4WJ3 | pdb_00004wj3

Crystal structure of the asparagine transamidosome from Pseudomonas aeruginosa

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)
C	SCOP2 Family	GatC-like	8082966	4001576	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	GatC-like	8082967	3001870	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	GatC-like	8082967	3001870	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	GatC-like	8082967	3001870	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	GatC-like	8082967	3001870	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Amidase signature (AS) enzymes	8082871	3001251	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Amidase signature (AS) enzymes	8082871	3001251	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Amidase signature (AS) enzymes	8082871	3001251	SCOP2B (2022-06-29)
A	SCOP2 Family	Amidase signature (AS) enzymes	8082870	4002446	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Amidase signature (AS) enzymes	8082871	3001251	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)
M	Ank, Ank_2, Ank_3, Ank_4	e4wj3M1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Ank, Ank_2, Ank_3, Ank_4	ECOD (v294.1)
N	Ank, Ank_2, Ank_3, Ank_4	e4wj3N1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Ank, Ank_2, Ank_3, Ank_4	ECOD (v294.1)
P	Ank, Ank_2, Ank_3, Ank_4	e4wj3P1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Ank, Ank_2, Ank_3, Ank_4	ECOD (v294.1)
O	Ank, Ank_2, Ank_3, Ank_4	e4wj3O1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Ank, Ank_2, Ank_3, Ank_4	ECOD (v294.1)
C	Ank, Ank_2, Ank_3, Ank_4	e4wj3C1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Ank, Ank_2, Ank_3, Ank_4	ECOD (v294.1)
F	Ank, Ank_2, Ank_3, Ank_4	e4wj3F1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Ank, Ank_2, Ank_3, Ank_4	ECOD (v294.1)
I	Ank, Ank_2, Ank_3, Ank_4	e4wj3I1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Ank, Ank_2, Ank_3, Ank_4	ECOD (v294.1)
L	Ank, Ank_2, Ank_3, Ank_4	e4wj3L1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Ank, Ank_2, Ank_3, Ank_4	ECOD (v294.1)
E	PCI	e4wj3E1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: PCI	ECOD (v294.1)
K	PCI	e4wj3K1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: PCI	ECOD (v294.1)
G	Ank, Ank_2, Ank_3, Ank_4	e4wj3G1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Ank, Ank_2, Ank_3, Ank_4	ECOD (v294.1)
J	Ank, Ank_2, Ank_3, Ank_4	e4wj3J1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Ank, Ank_2, Ank_3, Ank_4	ECOD (v294.1)
D	Ank, Ank_2, Ank_3, Ank_4	e4wj3D1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Ank, Ank_2, Ank_3, Ank_4	ECOD (v294.1)
A	Ank, Ank_2, Ank_3, Ank_4	e4wj3A1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Ank, Ank_2, Ank_3, Ank_4	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
M	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
M	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
M	3.30.1360.30	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
N	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
N	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
N	3.30.1360.30	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
P	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
P	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
P	3.30.1360.30	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
O	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
O	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
O	3.30.1360.30	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	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)
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)
G	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
M, N, O, P	PF02938	GAD domain (GAD)	GAD domain	This domain is found in some members of the GatB and aspartyl tRNA synthetases.	Domain
M, N, O, P	PF00152	tRNA synthetases class II (D, K and N) (tRNA-synt_2)	tRNA synthetases class II (D, K and N)		Domain
M, N, O, P	PF01336	OB-fold nucleic acid binding domain (tRNA_anti-codon)	OB-fold nucleic acid binding domain	This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an am ...	This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family [2,3]. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.	Domain
C, F, I, L	PF02686	Glu-tRNAGln amidotransferase C subunit (GatC)	Glu-tRNAGln amidotransferase C subunit	-	Family
B, E, H, K	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, E, H, K	PF02934	GatB/GatE catalytic domain (GatB_N)	GatB/GatE catalytic domain	This domain is found in the GatB and GatE proteins [1].	Domain
A, D, G, J	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
Q, R, S, T	76mer-tRNA	-	-	-
M, N, O, P	Aspartate--tRNA(Asp/Asn) ligase	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 aspartate-tRNA(Asn) ligase activity ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding 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 aspartate-tRNA(Asn) ligase activity ligase activity 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 nucleic acid binding aspartate-tRNA ligase activity	amino acid activation aspartyl-tRNA aminoacylation 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 aspartyl-tRNA aminoacylation 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	cellular anatomical structure intracellular anatomical structure cytoplasm
C, F, I, L	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	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	-
A, D, G, J	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
M, N, O, P	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
M, N, O, P	IPR002312	Aspartyl/Asparaginyl-tRNA synthetase, class IIb	Family
M, N, O, P	IPR047089	Aspartate-tRNA ligase, type 1, anticodon recognition domain	Domain
M, N, O, P	IPR047090	Aspartate-tRNA ligase, type 1, core domain	Domain
M, N, O, P	IPR004365	OB-fold nucleic acid binding domain, AA-tRNA synthetase-type	Domain
M, N, O, P	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
M, N, O, P	IPR029351	GAD domain	Domain
M, N, O, P	IPR004115	GAD-like domain superfamily	Homologous Superfamily
M, N, O, P	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
M, N, O, P	IPR004364	Aminoacyl-tRNA synthetase, class II (D/K/N)	Domain
M, N, O, P	IPR004524	Aspartate-tRNA ligase, type 1	Family
C, F, I, L	IPR003837	Glu-tRNAGln amidotransferase C subunit	Family
C, F, I, L	IPR036113	Glu-tRNAGln amidotransferase superfamily, subunit C	Homologous Superfamily
B, E, H, K	IPR006075	Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic	Domain
B, E, H, K	IPR042114	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1	Homologous Superfamily
B, E, H, K	IPR003789	Aspartyl/glutamyl-tRNA amidotransferase subunit B-like	Homologous Superfamily
B, E, H, K	IPR017959	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E	Family
B, E, H, K	IPR023168	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2	Homologous Superfamily
B, E, H, K	IPR018027	Asn/Gln amidotransferase	Domain
B, E, H, K	IPR017958	Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site	Conserved Site
B, E, H, K	IPR004413	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B	Family
B, E, H, K	IPR014746	Glutamine synthetase/guanido kinase, catalytic domain	Homologous Superfamily
A, D, G, J	IPR036928	Amidase signature (AS) superfamily	Homologous Superfamily
A, D, G, J	IPR004412	Glutamyl-tRNA(Gln) amidotransferase A subunit	Family
A, D, G, J	IPR000120	Amidase	Family
A, D, G, J	IPR023631	Amidase signature domain	Domain
A, D, G, J	IPR020556	Amidase, conserved site	Conserved Site