1WY5 | pdb_00001wy5

Crystal structure of isoluecyl-tRNA lysidine synthetase

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)
B	d1wy5b1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	PP-loop ATPase	TilS-like protein Aq_1887	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d1wy5b2	Alpha and beta proteins (a+b)	MesJ substrate recognition domain-like	MesJ substrate recognition domain-like	MesJ substrate recognition domain-like	TilS-like protein Aq_1887	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d1wy5a1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	PP-loop ATPase	TilS-like protein Aq_1887	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d1wy5a2	Alpha and beta proteins (a+b)	MesJ substrate recognition domain-like	MesJ substrate recognition domain-like	MesJ substrate recognition domain-like	TilS-like protein Aq_1887	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	MesJ substrate recognition domain-like	8033391	3000685	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8033389	3001593	SCOP2B (2022-06-29)
A	SCOP2 Family	PP-loop ATPase	8021009	4002958	SCOP2 (2022-06-29)
A	SCOP2 Family	MesJ substrate recognition domain-like	8021011	4003359	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Adenine nucleotide alpha hydrolases-like	8033389	3001593	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MesJ substrate recognition domain-like	8033391	3000685	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)
B	TilS_like	e1wy5B1	A: a+b two layers	X: MesJ substrate recognition domain-like (From Topology)	H: MesJ substrate recognition domain-like (From Topology)	T: MesJ substrate recognition domain-like	F: TilS_like	ECOD (1.6)
B	NAD_synthase	e1wy5B2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: NAD_synthase	ECOD (1.6)
A	TilS_like	e1wy5A2	A: a+b two layers	X: MesJ substrate recognition domain-like (From Topology)	H: MesJ substrate recognition domain-like (From Topology)	T: MesJ substrate recognition domain-like	F: TilS_like	ECOD (1.6)
A	NAD_synthase	e1wy5A1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: NAD_synthase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	1.20.59.20	Mainly Alpha	Up-down Bundle	Chorismate Mutase Domain, subunit A		CATH (4.3.0)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	1.20.59.20	Mainly Alpha	Up-down Bundle	Chorismate Mutase Domain, subunit A		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01171	PP-loop domain (ATP_bind_3)	PP-loop domain	The structure of tRNA(Ile)-lysidine synthetase consists of an N-terminal dinucleotide-binding fold domain (NTD), and a C-terminal globular domain (CTD). The structure of the NTD closely resembles that of a P-loop "N-type" ATP pyrophosphatase [2]. The ...	The structure of tRNA(Ile)-lysidine synthetase consists of an N-terminal dinucleotide-binding fold domain (NTD), and a C-terminal globular domain (CTD). The structure of the NTD closely resembles that of a P-loop "N-type" ATP pyrophosphatase [2]. These proteins belong to the PP-loop superfamily [1].	Domain
A, B	PF22132	TilS-like substrate binding domain (TilS-like)	TilS-like substrate binding domain	This entry represents a C-terminal domain (CTD) present in TilS ligases proteins, probably implicated in the recognition of the tRNA accetor stem [1]. TilS ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) th ...	This entry represents a C-terminal domain (CTD) present in TilS ligases proteins, probably implicated in the recognition of the tRNA accetor stem [1]. TilS ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Hypothetical UPF0072 protein AQ_1887	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 catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid tRNA(Ile)-lysidine synthase activity catalytic activity, acting on a tRNA catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity	tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification metabolic process cellular process macromolecule metabolic process RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR054377	tRNA(Ile)-lysidine synthase-like, C-terminal domain	Domain
A, B	IPR011063	tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal	Domain
A, B	IPR012795	tRNA(Ile)-lysidine synthase, N-terminal	Domain
A, B	IPR012094	tRNA(Ile)-lysidine synthase	Family
A, B	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily

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.