4RRF | pdb_00004rrf

Editing domain of threonyl-tRNA synthetase from Methanococcus jannaschii with L-Ser3AA

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)
F	d4rrff_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
E	d4rrfe_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
D	d4rrfd_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
C	d4rrfc_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
B	d4rrfb_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
A	d4rrfa_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	DTD-like	8055880	3000522	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DTD-like	8055880	3000522	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DTD-like	8055880	3000522	SCOP2B (2022-06-29)
C	SCOP2 Family	Threonyl-tRNA synthetase, editing domain	8051365	4007335	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	DTD-like	8055880	3000522	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	DTD-like	8055880	3000522	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DTD-like	8055880	3000522	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)
F		e4rrfF1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: PTR2	F:	ECOD (20:10:01)
E		e4rrfE1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: PTR2	F:	ECOD (20:10:01)
D		e4rrfD1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: PTR2	F:	ECOD (20:10:01)
C		e4rrfC1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: PTR2	F:	ECOD (20:10:01)
B		e4rrfB1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: PTR2	F:	ECOD (20:10:01)
A		e4rrfA1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: PTR2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.50.80.10	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
E	3.50.80.10	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
D	3.50.80.10	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
C	3.50.80.10	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
B	3.50.80.10	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
A	3.50.80.10	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF08915	Archaea-specific editing domain of threonyl-tRNA synthetase (tRNA-Thr_ED)	Archaea-specific editing domain of threonyl-tRNA synthetase	Archaea-specific editing domain of threonyl-tRNA synthetase, with marked structural similarity to D-amino acids deacylases found in eubacteria and eukaryotes. This domain can bind D-amino acids, and ensures high fidelity during translation. It is esp ...	Archaea-specific editing domain of threonyl-tRNA synthetase, with marked structural similarity to D-amino acids deacylases found in eubacteria and eukaryotes. This domain can bind D-amino acids, and ensures high fidelity during translation. It is especially responsible for removing incorrectly attached serine from tRNA-Thr. The domain forms a fold that can be be defined as two layers of beta-sheets (a three-stranded sheet and a five-stranded sheet), with two alpha-helices located adjacent to the five-stranded sheet [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	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 aminoacyl-tRNA deacylase activity hydrolase activity, acting on ester bonds deacylase activity carboxylic ester hydrolase activity hydrolase activity cation binding transition metal ion binding zinc ion binding metal ion binding RNA binding tRNA binding nucleic acid 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR033728	Threonine-tRNA ligase catalytic core domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR023509	D-aminoacyl-tRNA deacylase-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR004154	Anticodon-binding	Domain
A, B, C, D, E A, B, C, D, E, F	IPR015011	Threonyl-tRNA synthetase, editing domain, archaea	Domain
A, B, C, D, E A, B, C, D, E, F	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, B, C, D, E A, B, C, D, E, F	IPR047246	Threonine-tRNA ligase, class IIa, anticodon-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002314	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036621	Anticodon-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	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.