3TZU | pdb_00003tzu

Crystal structure of a glycine cleavage system H protein (GCVH) from Mycobacterium marinum

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)
D	d3tzud_	All beta proteins	Barrel-sandwich hybrid	Single hybrid motif	automated matches	automated matches	(Mycobacterium marinum M ) [TaxId: 216594 ],	SCOPe (2.08)
C	d3tzuc_	All beta proteins	Barrel-sandwich hybrid	Single hybrid motif	automated matches	automated matches	(Mycobacterium marinum M ) [TaxId: 216594 ],	SCOPe (2.08)
B	d3tzub_	All beta proteins	Barrel-sandwich hybrid	Single hybrid motif	automated matches	automated matches	(Mycobacterium marinum M ) [TaxId: 216594 ],	SCOPe (2.08)
A	d3tzua_	All beta proteins	Barrel-sandwich hybrid	Single hybrid motif	automated matches	automated matches	(Mycobacterium marinum M ) [TaxId: 216594 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Single hybrid motif	8077761	3001880	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Single hybrid motif	8077761	3001880	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Single hybrid motif	8077761	3001880	SCOP2B (2022-06-29)
A	SCOP2 Family	Biotinyl/lipoyl-carrier proteins and domains	8077760	4002909	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Single hybrid motif	8077761	3001880	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)
D	PNP_UDP_1	e3tzuD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: PNP_UDP_1	ECOD (v294.1)
C	PNP_UDP_1	e3tzuC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: PNP_UDP_1	ECOD (v294.1)
B	PNP_UDP_1	e3tzuB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: PNP_UDP_1	ECOD (v294.1)
A	ATP-synt_F	e3tzuA1	A: a/b three-layered sandwiches	X: Cystatin-like	H: Cystatin/monellin	T: Cystatin/monellin	F: ATP-synt_F	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Glycine cleavage system H protein 1	-	peptidyl-lysine modification primary metabolic process gene expression protein lipoylation macromolecule biosynthetic process protein maturation biosynthetic process macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process peptidyl-lysine modification primary metabolic process gene expression protein lipoylation macromolecule biosynthetic process protein maturation biosynthetic process macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process glycine decarboxylation via glycine cleavage system catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid 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 metabolic 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR017453	Glycine cleavage system H-protein, subgroup	Family
A, B, C, D	IPR002930	Glycine cleavage system H-protein	Family
A, B, C, D	IPR033753	Glycine cleavage system H-protein/Simiate	Family
A, B, C, D	IPR011053	Single hybrid motif	Homologous Superfamily
A, B, C, D	IPR003016	2-oxo acid dehydrogenase, lipoyl-binding site	Binding Site
A, B, C, D	IPR000089	Biotin/lipoyl attachment	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.