2D6F | pdb_00002d6f

Crystal structure of Glu-tRNA(Gln) amidotransferase in the complex with tRNA(Gln)

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)
D [auth B]	d2d6fb1	All beta proteins	Sm-like fold	GatD N-terminal domain-like	automated matches	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
D [auth B]	d2d6fb2	Alpha and beta proteins (a/b)	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Glutaminase/Asparaginase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
C [auth A]	d2d6fa1	All beta proteins	Sm-like fold	GatD N-terminal domain-like	GatD N-terminal domain-like	Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
C [auth A]	d2d6fa2	Alpha and beta proteins (a/b)	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
F [auth D]	d2d6fd1	All alpha proteins	GatB/YqeY motif	GatB/YqeY motif	GatB/GatE C-terminal domain-like	Glutamyl-tRNA(Gln) amidotransferase subunit E, GatE, C-terminal domain	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
F [auth D]	d2d6fd2	Alpha and beta proteins (a+b)	DCoH-like	GAD domain-like	GAD domain	Glutamyl-tRNA(gln) amidotransferase subunit E, GatE, insert domain	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
F [auth D]	d2d6fd3	Alpha and beta proteins (a+b)	Glutamine synthetase/guanido kinase	Glutamine synthetase/guanido kinase	GatB/GatE catalytic domain-like	Glutamyl-tRNA(Gln) amidotransferase subunit E, GatE	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
E [auth C]	d2d6fc1	All alpha proteins	GatB/YqeY motif	GatB/YqeY motif	GatB/GatE C-terminal domain-like	Glutamyl-tRNA(Gln) amidotransferase subunit E, GatE, C-terminal domain	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
E [auth C]	d2d6fc2	Alpha and beta proteins (a+b)	DCoH-like	GAD domain-like	GAD domain	Glutamyl-tRNA(gln) amidotransferase subunit E, GatE, insert domain	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
E [auth C]	d2d6fc3	Alpha and beta proteins (a+b)	Glutamine synthetase/guanido kinase	Glutamine synthetase/guanido kinase	GatB/GatE catalytic domain-like	Glutamyl-tRNA(Gln) amidotransferase subunit E, GatE	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth B]	SCOP2B Superfamily	GatD N-terminal domain-like	8039596	3000389	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Glutaminase/Asparaginase	8039600	3001625	SCOP2B (2022-06-29)
C [auth A]	SCOP2 Family	GatD N-terminal domain-like	8027217	4001791	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Family	Glutaminase/Asparaginase	8027221	4000833	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	GatD N-terminal domain-like	8039596	3000389	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	Glutaminase/Asparaginase	8039600	3001625	SCOP2 (2022-06-29)
F [auth D]	SCOP2B Superfamily	GAD domain-like	8039605	3000108	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	GatB/YqeY motif	8039602	3001497	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Glutamine synthetase/guanido kinase	8039606	3000676	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Glutamine synthetase/guanido kinase	8039606	3000676	SCOP2B (2022-06-29)
E [auth C]	SCOP2 Family	GatB/GatE C-terminal domain-like	8027223	4001495	SCOP2 (2022-06-29)
E [auth C]	SCOP2 Family	GAD domain	8027226	4001480	SCOP2 (2022-06-29)
E [auth C]	SCOP2 Family	GatB/GatE catalytic domain-like	8027227	4003972	SCOP2 (2022-06-29)
E [auth C]	SCOP2 Superfamily	GatB/YqeY motif	8039602	3001497	SCOP2 (2022-06-29)
E [auth C]	SCOP2 Superfamily	GAD domain-like	8039605	3000108	SCOP2 (2022-06-29)
E [auth C]	SCOP2 Superfamily	Glutamine synthetase/guanido kinase	8039606	3000676	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)
D [auth B]	Glyco_hydro_32C	e2d6fB3	A: alpha bundles	X: POZ domain	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Glyco_hydro_32C	ECOD (develop294)
C [auth A]	Glyco_hydro_32C	e2d6fA3	A: alpha bundles	X: POZ domain	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Glyco_hydro_32C	ECOD (develop294)
F [auth D]	tRNA_int_endo_N	e2d6fD2	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: tRNA_int_endo_N	ECOD (develop294)
F [auth D]	Ribosomal_L24e	e2d6fD4	A: alpha bundles	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: Ribosomal_L24e	ECOD (develop294)
E [auth C]	tRNA_int_endo_N	e2d6fC2	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: tRNA_int_endo_N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	2.30.30.520	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
D [auth B]	3.40.50.1170	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	L-asparaginase, N-terminal domain	CATH (4.3.0)
D [auth B]	3.40.50.40	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C [auth A]	2.30.30.520	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C [auth A]	3.40.50.1170	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	L-asparaginase, N-terminal domain	CATH (4.3.0)
C [auth A]	3.40.50.40	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
F [auth D]	3.30.1360.30	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
E [auth C]	3.30.1360.30	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
E [auth C]	1.10.150.380	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF00710	Asparaginase, N-terminal (Asparaginase)	Asparaginase, N-terminal	This is the N-terminal domain of this enzyme.	Domain
C [auth A], D [auth B]	PF18195	GatD N-terminal domain (GatD_N)	GatD N-terminal domain	This is the N-terminal domain of GatD protein present in Pyrococcus abyssi. Two GatD and two GatE associate to form a tetramer complex. The tetramer complex is able to mature Glutamic acid-tRNA Glutamine into Glutamine-tRNA Glutamine, a necessary ste ...	This is the N-terminal domain of GatD protein present in Pyrococcus abyssi. Two GatD and two GatE associate to form a tetramer complex. The tetramer complex is able to mature Glutamic acid-tRNA Glutamine into Glutamine-tRNA Glutamine, a necessary step in the translation of proteins. The N-terminal domain is involved in anchoring GatD to GatE in order to form the tetramer [1].	Domain
C [auth A], D [auth B]	PF17763	Glutaminase/Asparaginase C-terminal domain (Asparaginase_C)	Glutaminase/Asparaginase C-terminal domain	This domain is found at the C-terminus of asparaginase enzymes.	Domain
E [auth C], F [auth D]	PF02934	GatB/GatE catalytic domain (GatB_N)	GatB/GatE catalytic domain	This domain is found in the GatB and GatE proteins [1].	Domain
E [auth C], F [auth D]	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
E [auth C], F [auth D]	PF02938	GAD domain (GAD)	GAD domain	This domain is found in some members of the GatB and aspartyl tRNA synthetases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], B [auth F]	tRNA	-	-	-
C [auth A], D [auth B]	Glutamyl-tRNA(Gln) amidotransferase subunit D	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 asparaginase activity amidase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	biological regulation regulation of biological quality regulation of translational fidelity amino acid metabolic process primary metabolic process metabolic process cellular process biosynthetic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	-
E [auth C], F [auth D]	Glutamyl-tRNA(Gln) amidotransferase subunit E	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 ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase 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	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR027473	L-asparaginase, C-terminal	Homologous Superfamily
C [auth A], D [auth B]	IPR027475	Asparaginase/glutaminase, active site 2	Active Site
C [auth A], D [auth B]	IPR006033	Type I L-asparaginase family	Family
C [auth A], D [auth B]	IPR036152	Asparaginase/glutaminase-like superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR020827	Asparaginase/glutaminase, active site 1	Active Site
C [auth A], D [auth B]	IPR037152	L-asparaginase, N-terminal domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR040919	Asparaginase/glutaminase, C-terminal	Domain
C [auth A], D [auth B]	IPR027474	L-asparaginase, N-terminal	Domain
C [auth A], D [auth B]	IPR011878	Glutamyl-tRNA(Gln) amidotransferase subunit D	Family
C [auth A], D [auth B]	IPR037222	GatD, N-terminal superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR006034	Asparaginase/glutaminase-like	Family
C [auth A], D [auth B]	IPR040918	GatD, N-terminal	Domain
E [auth C], F [auth D]	IPR006075	Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic	Domain
E [auth C], F [auth D]	IPR042114	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1	Homologous Superfamily
E [auth C], F [auth D]	IPR003789	Aspartyl/glutamyl-tRNA amidotransferase subunit B-like	Homologous Superfamily
E [auth C], F [auth D]	IPR017959	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E	Family
E [auth C], F [auth D]	IPR023168	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2	Homologous Superfamily
E [auth C], F [auth D]	IPR029351	GAD domain	Domain
E [auth C], F [auth D]	IPR018027	Asn/Gln amidotransferase	Domain
E [auth C], F [auth D]	IPR004115	GAD-like domain superfamily	Homologous Superfamily
E [auth C], F [auth D]	IPR004414	Glutamyl-tRNA(Gln) amidotransferase subunit E	Family
E [auth C], F [auth D]	IPR017958	Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site	Conserved Site
E [auth C], F [auth D]	IPR014746	Glutamine synthetase/guanido kinase, catalytic domain	Homologous Superfamily