3A8I | pdb_00003a8i

Crystal Structure of ET-EHred-5-CH3-THF complex

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)
F	d3a8if_	All beta proteins	Barrel-sandwich hybrid	Single hybrid motif	Biotinyl/lipoyl-carrier proteins and domains	Protein H of glycine cleavage system	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d3a8ie_	All beta proteins	Barrel-sandwich hybrid	Single hybrid motif	Biotinyl/lipoyl-carrier proteins and domains	Protein H of glycine cleavage system	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d3a8id2	All beta proteins	Elongation factor/aminomethyltransferase common domain	Aminomethyltransferase beta-barrel domain	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d3a8id1	Alpha and beta proteins (a+b)	Folate-binding domain	Folate-binding domain	Aminomethyltransferase folate-binding domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3a8ic2	All beta proteins	Elongation factor/aminomethyltransferase common domain	Aminomethyltransferase beta-barrel domain	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3a8ic1	Alpha and beta proteins (a+b)	Folate-binding domain	Folate-binding domain	Aminomethyltransferase folate-binding domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3a8ib2	All beta proteins	Elongation factor/aminomethyltransferase common domain	Aminomethyltransferase beta-barrel domain	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3a8ib1	Alpha and beta proteins (a+b)	Folate-binding domain	Folate-binding domain	Aminomethyltransferase folate-binding domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3a8ia2	All beta proteins	Elongation factor/aminomethyltransferase common domain	Aminomethyltransferase beta-barrel domain	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3a8ia1	Alpha and beta proteins (a+b)	Folate-binding domain	Folate-binding domain	Aminomethyltransferase folate-binding domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Single hybrid motif	8077749	3001880	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Single hybrid motif	8077749	3001880	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Aminomethyltransferase beta-barrel domain-like	8056085	3000024	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Folate-binding domain-like	8056084	3000025	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Folate-binding domain-like	8056084	3000025	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aminomethyltransferase beta-barrel domain-like	8056085	3000024	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Folate-binding domain-like	8056084	3000025	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aminomethyltransferase beta-barrel domain-like	8056085	3000024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Aminomethyltransferase beta-barrel domain-like	8056085	3000024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Folate-binding domain-like	8056084	3000025	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)
F	GCV_H	e3a8iF1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: GCV_H	ECOD (1.6)
E	GCV_H	e3a8iE1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: GCV_H	ECOD (1.6)
D	GCV_T_C	e3a8iD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GCV_T_C	ECOD (1.6)
D	GCV_T_N	e3a8iD3	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: GCV_T_N	ECOD (1.6)
D	GCV_T_N1	e3a8iD2	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: GCV_T_N1	ECOD (1.6)
C	GCV_T_C	e3a8iC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GCV_T_C	ECOD (1.6)
C	GCV_T_N	e3a8iC3	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: GCV_T_N	ECOD (1.6)
C	GCV_T_N1	e3a8iC2	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: GCV_T_N1	ECOD (1.6)
B	GCV_T_C	e3a8iB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GCV_T_C	ECOD (1.6)
B	GCV_T_N	e3a8iB3	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: GCV_T_N	ECOD (1.6)
B	GCV_T_N1	e3a8iB2	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: GCV_T_N1	ECOD (1.6)
A	GCV_T_C	e3a8iA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GCV_T_C	ECOD (1.6)
A	GCV_T_N	e3a8iA3	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: GCV_T_N	ECOD (1.6)
A	GCV_T_N1	e3a8iA2	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: GCV_T_N1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
E	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
D	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
D	3.30.70.1400	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Aminomethyltransferase beta-barrel domains	CATH (4.3.0)
D	4.10.1250.10	Few Secondary Structures	Irregular	Aminomethyltransferase fragment	Aminomethyltransferase fragment	CATH (4.3.0)
D	2.40.30.110	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
C	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
C	3.30.70.1400	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Aminomethyltransferase beta-barrel domains	CATH (4.3.0)
C	4.10.1250.10	Few Secondary Structures	Irregular	Aminomethyltransferase fragment	Aminomethyltransferase fragment	CATH (4.3.0)
C	2.40.30.110	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
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	4.10.1250.10	Few Secondary Structures	Irregular	Aminomethyltransferase fragment	Aminomethyltransferase fragment	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	4.10.1250.10	Few Secondary Structures	Irregular	Aminomethyltransferase fragment	Aminomethyltransferase fragment	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
E, F	PF01597	Glycine cleavage H-protein (GCV_H)	Glycine cleavage H-protein	This is a family of glycine cleavage H-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. A lipoyl group is attached to a comp ...	This is a family of glycine cleavage H-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. A lipoyl group is attached to a completely conserved lysine residue. The H protein shuttles the methylamine group of glycine from the P protein to the T protein.	Domain
A, B, C, D	PF01571	GCVT N-terminal domain (GCV_T)	GCVT N-terminal domain	This entry represents the N-terminal domain in glycine cleavage T-proteins (GCVT) which are part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCVT proteins are involved in various biochemical ...	This entry represents the N-terminal domain in glycine cleavage T-proteins (GCVT) which are part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCVT proteins are involved in various biochemical processes, mainly on the degradation and transformation of small molecules. A significant function of these proteins is their role in the glycine cleavage system, which is responsible for the degradation of glycine. This system is composed of four proteins: P, T, L, and H. These proteins also participate in the demethylation of compounds such as N,N-dimethylglycine and sarcosine, converting them into simpler molecules like sarcosine and glycine, respectively. Additionally, they are involved in the catabolism of compounds like syringate and vanillate, contributing to the breakdown and assimilation of these molecules. GCVT proteins also include proteins that regulate enzymatic activity, such as the pyruvate dehydrogenase phosphatase regulatory subunit, which modulates sensitivity to magnesium ions [1-2].	Domain
A, B, C, D	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
E, F	Glycine cleavage system H protein	-	small molecule metabolic process metabolic process cellular process one-carbon metabolic process glycine decarboxylation via glycine cleavage system catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process small molecule metabolic process metabolic process cellular process one-carbon metabolic process glycine decarboxylation via glycine cleavage system catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process glycine catabolic process carboxylic acid catabolic process small molecule catabolic process amino acid catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex oxidoreductase complex transferase complex glycine cleavage complex
A, B, C, D	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	small molecule metabolic process metabolic process cellular process one-carbon metabolic process glycine decarboxylation via glycine cleavage system catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process small molecule metabolic process metabolic process cellular process one-carbon metabolic process glycine decarboxylation via glycine cleavage system catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process glycine catabolic process carboxylic acid catabolic process small molecule catabolic process amino acid catabolic process	protein-containing complex catalytic complex oxidoreductase complex transferase complex glycine cleavage complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F	IPR017453	Glycine cleavage system H-protein, subgroup	Family
E, F	IPR002930	Glycine cleavage system H-protein	Family
E, F	IPR033753	Glycine cleavage system H-protein/Simiate	Family
E, F	IPR011053	Single hybrid motif	Homologous Superfamily
E, F	IPR003016	2-oxo acid dehydrogenase, lipoyl-binding site	Binding Site
E, F	IPR000089	Biotin/lipoyl attachment	Domain
A, B, C, D	IPR013977	Aminomethyltransferase, C-terminal domain	Domain
A, B, C, D	IPR028896	Aminomethyltransferase-like	Family
A, B, C, D	IPR027266	Aminomethyltransferase superfamily	Homologous Superfamily
A, B, C, D	IPR022903	Glycine cleavage system T protein, bacteria	Family
A, B, C, D	IPR006223	Glycine cleavage system T protein	Family
A, B, C, D	IPR006222	GCVT, N-terminal domain	Domain
A, B, C, D	IPR029043	Glycine cleavage T-protein/YgfZ, C-terminal	Homologous Superfamily

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.