1ASY

CLASS II AMINOACYL TRANSFER RNA SYNTHETASES: CRYSTAL STRUCTURE OF YEAST ASPARTYL-TRNA SYNTHETASE COMPLEXED WITH TRNA ASP

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth A]	d1asya1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Anticodon-binding domain	Aspartyl-tRNA synthetase (AspRS)	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C [auth A]	d1asya2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Aspartyl-tRNA synthetase (AspRS)	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D [auth B]	d1asyb1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Anticodon-binding domain	Aspartyl-tRNA synthetase (AspRS)	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D [auth B]	d1asyb2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Aspartyl-tRNA synthetase (AspRS)	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035952	3000058	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Nucleic acid-binding proteins	8041908	3000135	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Nucleic acid-binding proteins	8041908	3000135	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035952	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)
C [auth A]	tRNA_anti-codon	e1asyA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: tRNA_anti-codon	ECOD (1.6)
C [auth A]	tRNA-synt_2	e1asyA2	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2	ECOD (1.6)
D [auth B]	tRNA_anti-codon	e1asyB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: tRNA_anti-codon	ECOD (1.6)
D [auth B]	tRNA-synt_2	e1asyB2	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C [auth A]	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
D [auth B]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
D [auth B]	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF00152	tRNA synthetases class II (D, K and N) (tRNA-synt_2)	tRNA synthetases class II (D, K and N)	-	Domain
C [auth A], D [auth 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 [auth R], B [auth S]	T-RNA (75-MER)	-	-	-
C [auth A], D [auth B]	ASPARTYL-tRNA SYNTHETASE	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 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 RNA binding nucleic acid 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 aspartate-tRNA ligase activity catalytic activity ligase activity	amino acid activation tRNA aminoacylation cellular biosynthetic process organonitrogen compound biosynthetic process RNA metabolic process amino acid metabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process protein metabolic process organonitrogen compound metabolic process aspartyl-tRNA aminoacylation cellular metabolic process primary metabolic process amino acid activation tRNA aminoacylation cellular biosynthetic process organonitrogen compound biosynthetic process RNA metabolic process amino acid metabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process protein metabolic process organonitrogen compound metabolic process aspartyl-tRNA aminoacylation cellular metabolic process primary metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process biosynthetic process ncRNA metabolic process metabolic process cellular process macromolecule metabolic process	protein-containing complex catalytic complex aminoacyl-tRNA synthetase multienzyme complex intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
C [auth A], D [auth B]	IPR002312	Aspartyl/Asparaginyl-tRNA synthetase, class IIb	Family
C [auth A], D [auth B]	IPR004523	Aspartate-tRNA synthetase, type 2	Family
C [auth A], D [auth B]	IPR004365	OB-fold nucleic acid binding domain, AA-tRNA synthetase-type	Domain
C [auth A], D [auth B]	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
C [auth A], D [auth B]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
C [auth A], D [auth B]	IPR004364	Aminoacyl-tRNA synthetase, class II (D/K/N)	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
C [auth A]	aspartate---tRNA ligase M-CSA #404	Catalyzes the attachment of aspartmate to tRNA(Asp) in a two-step reaction: aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). Is specific for tRNA(Asp) since it aspartylates tRNA(Asn) 3 orders of magnitude less efficiently than tRNA(Asp). Aspartyl tRNA synthetase is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module.	Defined by 7 residues: ARG:C-258 [auth A-325]GLU:C-260 [auth A-327]ARG:C-266 [auth A-333]HIS:C-267 [auth A-334]GLU:C-411 [auth A-478]SER:C-414 [auth A-481]ARG:C-464 [auth A-531] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif

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.