1ZQ1 | pdb_00001zq1

Structure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d1zq1d1	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	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
D	d1zq1d2	Alpha and beta proteins (a+b)	DCoH-like	GAD domain-like	GAD domain	Glutamyl-tRNA(gln) amidotransferase subunit E, GatE, insert domain	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
D	d1zq1d3	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	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
C	d1zq1c1	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	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
C	d1zq1c2	Alpha and beta proteins (a+b)	DCoH-like	GAD domain-like	GAD domain	Glutamyl-tRNA(gln) amidotransferase subunit E, GatE, insert domain	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
C	d1zq1c3	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	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
B	d1zq1b1	All beta proteins	Sm-like fold	GatD N-terminal domain-like	GatD N-terminal domain-like	Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
B	d1zq1b2	Alpha and beta proteins (a/b)	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
A	d1zq1a1	All beta proteins	Sm-like fold	GatD N-terminal domain-like	GatD N-terminal domain-like	Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
A	d1zq1a2	Alpha and beta proteins (a/b)	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Glutamine synthetase/guanido kinase	8036136	3000676	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GAD domain-like	8036135	3000108	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glutamine synthetase/guanido kinase	8036136	3000676	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GatB/YqeY motif	8036134	3001497	SCOP2B (2022-06-29)
C	SCOP2 Family	GatB/GatE C-terminal domain-like	8023754	4001495	SCOP2 (2022-06-29)
C	SCOP2 Family	GAD domain	8023755	4001480	SCOP2 (2022-06-29)
C	SCOP2 Family	GatB/GatE catalytic domain-like	8023756	4003972	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	GatB/YqeY motif	8036134	3001497	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	GAD domain-like	8036135	3000108	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Glutamine synthetase/guanido kinase	8036136	3000676	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	GatD N-terminal domain-like	8036129	3000389	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glutaminase/Asparaginase	8036131	3001625	SCOP2B (2022-06-29)
A	SCOP2 Family	GatD N-terminal domain-like	8023749	4001791	SCOP2 (2022-06-29)
A	SCOP2 Family	Glutaminase/Asparaginase	8023751	4000833	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GatD N-terminal domain-like	8036129	3000389	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glutaminase/Asparaginase	8036131	3001625	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	PRK04028	e1zq1D1	A: alpha arrays	X: ERP29 C domain-like	H: GatB/GatE C-terminal domain (From Topology)	T: GatB/GatE C-terminal domain	F: PRK04028	ECOD (1.6)
D	GatB_N	e1zq1D2	A: a+b two layers	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase (From Topology)	T: Glutamine synthetase/guanido kinase	F: GatB_N	ECOD (1.6)
D	GAD	e1zq1D3	A: a+b two layers	X: Prokaryotic AspRS, insert domain (From Topology)	H: Prokaryotic AspRS, insert domain (From Topology)	T: Prokaryotic AspRS, insert domain	F: GAD	ECOD (1.6)
C	PRK04028	e1zq1C1	A: alpha arrays	X: ERP29 C domain-like	H: GatB/GatE C-terminal domain (From Topology)	T: GatB/GatE C-terminal domain	F: PRK04028	ECOD (1.6)
C	GatB_N	e1zq1C2	A: a+b two layers	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase (From Topology)	T: Glutamine synthetase/guanido kinase	F: GatB_N	ECOD (1.6)
C	GAD	e1zq1C3	A: a+b two layers	X: Prokaryotic AspRS, insert domain (From Topology)	H: Prokaryotic AspRS, insert domain (From Topology)	T: Prokaryotic AspRS, insert domain	F: GAD	ECOD (1.6)
B	GatD	e1zq1B1	A: beta barrels	X: SH3	H: GatD N-terminal domain-like (From Topology)	T: GatD N-terminal domain-like	F: GatD	ECOD (1.6)
B	PRK04183	e1zq1B3	A: a/b three-layered sandwiches	X: Glutaminase/Asparaginase C-terminal domain (From Topology)	H: Glutaminase/Asparaginase C-terminal domain (From Topology)	T: Glutaminase/Asparaginase C-terminal domain	F: PRK04183	ECOD (1.6)
B	Asparaginase	e1zq1B4	A: a/b three-layered sandwiches	X: Glutaminase/Asparaginase N-terminal domain (From Topology)	H: Glutaminase/Asparaginase N-terminal domain (From Topology)	T: Glutaminase/Asparaginase N-terminal domain	F: Asparaginase	ECOD (1.6)
A	GatD	e1zq1A1	A: beta barrels	X: SH3	H: GatD N-terminal domain-like (From Topology)	T: GatD N-terminal domain-like	F: GatD	ECOD (1.6)
A	PRK04183	e1zq1A4	A: a/b three-layered sandwiches	X: Glutaminase/Asparaginase C-terminal domain (From Topology)	H: Glutaminase/Asparaginase C-terminal domain (From Topology)	T: Glutaminase/Asparaginase C-terminal domain	F: PRK04183	ECOD (1.6)
A	Asparaginase	e1zq1A3	A: a/b three-layered sandwiches	X: Glutaminase/Asparaginase N-terminal domain (From Topology)	H: Glutaminase/Asparaginase N-terminal domain (From Topology)	T: Glutaminase/Asparaginase N-terminal domain	F: Asparaginase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, 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
A, 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	-

InterPro: Protein Family Classification InterPro Database Homepage

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