2D54 | pdb_00002d54

Crystal Structure of Methionyl tRNA Synthetase Y225A Mutant from Thermus Thermophilus

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)
A	d2d54a1	All alpha proteins	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	automated matches	automated matches	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d2d54a2	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	automated matches	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	8039576	3001786	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotidylyl transferase	8039578	3001541	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		e2d54A1	A: P-loop domains-like	X: P-loop domains-related	H: P-loop containing nucleoside triphosphate hydrolases	T: DPRP	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	2.170.220.10	Mainly Beta	Beta Complex	Methionyl-trna Synthetase	domain 2	CATH (4.3.0)
A	1.10.730.10	Mainly Alpha	Orthogonal Bundle	Isoleucyl-tRNA Synthetase	Domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF09334	tRNA synthetases class I (M) (tRNA-synt_1g)	tRNA synthetases class I (M)	-	Family
A	PF19303	Anticodon binding domain of methionyl tRNA ligase (Anticodon_3)	Anticodon binding domain of methionyl tRNA ligase	This domain is found in methionyl tRNA ligase. The domain binds to the anticodon of the tRNA ligase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Methionyl-tRNA synthetase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity methionine-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity RNA binding tRNA binding nucleic acid binding cation binding metal ion binding	amino acid activation tRNA aminoacylation methionyl-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 methionyl-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	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023457	Methionine-tRNA synthetase, type 2	Family
A	IPR041872	Methionyl-tRNA synthetase, anticodon-binding domain	Domain
A	IPR002547	tRNA-binding domain	Domain
A	IPR015413	Methionyl/Leucyl tRNA synthetase	Domain
A	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A	IPR004495	Methionyl-tRNA synthetase, beta subunit, C-terminal	Domain
A	IPR014758	Methionyl-tRNA synthetase	Family
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR009080	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Homologous Superfamily
A	IPR033911	Methioninyl-tRNA synthetase core domain	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.