1QF6

STRUCTURE OF E. COLI THREONYL-TRNA SYNTHETASE COMPLEXED WITH ITS COGNATE TRNA

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth A]	d1qf6a1	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	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B [auth A]	d1qf6a2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	TGS-like	TGS domain	Threonyl-tRNA synthetase (ThrRS), N-terminal 'additional' domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B [auth A]	d1qf6a3	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	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B [auth A]	d1qf6a4	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)	(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)
B [auth A]	SCOP2 Family	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	8023571	4001782	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Family	TGS domain	8030120	4001813	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Family	Threonyl-tRNA synthetase (ThrRS), second 'additional' domain	8030122	4001406	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Family	Anticodon-binding domain of Class II aaRS	8032040	4000507	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Class II aaRS and biotin synthetases	8035951	3000058	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	TGS-like	8042499	3000423	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	ThrRS/AlaRS editing domain-like	8042501	3001504	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Class II aaRS ABD-related	8044418	3000465	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 [auth A]	TGS	e1qf6A2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: TGS	ECOD (1.6)
B [auth A]	tRNA_SAD	e1qf6A1	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 [auth A]	tRNA-synt_2b	e1qf6A3	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 [auth A]	HGTP_anticodon	e1qf6A4	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)
B [auth A]	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
B [auth A]	3.30.980.10	Alpha Beta	2-Layer Sandwich	Threonyl-tRNA Synthetase	Chain A, domain 2	CATH (4.3.0)
B [auth A]	3.30.54.20	Alpha Beta	2-Layer Sandwich	Replication Terminator Protein	Chain A, domain 2	CATH (4.3.0)
B [auth A]	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B [auth A]	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
B [auth A]	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
B [auth A]	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
B [auth A]	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
B [auth A]	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 [auth B]	THREONINE TRNA	-	-	-
B [auth A]	THREONYL-TRNA SYNTHETASE	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 ligase activity translation regulator activity binding mRNA regulatory element binding translation repressor activity organic cyclic compound binding translation regulator activity, nucleic acid binding nucleic acid binding translation repressor activity 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 ligase activity translation regulator activity binding mRNA regulatory element binding translation repressor activity organic cyclic compound binding translation regulator activity, nucleic acid binding nucleic acid binding translation repressor activity RNA binding tRNA 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 identical protein binding protein binding protein homodimerization activity protein dimerization activity threonine-tRNA ligase activity hydrolase activity, acting on ester bonds carboxylic ester hydrolase activity aminoacyl-tRNA editing activity hydrolase activity mRNA 5'-UTR binding mRNA binding cation binding transition metal ion binding zinc ion binding metal ion binding	response to stimulus response to chemical response to antibiotic regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of primary metabolic process response to stimulus response to chemical response to antibiotic regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process regulation of metabolic process amino acid activation tRNA aminoacylation RNA metabolic process amino acid metabolic process tRNA aminoacylation for protein translation nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process threonyl-tRNA aminoacylation negative regulation of biological process negative regulation of translation negative regulation of cellular process translational initiation negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of translational initiation negative regulation of metabolic process negative regulation of translational initiation negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

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

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
B [auth A]	threonine---tRNA ligase M-CSA #540	threonyl tRNA synthase from E.coli is able to catalyse the attachment of a threonine residue to its corresponding tRNA, displaying remarkable specificity as it only works on the specific amino acid and on the specific tRNA. It is part of the class II tRNA synthases, which make up approximately half of the known tRNA synthases. It is rare among class II synthases because of the presence of a Zinc ion in the active site, which is catalytic rather than structural.	Defined by 7 residues: CYS:B-334 [auth A-334]ARG:B-363 [auth A-363]GLN:B-381 [auth A-381]ASP:B-383 [auth A-383]HIS:B-385 [auth A-385]LYS:B-465 [auth A-465]HIS:B-511 [auth A-511] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 6.1.1.3 (PDB Primary Data) Search M-CSA Motif + EC 6.1.1.3

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.