1V4P | pdb_00001v4p

Crystal structure of Alanyl-tRNA Synthetase from Pyrococcus horikoshii OT3

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)
C	d1v4pc_	Alpha and beta proteins (a+b)	RRF/tRNA synthetase additional domain-like	ThrRS/AlaRS common domain	AlaX-like	Hypothetical protein PH0574	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B	d1v4pb_	Alpha and beta proteins (a+b)	RRF/tRNA synthetase additional domain-like	ThrRS/AlaRS common domain	AlaX-like	Hypothetical protein PH0574	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
A	d1v4pa_	Alpha and beta proteins (a+b)	RRF/tRNA synthetase additional domain-like	ThrRS/AlaRS common domain	AlaX-like	Hypothetical protein PH0574	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	ThrRS/AlaRS editing domain-like	8042986	3001504	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ThrRS/AlaRS editing domain-like	8042986	3001504	SCOP2B (2022-06-29)
A	SCOP2 Family	AlaX-like	8030607	4001430	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ThrRS/AlaRS editing domain-like	8042986	3001504	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)
C	tRNA_SAD	e1v4pC1	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_SAD	e1v4pB1	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_SAD	e1v4pA1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.980.10	Alpha Beta	2-Layer Sandwich	Threonyl-tRNA Synthetase	Chain A, domain 2	CATH (4.3.0)
C	3.30.54.20	Alpha Beta	2-Layer Sandwich	Replication Terminator Protein	Chain A, domain 2	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	3.30.54.20	Alpha Beta	2-Layer Sandwich	Replication Terminator Protein	Chain A, domain 2	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	3.30.54.20	Alpha Beta	2-Layer Sandwich	Replication Terminator Protein	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	alanyl-tRNA synthetase	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 aminoacyl-tRNA deacylase activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid deacylase activity carboxylic ester hydrolase activity hydrolase activity catalytic activity, acting on a tRNA catalytic activity ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity ligase activity cation binding metal ion binding	amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR018163	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily	Homologous Superfamily
A, B, C	IPR012947	Threonyl/alanyl tRNA synthetase, SAD	Domain
A, B, C	IPR051335	Alanyl-tRNA Editing Enzymes	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.