5GRO

Crystal structure of the N-terminal anticodon-binding domain of non-discriminating aspartyl-tRNA synthetase from Helicobacter pylori

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)
A	SCOP2 Family	Anticodon-binding domain	8098761	4001884	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8098762	3000135	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8098762	3000135	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)
A	PF01336	e5groA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01336	ECOD (1.6)
B	PF01336	e5groB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01336	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01336	OB-fold nucleic acid binding domain (tRNA_anti-codon)	OB-fold nucleic acid binding domain	This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an a ...	This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family [2,3]. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Aspartate--tRNA(Asp/Asn) ligase	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 catalytic activity aspartate-tRNA(Asn) ligase activity ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding 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 catalytic activity aspartate-tRNA(Asn) ligase activity ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding nucleic acid binding aspartate-tRNA ligase activity	amino acid activation tRNA aminoacylation cellular biosynthetic process organonitrogen compound biosynthetic process RNA metabolic process amino acid metabolic process cellular nitrogen compound biosynthetic process nucleobase-containing compound metabolic process organic substance metabolic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process protein metabolic process amide metabolic process amino acid activation tRNA aminoacylation cellular biosynthetic process organonitrogen compound biosynthetic process RNA metabolic process amino acid metabolic process cellular nitrogen compound biosynthetic process nucleobase-containing compound metabolic process organic substance metabolic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process protein metabolic process amide metabolic process organonitrogen compound metabolic process aspartyl-tRNA aminoacylation cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process amide biosynthetic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process peptide biosynthetic process biosynthetic process ncRNA metabolic process metabolic process cellular process macromolecule metabolic process cellular aromatic compound metabolic process peptide metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B	IPR002312	Aspartyl/Asparaginyl-tRNA synthetase, class IIb	Family
A, B	IPR047089	Aspartate-tRNA ligase, type 1, anticodon recognition domain	Domain
A, B	IPR047090	Aspartate-tRNA ligase, type 1, core domain	Domain
A, B	IPR004365	OB-fold nucleic acid binding domain, AA-tRNA synthetase-type	Domain
A, B	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, B	IPR029351	GAD domain	Domain
A, B	IPR004115	GAD-like domain superfamily	Homologous Superfamily
A, B	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B	IPR004364	Aminoacyl-tRNA synthetase, class II (D/K/N)	Domain
A, B	IPR004524	Aspartate-tRNA ligase, type 1	Family

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.