3H0M | pdb_00003h0m

Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus

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)
V	SCOP2B Superfamily	Amidase signature (AS) enzymes	8082869	3001251	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	Amidase signature (AS) enzymes	8082869	3001251	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Amidase signature (AS) enzymes	8082869	3001251	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Amidase signature (AS) enzymes	8082869	3001251	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Amidase signature (AS) enzymes	8082869	3001251	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Amidase signature (AS) enzymes	8082869	3001251	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Amidase signature (AS) enzymes	8082869	3001251	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Amidase signature (AS) enzymes	8082869	3001251	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	GatC-like	8082963	3001870	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	GatC-like	8082963	3001870	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	GatC-like	8082963	3001870	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	GatC-like	8082963	3001870	SCOP2B (2022-06-29)
U	SCOP2B Superfamily	GatC-like	8082963	3001870	SCOP2B (2022-06-29)
X	SCOP2B Superfamily	GatC-like	8082963	3001870	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	GatC-like	8082963	3001870	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GatC-like	8082963	3001870	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
V	HCV_NS2	e3h0mV1	A: alpha arrays	X: HTH	H: HTH	T: Catalytic domain of hepatitis C virus NS2-3 protease	F: HCV_NS2	ECOD (v295)
S	YgbB	e3h0mS1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
P	YgbB	e3h0mP1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
M	YgbB	e3h0mM1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
J	YgbB	e3h0mJ1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
G	YgbB	e3h0mG1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
D	YgbB	e3h0mD1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
A	YgbB	e3h0mA1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
F	YgbB	e3h0mF1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
I	YgbB	e3h0mI1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
L	YgbB	e3h0mL1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
R	YgbB	e3h0mR1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
U	YgbB	e3h0mU1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
X	YgbB	e3h0mX1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
O	YgbB	e3h0mO1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
C	YgbB	e3h0mC1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
W	YgbB	e3h0mW1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
T	YgbB	e3h0mT1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
Q	YgbB	e3h0mQ1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
N	YgbB	e3h0mN1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
K	YgbB	e3h0mK1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
H	YgbB	e3h0mH1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
E	YgbB	e3h0mE1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
B	YgbB	e3h0mB1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
V	3.90.1300.10	Alpha Beta	Alpha-Beta Complex	Amidase signature (AS) enzymes	Amidase signature (AS) domain	CATH (4.3.0)
S	3.90.1300.10	Alpha Beta	Alpha-Beta Complex	Amidase signature (AS) enzymes	Amidase signature (AS) domain	CATH (4.3.0)
P	3.90.1300.10	Alpha Beta	Alpha-Beta Complex	Amidase signature (AS) enzymes	Amidase signature (AS) domain	CATH (4.3.0)
M	3.90.1300.10	Alpha Beta	Alpha-Beta Complex	Amidase signature (AS) enzymes	Amidase signature (AS) domain	CATH (4.3.0)
J	3.90.1300.10	Alpha Beta	Alpha-Beta Complex	Amidase signature (AS) enzymes	Amidase signature (AS) domain	CATH (4.3.0)
G	3.90.1300.10	Alpha Beta	Alpha-Beta Complex	Amidase signature (AS) enzymes	Amidase signature (AS) domain	CATH (4.3.0)
D	3.90.1300.10	Alpha Beta	Alpha-Beta Complex	Amidase signature (AS) enzymes	Amidase signature (AS) domain	CATH (4.3.0)
A	3.90.1300.10	Alpha Beta	Alpha-Beta Complex	Amidase signature (AS) enzymes	Amidase signature (AS) domain	CATH (4.3.0)
F	1.10.20.60	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Glu-tRNAGln amidotransferase C subunit, N-terminal domain	CATH (4.3.0)
I	1.10.20.60	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Glu-tRNAGln amidotransferase C subunit, N-terminal domain	CATH (4.3.0)
L	1.10.20.60	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Glu-tRNAGln amidotransferase C subunit, N-terminal domain	CATH (4.3.0)
R	1.10.20.60	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Glu-tRNAGln amidotransferase C subunit, N-terminal domain	CATH (4.3.0)
U	1.10.20.60	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Glu-tRNAGln amidotransferase C subunit, N-terminal domain	CATH (4.3.0)
X	1.10.20.60	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Glu-tRNAGln amidotransferase C subunit, N-terminal domain	CATH (4.3.0)
O	1.10.20.60	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Glu-tRNAGln amidotransferase C subunit, N-terminal domain	CATH (4.3.0)
C	1.10.20.60	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Glu-tRNAGln amidotransferase C subunit, N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G, J, M A, D, G, J, M, P, S, V	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
C, F, I, L, O C, F, I, L, O, R, U, X	PF02686	Glu-tRNAGln amidotransferase C subunit (GatC)	Glu-tRNAGln amidotransferase C subunit	-	Family
B, E, H, K, N B, E, H, K, N, Q, T, W	PF02934	GatB/GatE catalytic domain (GatB_N)	GatB/GatE catalytic domain	This domain is found in the GatB and GatE proteins [1].	Domain
B, E, H, K, N B, E, H, K, N, Q, T, W	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G, J, M A, D, G, J, M, P, S, V	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
C, F, I, L, O C, F, I, L, O, R, U, X	Glutamyl-tRNA(Gln) amidotransferase subunit C	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	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	-
B, E, H, K, N B, E, H, K, N, Q, T, W	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G, J, M A, D, G, J, M, P, S, V	IPR036928	Amidase signature (AS) superfamily	Homologous Superfamily
A, D, G, J, M A, D, G, J, M, P, S, V	IPR004412	Glutamyl-tRNA(Gln) amidotransferase A subunit	Family
A, D, G, J, M A, D, G, J, M, P, S, V	IPR000120	Amidase	Family
A, D, G, J, M A, D, G, J, M, P, S, V	IPR023631	Amidase signature domain	Domain
A, D, G, J, M A, D, G, J, M, P, S, V	IPR020556	Amidase, conserved site	Conserved Site
C, F, I, L, O C, F, I, L, O, R, U, X	IPR003837	Glu-tRNAGln amidotransferase C subunit	Family
C, F, I, L, O C, F, I, L, O, R, U, X	IPR036113	Glu-tRNAGln amidotransferase superfamily, subunit C	Homologous Superfamily
B, E, H, K, N B, E, H, K, N, Q, T, W	IPR006075	Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic	Domain
B, E, H, K, N B, E, H, K, N, Q, T, W	IPR042114	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1	Homologous Superfamily
B, E, H, K, N B, E, H, K, N, Q, T, W	IPR003789	Aspartyl/glutamyl-tRNA amidotransferase subunit B-like	Homologous Superfamily
B, E, H, K, N B, E, H, K, N, Q, T, W	IPR017959	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E	Family
B, E, H, K, N B, E, H, K, N, Q, T, W	IPR023168	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2	Homologous Superfamily
B, E, H, K, N B, E, H, K, N, Q, T, W	IPR018027	Asn/Gln amidotransferase	Domain
B, E, H, K, N B, E, H, K, N, Q, T, W	IPR017958	Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site	Conserved Site
B, E, H, K, N B, E, H, K, N, Q, T, W	IPR004413	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B	Family
B, E, H, K, N B, E, H, K, N, Q, T, W	IPR014746	Glutamine synthetase/guanido kinase, catalytic domain	Homologous Superfamily

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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.