4DLP | pdb_00004dlp

Crystal structure of methionyl-tRNA synthetase MetRS from Brucella melitensis bound to selenomethionine

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B	d4dlpb2	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	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
B	d4dlpb1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
C	d4dlpc2	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	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
C	d4dlpc1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
A	d4dlpa2	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	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
A	d4dlpa1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Hydrolase_3, HAD	e4dlpB1	A: alpha bundles	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: Hydrolase_3, HAD	ECOD (develop294)
C	Hydrolase_3, HAD	e4dlpC1	A: alpha bundles	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: Hydrolase_3, HAD	ECOD (develop294)
A	Hydrolase_3, HAD	e4dlpA1	A: alpha bundles	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: Hydrolase_3, HAD	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	2.170.220.10	Mainly Beta	Beta Complex	Methionyl-trna Synthetase	domain 2	CATH (4.3.0)
B	1.10.730.10	Mainly Alpha	Orthogonal Bundle	Isoleucyl-tRNA Synthetase	Domain 1	CATH (4.3.0)
C	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
C	2.170.220.10	Mainly Beta	Beta Complex	Methionyl-trna Synthetase	domain 2	CATH (4.3.0)
C	1.10.730.10	Mainly Alpha	Orthogonal Bundle	Isoleucyl-tRNA Synthetase	Domain 1	CATH (4.3.0)
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, B, C	PF09334	tRNA synthetases class I (M) (tRNA-synt_1g)	tRNA synthetases class I (M)	-	Family
A, B, C	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, B, C	Aminoacyl-tRNA synthetase, class I:Aminoacyl-tRNA synthetase, class Ia:Methionyl-tRNA synthetase, class Ia	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 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 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 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	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, B, C	IPR014758	Methionyl-tRNA synthetase	Family
A, B, C	IPR023457	Methionine-tRNA synthetase, type 2	Family
A, B, C	IPR041872	Methionyl-tRNA synthetase, anticodon-binding domain	Domain
A, B, C	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
A, B, C	IPR009080	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Homologous Superfamily
A, B, C	IPR033911	Methioninyl-tRNA synthetase core domain	Domain
A, B, C	IPR015413	Methionyl/Leucyl tRNA synthetase	Domain
A, B, C	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily

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.