5H4V | pdb_00005h4v

Structure of glutamyl-tRNA synthetase (Xoo1504) from Xanthomonas oryzae pv. oryzae

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	d5h4vb2	All alpha proteins	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
B	d5h4vb1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
C	d5h4vc2	All alpha proteins	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
C	d5h4vc1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
D	d5h4vd2	All alpha proteins	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
D	d5h4vd1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
E	d5h4ve2	All alpha proteins	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
E	d5h4ve1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
F	d5h4vf2	All alpha proteins	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
F	d5h4vf1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
A	d5h4va2	All alpha proteins	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
A	d5h4va1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	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	Terminase_6N	e5h4vB2	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (v294.1)
B	BNR_6, Sortilin-Vps10	e5h4vB3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: BNR_6, Sortilin-Vps10	ECOD (v294.1)
C	Terminase_6N	e5h4vC1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (v294.1)
C	BNR_6, Sortilin-Vps10	e5h4vC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: BNR_6, Sortilin-Vps10	ECOD (v294.1)
D	Terminase_6N	e5h4vD2	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (v294.1)
D	BNR_6, Sortilin-Vps10	e5h4vD3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: BNR_6, Sortilin-Vps10	ECOD (v294.1)
E	Terminase_6N	e5h4vE1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (v294.1)
E	BNR_6, Sortilin-Vps10	e5h4vE2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: BNR_6, Sortilin-Vps10	ECOD (v294.1)
F	Terminase_6N	e5h4vF1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (v294.1)
F	BNR_6, Sortilin-Vps10	e5h4vF2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: BNR_6, Sortilin-Vps10	ECOD (v294.1)
A	Terminase_6N	e5h4vA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (v294.1)
A	BNR_6, Sortilin-Vps10	e5h4vA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: BNR_6, Sortilin-Vps10	ECOD (v294.1)

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	3.90.800.10	Alpha Beta	Alpha-Beta Complex	Glutamyl-tRNA Synthetase	domain 3	CATH (4.3.0)
B	1.10.1160.10	Mainly Alpha	Orthogonal Bundle	Glutamyl-tRNA Synthetase	domain 2	CATH (4.3.0)
C	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
C	3.90.800.10	Alpha Beta	Alpha-Beta Complex	Glutamyl-tRNA Synthetase	domain 3	CATH (4.3.0)
C	1.10.1160.10	Mainly Alpha	Orthogonal Bundle	Glutamyl-tRNA Synthetase	domain 2	CATH (4.3.0)
D	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
D	3.90.800.10	Alpha Beta	Alpha-Beta Complex	Glutamyl-tRNA Synthetase	domain 3	CATH (4.3.0)
D	1.10.1160.10	Mainly Alpha	Orthogonal Bundle	Glutamyl-tRNA Synthetase	domain 2	CATH (4.3.0)
E	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
E	3.90.800.10	Alpha Beta	Alpha-Beta Complex	Glutamyl-tRNA Synthetase	domain 3	CATH (4.3.0)
E	1.10.1160.10	Mainly Alpha	Orthogonal Bundle	Glutamyl-tRNA Synthetase	domain 2	CATH (4.3.0)
F	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
F	3.90.800.10	Alpha Beta	Alpha-Beta Complex	Glutamyl-tRNA Synthetase	domain 3	CATH (4.3.0)
F	1.10.1160.10	Mainly Alpha	Orthogonal Bundle	Glutamyl-tRNA Synthetase	domain 2	CATH (4.3.0)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	3.90.800.10	Alpha Beta	Alpha-Beta Complex	Glutamyl-tRNA Synthetase	domain 3	CATH (4.3.0)
A	1.10.1160.10	Mainly Alpha	Orthogonal Bundle	Glutamyl-tRNA Synthetase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF19269	Anticodon binding domain (Anticodon_2)	Anticodon binding domain	This entry represents the anticodon binding domain found at the C-terminus of the class-I glutamyl tRNA synthetase enzyme.	Domain
A, B, C, D, E A, B, C, D, E, F	PF00749	tRNA synthetases class I (E and Q), catalytic domain (tRNA-synt_1c)	tRNA synthetases class I (E and Q), catalytic domain	Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Glutamate--tRNA ligase	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 glutamate-tRNA ligase activity 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 ligase activity cation binding transition metal ion binding zinc ion binding metal ion binding RNA binding tRNA binding nucleic acid binding	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 glutamyl-tRNA aminoacylation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR020751	Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000924	Glutamyl/glutaminyl-tRNA synthetase	Family
A, B, C, D, E A, B, C, D, E, F	IPR033910	Glutamyl-tRNA synthetase	Domain
A, B, C, D, E A, B, C, D, E, F	IPR020058	Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR045462	Aminoacyl-tRNA synthetase, class I, anticodon-binding	Domain
A, B, C, D, E A, B, C, D, E, F	IPR049940	Glutamyl-Q tRNA(Asp) synthetase/Glutamate--tRNA ligase	Family
A, B, C, D, E A, B, C, D, E, F	IPR004527	Glutamate-tRNA ligase, bacterial/mitochondrial	Family
A, B, C, D, E A, B, C, D, E, F	IPR008925	Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily	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.