3OD1 | pdb_00003od1

The crystal structure of an ATP phosphoribosyltransferase regulatory subunit/histidyl-tRNA synthetase from Bacillus halodurans C

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	8100561	4001782	SCOP2 (2022-06-29)
B	SCOP2 Family	Anticodon-binding domain of Class II aaRS	8101135	4000507	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Class II aaRS and biotin synthetases	8100562	3000058	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Class II aaRS ABD-related	8101136	3000465	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS ABD-related	8101136	3000465	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8100562	3000058	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	RA	e3od1B1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: RA	ECOD (v294.1)
B	FlaF_Ig-like	e3od1B2	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: FlaF_Ig-like	ECOD (v294.1)
A	SBP_bac_5	e3od1A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_5	ECOD (v294.1)
A	Homoserine_dh	e3od1A1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: Homoserine_dh	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	3.40.50.12590	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
A	3.40.50.12590	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13393	Histidyl-tRNA synthetase (tRNA-synt_His)	Histidyl-tRNA synthetase	This is a family of class II aminoacyl-tRNA synthetase-like and ATP phosphoribosyltransferase regulatory subunits.	Domain
A, B	PF21996	Histidyl-tRNA synthetase HisZ, C-terminal domain (HisZ-like)	Histidyl-tRNA synthetase HisZ, C-terminal domain	HisZ is composed of two domains for the catalytic reaction and for anticodon binding. In contrast to other class-II aminoacyl-tRNA synthetases it lacks the essential editing domain. The C-terminal anicodon binding domain consists of three-stranded pa ...	HisZ is composed of two domains for the catalytic reaction and for anticodon binding. In contrast to other class-II aminoacyl-tRNA synthetases it lacks the essential editing domain. The C-terminal anicodon binding domain consists of three-stranded parallel beta-sheet flanked on each side with helices.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	ATP phosphoribosyltransferase regulatory subunit	ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA histidine-tRNA ligase activity catalytic activity ligase activity catalytic activity, acting on a protein transferase activity	amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process histidyl-tRNA aminoacylation oxoacid metabolic process organic acid biosynthetic process organic acid metabolic process imidazole-containing compound metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process L-histidine biosynthetic process proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004517	ATP phosphoribosyltransferase regulatory subunit	Family
A, B	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, B	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B	IPR041715	Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain	Domain
A, B	IPR004516	Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit	Family
A, B	IPR053846	Histidyl-tRNA synthetase HisZ, C-terminal domain, Bacillales	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.