_T)	Aminomethyltransferase folate-binding domain	This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl tran ...	This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase.	Domain
A, B	PF08669	Glycine cleavage T-protein C-terminal barrel domain (GCV_T_C)	Glycine cleavage T-protein C-terminal barrel domain	This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl tran ...	This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	aminomethyltransferase	transferase activity, transferring nitrogenous groups transaminase activity transferase activity catalytic activity transferase activity, transferring one-carbon groups aminomethyltransferase activity hydroxymethyl-, formyl- and related transferase activity	catabolic process serine family amino acid metabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process cellular catabolic process organic substance metabolic process glycine catabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process catabolic process serine family amino acid metabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process cellular catabolic process organic substance metabolic process glycine catabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process glycine decarboxylation via glycine cleavage system organonitrogen compound catabolic process organonitrogen compound metabolic process cellular metabolic process L-amino acid catabolic process carboxylic acid metabolic process primary metabolic process L-amino acid metabolic process serine family amino acid catabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process small molecule catabolic process organic substance catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR013977	Glycine cleavage T-protein, C-terminal barrel domain	Domain
A, B	IPR028896	Aminomethyltransferase-like	Family
A, B	IPR022903	Glycine cleavage system T protein, bacteria	Family
A, B	IPR029043	Glycine cleavage T-protein/YgfZ, C-terminal	Homologous Superfamily
A, B	IPR006223	Glycine cleavage system T protein	Family
A, B	IPR006222	Aminomethyltransferase, folate-binding domain	Domain
A, B	IPR027266	GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1	Homologous Superfamily

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.