6VU9 | pdb_00006vu9

Crystal structure of threonyl-tRNA synthetase (ThrRS) from Stenotrophomonas maltophilia K279a

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	MacB_PCD	e6vu9A1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit 8 (Nqo8)-related	F: MacB_PCD	ECOD (v294.1)

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 (utative)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (utative)
A	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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
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	Threonine--tRNA ligase	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	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 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 protein biosynthetic process 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 cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR012676	TGS-like	Homologous Superfamily
A	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A	IPR033728	Threonine-tRNA ligase catalytic core domain	Domain
A	IPR004095	TGS	Domain
A	IPR012947	Threonyl/alanyl tRNA synthetase, SAD	Domain
A	IPR004154	Anticodon-binding	Domain
A	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A	IPR047246	Threonine-tRNA ligase, class IIa, anticodon-binding domain	Domain
A	IPR002314	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Domain
A	IPR018163	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily	Homologous Superfamily
A	IPR036621	Anticodon-binding domain superfamily	Homologous Superfamily
A	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily
A	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.