1LI5 | pdb_00001li5

Crystal Structure of Cysteinyl-tRNA 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)
A	d1li5a1	All alpha proteins	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Cysteinyl-tRNA synthetase (CysRS)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1li5a2	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	Cysteinyl-tRNA synthetase (CysRS)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1li5b1	All alpha proteins	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Cysteinyl-tRNA synthetase (CysRS)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1li5b2	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	Cysteinyl-tRNA synthetase (CysRS)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotidylyl transferase	8042745	3001541	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotidylyl transferase	8042745	3001541	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)
A	DALR_2,tRNA-synt_1g	e1li5A1	A: alpha bundles	X: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: DALR_2,tRNA-synt_1g	ECOD (1.6)
A	tRNA-synt_1g	e1li5A2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1g	ECOD (1.6)
A	UNK_F_TYPE	e1li5A3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: UNK_F_TYPE	ECOD (1.6)
B	DALR_2,tRNA-synt_1g	e1li5B1	A: alpha bundles	X: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: DALR_2,tRNA-synt_1g	ECOD (1.6)
B	tRNA-synt_1g	e1li5B3	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1g	ECOD (1.6)
B	UNK_F_TYPE	e1li5B2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	1.20.120.640	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	CATH (4.3.0)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	1.20.120.640	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01406	tRNA synthetases class I (C) catalytic domain (tRNA-synt_1e)	tRNA synthetases class I (C) catalytic domain	This entry represents the catalytic (Rossmann-fold) domain found in cysteinyl tRNA synthetases [3] which is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS m ...	This entry represents the catalytic (Rossmann-fold) domain found in cysteinyl tRNA synthetases [3] which is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Cysteine-tRNA ligase (also known as cysteinyl-tRNA synthetase) (6.1.1.16) is an alpha monomer and belongs to class Ia [1]. It aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. It is highly specific despite not possessing the amino acid editing activity characteristic of many other tRNA ligases [2][4].	Domain
A, B	PF09190	DALR domain (DALR_2)	DALR domain	This DALR domain is found in cysteinyl-tRNA-synthetases [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	CYSTEINYL-TRNA SYNTHETASE	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 ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity cysteine-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity cation binding transition metal ion binding zinc ion binding metal ion binding	amino acid activation tRNA aminoacylation RNA metabolic process cysteinyl-tRNA aminoacylation primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process amino acid activation tRNA aminoacylation RNA metabolic process cysteinyl-tRNA aminoacylation primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation 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	IPR032678	tRNA synthetases class I, catalytic domain	Domain
A, B	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A, B	IPR015803	Cysteine-tRNA ligase	Family
A, B	IPR056411	Cysteinyl-tRNA ligase, anticodon binding domain	Domain
A, B	IPR015273	Cysteinyl-tRNA synthetase, class Ia, DALR	Domain
A, B	IPR009080	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Homologous Superfamily
A, B	IPR024909	Cysteinyl-tRNA synthetase/mycothiol ligase	Family

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.