3AL0 | pdb_00003al0

Crystal structure of the glutamine transamidosome from Thermotoga maritima in the glutamylation state.

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	SCOP2B Superfamily	Amidase signature (AS) enzymes	8041897	3001251	SCOP2B (2022-06-29)
C	SCOP2 Family	GatC-like	8082964	4001576	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	GatC-like	8082965	3001870	SCOP2 (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	Thi4, NAD_binding_8	e3al0A1	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: Ankyrin repeat	T: Ankyrin repeat	F: Thi4, NAD_binding_8	ECOD (v294.1)
B	zf-CXXC	e3al0B1	A: a/b three-layered sandwiches	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F: zf-CXXC	ECOD (v294.1)
C	GatC	e3al0C2	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: Glu-tRNAGln amidotransferase C subunit	T: Glu-tRNAGln amidotransferase C subunit	F: GatC	ECOD (v294.1)
C	PKD_4	e3al0C3	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: Ankyrin repeat	T: Ankyrin repeat	F: PKD_4	ECOD (v294.1)
C	Glyco_hydro_32C	e3al0C4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: Glyco_hydro_32C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.1300.10	Alpha Beta	Alpha-Beta Complex	Amidase signature (AS) enzymes	Amidase signature (AS) domain	CATH (4.3.0)
B	1.10.10.410	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		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)
C	1.10.8.70	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	1.10.10.350	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01425	Amidase (Amidase)	Amidase	This entry represents the amidase signature domain that consists structurally of a core domain that is covered by alpha-helices. In most members, this is found as a standalone domain, while in others, such as Scytalone dehydratase-like protein Arp1, ...	This entry represents the amidase signature domain that consists structurally of a core domain that is covered by alpha-helices. In most members, this is found as a standalone domain, while in others, such as Scytalone dehydratase-like protein Arp1, it is found in association with other domains.	Domain
B	PF02637	GatB domain (GatB_Yqey)	GatB domain	This domain is found in GatB. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB Swiss:O30509 which transamidates Glu-tRNA to Gln-tRNA.	Domain
B	PF02934	GatB/GatE catalytic domain (GatB_N)	GatB/GatE catalytic domain	This domain is found in the GatB and GatE proteins [1].	Domain
C	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
C	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
C	PF02686	Glu-tRNAGln amidotransferase C subunit (GatC)	Glu-tRNAGln amidotransferase C subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Glutamyl-tRNA(Gln) amidotransferase subunit A	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 carbon-nitrogen ligase activity, with glutamine as amido-N-donor catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex catalytic complex glutamyl-tRNA(Gln) amidotransferase complex intracellular protein-containing complex
B	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B	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 carbon-nitrogen ligase activity, with glutamine as amido-N-donor catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity asparaginyl-tRNA synthase (glutamine-hydrolyzing) activity	amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process glutaminyl-tRNAGln biosynthesis via transamidation nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process metabolic process cellular process macromolecule metabolic process biosynthetic process protein metabolic process amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process glutaminyl-tRNAGln biosynthesis via transamidation nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process metabolic process cellular process macromolecule metabolic process biosynthetic process protein metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	-
C	Glutamyl-tRNA(Gln) amidotransferase subunit C,Linker,Glutamate--tRNA ligase 2	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 carbon-nitrogen ligase activity, with glutamine as amido-N-donor catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity asparaginyl-tRNA synthase (glutamine-hydrolyzing) activity glutamate-tRNA ligase activity ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity cation binding transition metal ion binding zinc ion binding metal ion binding RNA binding tRNA binding nucleic acid binding	biological regulation regulation of biological quality regulation of translational fidelity amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process glutaminyl-tRNAGln biosynthesis via transamidation nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process metabolic process cellular process biological regulation regulation of biological quality regulation of translational fidelity amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process glutaminyl-tRNAGln biosynthesis via transamidation nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process metabolic process cellular process macromolecule metabolic process biosynthetic process protein metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process tRNA aminoacylation for protein translation glutamyl-tRNA aminoacylation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
D [auth E]	tRNAGln	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036928	Amidase signature (AS) superfamily	Homologous Superfamily
A	IPR004412	Glutamyl-tRNA(Gln) amidotransferase A subunit	Family
A	IPR000120	Amidase	Family
A	IPR023631	Amidase signature domain	Domain
A	IPR020556	Amidase, conserved site	Conserved Site
B	IPR006075	Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic	Domain
B	IPR042114	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1	Homologous Superfamily
B	IPR003789	Aspartyl/glutamyl-tRNA amidotransferase subunit B-like	Homologous Superfamily
B	IPR017959	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E	Family
B	IPR023168	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2	Homologous Superfamily
B	IPR018027	Asn/Gln amidotransferase	Domain
B	IPR017958	Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site	Conserved Site
B	IPR004413	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B	Family
B	IPR014746	Glutamine synthetase/guanido kinase, catalytic domain	Homologous Superfamily
C	IPR003837	Glu-tRNAGln amidotransferase C subunit	Family
C	IPR036113	Glu-tRNAGln amidotransferase superfamily, subunit C	Homologous Superfamily
C	IPR020751	Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2	Homologous Superfamily
C	IPR000924	Glutamyl/glutaminyl-tRNA synthetase	Family
C	IPR033910	Glutamyl-tRNA synthetase	Domain
C	IPR020061	Glutamine-tRNA ligase, alpha-bundle domain superfamily	Homologous Superfamily
C	IPR020058	Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain	Domain
C	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
C	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
C	IPR045462	Aminoacyl-tRNA synthetase, class I, anticodon-binding	Domain
C	IPR049940	Glutamyl-Q tRNA(Asp) synthetase/Glutamate--tRNA ligase	Family
C	IPR004527	Glutamate-tRNA ligase, bacterial/mitochondrial	Family
C	IPR020752	Glutamate-tRNA synthetase, class I, anticodon-binding domain, subdomain 1	Homologous Superfamily
C	IPR008925	Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily	Homologous Superfamily