1KOG | pdb_00001kog

Crystal structure of E. coli threonyl-tRNA synthetase interacting with the essential domain of its mRNA operator

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)
I [auth A]	d1koga1	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)
I [auth A]	d1koga2	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)
K [auth C]	d1kogc1	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)
K [auth C]	d1kogc2	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)
L [auth D]	d1kogd1	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)
L [auth D]	d1kogd2	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)
M [auth E]	d1koge1	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)
M [auth E]	d1koge2	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)
O [auth G]	d1kogg1	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)
O [auth G]	d1kogg2	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)
P [auth H]	d1kogh1	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)
P [auth H]	d1kogh2	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)
N [auth F]	d1kogf1	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)
N [auth F]	d1kogf2	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)
J [auth B]	d1kogb1	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)
J [auth B]	d1kogb2	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)
I [auth A]	SCOP2B Superfamily	Class II aaRS ABD-related	8044418	3000465	SCOP2B (2022-06-29)
I [auth A]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035951	3000058	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	Class II aaRS ABD-related	8044418	3000465	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035951	3000058	SCOP2B (2022-06-29)
L [auth D]	SCOP2B Superfamily	Class II aaRS ABD-related	8044418	3000465	SCOP2B (2022-06-29)
L [auth D]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035951	3000058	SCOP2B (2022-06-29)
M [auth E]	SCOP2B Superfamily	Class II aaRS ABD-related	8044418	3000465	SCOP2B (2022-06-29)
M [auth E]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035951	3000058	SCOP2B (2022-06-29)
O [auth G]	SCOP2B Superfamily	Class II aaRS ABD-related	8044418	3000465	SCOP2B (2022-06-29)
O [auth G]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035951	3000058	SCOP2B (2022-06-29)
P [auth H]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035951	3000058	SCOP2B (2022-06-29)
P [auth H]	SCOP2B Superfamily	Class II aaRS ABD-related	8044418	3000465	SCOP2B (2022-06-29)
N [auth F]	SCOP2B Superfamily	Class II aaRS ABD-related	8044418	3000465	SCOP2B (2022-06-29)
N [auth F]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035951	3000058	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035951	3000058	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	Class II aaRS ABD-related	8044418	3000465	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)
I [auth A]	tRNA-synt_2b	e1kogA1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: tRNA-synt_2b	ECOD (develop294)
I [auth A]	HGTP_anticodon	e1kogA2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)
K [auth C]	tRNA-synt_2b	e1kogC1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: tRNA-synt_2b	ECOD (develop294)
K [auth C]	HGTP_anticodon	e1kogC2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)
L [auth D]	tRNA-synt_2b	e1kogD1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: tRNA-synt_2b	ECOD (develop294)
L [auth D]	HGTP_anticodon	e1kogD2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)
M [auth E]	tRNA-synt_2b	e1kogE1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: tRNA-synt_2b	ECOD (develop294)
M [auth E]	HGTP_anticodon	e1kogE2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)
O [auth G]	tRNA-synt_2b	e1kogG1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: tRNA-synt_2b	ECOD (develop294)
O [auth G]	HGTP_anticodon	e1kogG2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)
P [auth H]	tRNA-synt_2b	e1kogH1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: tRNA-synt_2b	ECOD (develop294)
P [auth H]	HGTP_anticodon	e1kogH2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)
N [auth F]	tRNA-synt_2b	e1kogF1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: tRNA-synt_2b	ECOD (develop294)
N [auth F]	HGTP_anticodon	e1kogF2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)
J [auth B]	tRNA-synt_2b	e1kogB1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: tRNA-synt_2b	ECOD (develop294)
J [auth B]	HGTP_anticodon	e1kogB2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I [auth A]	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
I [auth A]	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
K [auth C]	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
K [auth C]	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
L [auth D]	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
L [auth D]	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
M [auth E]	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
M [auth E]	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
O [auth G]	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
O [auth G]	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
P [auth H]	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
P [auth H]	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
N [auth F]	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
N [auth F]	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
J [auth B]	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
J [auth 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
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	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
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	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
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	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 mRNA regulatory element binding translation repressor activity translation repressor activity RNA binding binding nucleic acid binding tRNA 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 catalytic activity ligase activity translation regulator activity mRNA regulatory element binding translation repressor activity translation repressor activity RNA binding binding nucleic acid 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 aminoacyl-tRNA deacylase activity hydrolase activity, acting on ester bonds deacylase activity carboxylic ester hydrolase 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 protein biosynthetic 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 protein 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
A [auth I], B [auth J], C [auth K], D [auth L], E [auth M], A [auth I], B [auth J], C [auth K], D [auth L], E [auth M], F [auth N], G [auth O], H [auth P]	Threonyl-tRNA synthetase mRNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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.