6AQG | pdb_00006aqg

Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine and Cladosporin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d6aqgd1	All beta proteins	OB-fold	Nucleic acid-binding proteins	automated matches	automated matches	(Mycobacterium ulcerans Agy99 ) [TaxId: 362242 ],	SCOPe (2.08)
D	d6aqgd2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	automated matches	automated matches	(Mycobacterium ulcerans Agy99 ) [TaxId: 362242 ],	SCOPe (2.08)
C	d6aqgc1	All beta proteins	OB-fold	Nucleic acid-binding proteins	automated matches	automated matches	(Mycobacterium ulcerans Agy99 ) [TaxId: 362242 ],	SCOPe (2.08)
C	d6aqgc2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	automated matches	automated matches	(Mycobacterium ulcerans Agy99 ) [TaxId: 362242 ],	SCOPe (2.08)
B	d6aqgb1	All beta proteins	OB-fold	Nucleic acid-binding proteins	automated matches	automated matches	(Mycobacterium ulcerans Agy99 ) [TaxId: 362242 ],	SCOPe (2.08)
B	d6aqgb2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	automated matches	automated matches	(Mycobacterium ulcerans Agy99 ) [TaxId: 362242 ],	SCOPe (2.08)
A	d6aqga1	All beta proteins	OB-fold	Nucleic acid-binding proteins	automated matches	automated matches	(Mycobacterium ulcerans Agy99 ) [TaxId: 362242 ],	SCOPe (2.08)
A	d6aqga2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	automated matches	automated matches	(Mycobacterium ulcerans Agy99 ) [TaxId: 362242 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Ribosomal_L23	e6aqgD1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ribosomal_L23	ECOD (v294.1)
C	Ribosomal_L23	e6aqgC1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ribosomal_L23	ECOD (v294.1)
B	Ribosomal_L23	e6aqgB1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ribosomal_L23	ECOD (v294.1)
A	Ribosomal_L23	e6aqgA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ribosomal_L23	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
D	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Lysine--tRNA ligase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide 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 lysine-tRNA ligase activity catalytic activity ligase activity RNA binding tRNA binding nucleic acid binding	lysyl-tRNA aminoacylation amino acid activation 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 lysyl-tRNA aminoacylation amino acid activation 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 cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B, C, D	IPR004365	OB-fold nucleic acid binding domain, AA-tRNA synthetase-type	Domain
A, B, C, D	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, B, C, D	IPR018149	Lysyl-tRNA synthetase, class II, C-terminal	Domain
A, B, C, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B, C, D	IPR004364	Aminoacyl-tRNA synthetase, class II (D/K/N)	Domain
A, B, C, D	IPR002313	Lysine-tRNA ligase, class II	Family
A, B, C, D	IPR044136	Lysine-tRNA ligase, class II, N-terminal	Domain

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.