1NYR | pdb_00001nyr

Structure of Staphylococcus aureus threonyl-tRNA synthetase complexed with ATP

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	d1nyra1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	Class II aaRS ABD-related	Anticodon-binding domain of Class II aaRS	Threonyl-tRNA synthetase (ThrRS), C-terminal domain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d1nyra2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	TGS-like	TGS domain	Threonyl-tRNA synthetase (ThrRS), N-terminal 'additional' domain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d1nyra3	Alpha and beta proteins (a+b)	RRF/tRNA synthetase additional domain-like	ThrRS/AlaRS common domain	Threonyl-tRNA synthetase (ThrRS), second 'additional' domain	Threonyl-tRNA synthetase (ThrRS), second 'additional' domain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d1nyra4	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Threonyl-tRNA synthetase (ThrRS)	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d1nyrb1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	Class II aaRS ABD-related	Anticodon-binding domain of Class II aaRS	Threonyl-tRNA synthetase (ThrRS), C-terminal domain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d1nyrb2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	TGS-like	TGS domain	Threonyl-tRNA synthetase (ThrRS), N-terminal 'additional' domain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d1nyrb3	Alpha and beta proteins (a+b)	RRF/tRNA synthetase additional domain-like	ThrRS/AlaRS common domain	Threonyl-tRNA synthetase (ThrRS), second 'additional' domain	Threonyl-tRNA synthetase (ThrRS), second 'additional' domain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d1nyrb4	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Threonyl-tRNA synthetase (ThrRS)	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Anticodon-binding domain of Class II aaRS	8024721	4000507	SCOP2 (2022-06-29)
A	SCOP2 Family	TGS domain	8024723	4001813	SCOP2 (2022-06-29)
A	SCOP2 Family	Threonyl-tRNA synthetase (ThrRS), second 'additional' domain	8024724	4001406	SCOP2 (2022-06-29)
A	SCOP2 Family	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	8024725	4001782	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Class II aaRS ABD-related	8037100	3000465	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TGS-like	8037102	3000423	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ThrRS/AlaRS editing domain-like	8037103	3001504	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Class II aaRS and biotin synthetases	8037104	3000058	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8037104	3000058	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TGS-like	8037102	3000423	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS ABD-related	8037100	3000465	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ThrRS/AlaRS editing domain-like	8037103	3001504	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	TGS	e1nyrA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: TGS	ECOD (1.6)
A	tRNA_SAD	e1nyrA1	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: ThrRS/AlaRS editing domain	F: tRNA_SAD	ECOD (1.6)
A	tRNA-synt_2b	e1nyrA3	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2b	ECOD (1.6)
A	HGTP_anticodon	e1nyrA4	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS (From Topology)	H: Anticodon-binding domain of Class II aaRS (From Topology)	T: Anticodon-binding domain of Class II aaRS	F: HGTP_anticodon	ECOD (1.6)
B	TGS	e1nyrB2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: TGS	ECOD (1.6)
B	tRNA_SAD	e1nyrB1	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: ThrRS/AlaRS editing domain	F: tRNA_SAD	ECOD (1.6)
B	tRNA-synt_2b	e1nyrB3	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2b	ECOD (1.6)
B	HGTP_anticodon	e1nyrB4	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS (From Topology)	H: Anticodon-binding domain of Class II aaRS (From Topology)	T: Anticodon-binding domain of Class II aaRS	F: HGTP_anticodon	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
A	3.30.980.10	Alpha Beta	2-Layer Sandwich	Threonyl-tRNA Synthetase	Chain A, domain 2	CATH (4.3.0)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
A	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
B	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
B	3.30.980.10	Alpha Beta	2-Layer Sandwich	Threonyl-tRNA Synthetase	Chain A, domain 2	CATH (4.3.0)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02824	TGS domain (TGS)	TGS domain	The TGS domain is named after ThrRS, GTPase, and SpoT [1]. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete ...	The TGS domain is named after ThrRS, GTPase, and SpoT [1]. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role [1].	Domain
A, B	PF07973	Threonyl and Alanyl tRNA synthetase second additional domain (tRNA_SAD)	Threonyl and Alanyl tRNA synthetase second additional domain	The catalytically active from of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and thi ...	The catalytically active from of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and this domain (the second additional domain). The second additional domain is comprised of a pair of perpendicularly orientated antiparallel beta sheets, of four and three strands, respectively, that surround a central alpha helix that forms the core of the domain [1].	Domain
A, B	PF03129	Anticodon binding domain (HGTP_anticodon)	Anticodon binding domain	This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [1] it is probably the anticodon binding domain [2].	Domain
A, B	PF00587	tRNA synthetase class II core domain (G, H, P, S and T) (tRNA-synt_2b)	tRNA synthetase class II core domain (G, H, P, S and T)	tRNA-synt_2b is a family of largely threonyl-tRNA members.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	threonyl-tRNA synthetase 1	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 threonine-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 RNA binding tRNA binding nucleic acid binding cation binding metal ion binding transferase activity	amino acid activation tRNA aminoacylation RNA metabolic process 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 threonyl-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 macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process threonyl-tRNA aminoacylation metabolic process cellular process macromolecule metabolic process protein metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012676	TGS-like	Homologous Superfamily
A, B	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B	IPR033728	Threonine-tRNA ligase catalytic core domain	Domain
A, B	IPR004095	TGS	Domain
A, B	IPR012947	Threonyl/alanyl tRNA synthetase, SAD	Domain
A, B	IPR004154	Anticodon-binding	Domain
A, B	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, B	IPR047246	Threonine-tRNA ligase, class IIa, anticodon-binding domain	Domain
A, B	IPR002314	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Domain
A, B	IPR018163	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily	Homologous Superfamily
A, B	IPR036621	Anticodon-binding domain superfamily	Homologous Superfamily
A, B	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily
A, B	IPR002320	Threonine-tRNA ligase, class IIa	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.