2E1B

Crystal structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii

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)
A	d2e1ba1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	AlaX-M N-terminal domain-like	AlaX-M trans-editing enzyme, N-terminal domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
A	d2e1ba2	Alpha and beta proteins (a+b)	RRF/tRNA synthetase additional domain-like	ThrRS/AlaRS common domain	AlaX-like	AlaX-M trans-editing enzyme, C-terminal domain	(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)
A	SCOP2 Family	AlaX-like	8021461	4001430	SCOP2 (2022-06-29)
A	SCOP2 Family	AlaX-M N-terminal domain-like	8021460	4001789	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ThrRS/AlaRS editing domain-like	8033841	3001504	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Translational proteins	8033840	3000811	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)
A	PF01411	e2e1bA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PF01411	ECOD (1.6)
A	PF07973	e2e1bA2	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: PF07973	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.30.130	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01411	tRNA synthetases class II (A) (tRNA-synt_2c)	tRNA synthetases class II (A)	-	Family
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	216aa long hypothetical alanyl-tRNA synthetase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding nucleic acid binding ligase activity, forming carbon-oxygen bonds alanine-tRNA ligase activity 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 cation binding metal ion binding hydrolase activity, acting on ester bonds carboxylic ester hydrolase activity aminoacyl-tRNA editing activity hydrolase activity	amino acid activation tRNA aminoacylation cellular biosynthetic process organonitrogen compound biosynthetic process RNA metabolic process amino acid metabolic process nucleobase-containing compound metabolic process organic substance metabolic process alanyl-tRNA aminoacylation organic substance biosynthetic process protein metabolic process organonitrogen compound metabolic process cellular metabolic process primary metabolic process amino acid activation tRNA aminoacylation cellular biosynthetic process organonitrogen compound biosynthetic process RNA metabolic process amino acid metabolic process nucleobase-containing compound metabolic process organic substance metabolic process alanyl-tRNA aminoacylation organic substance biosynthetic process protein metabolic process organonitrogen compound metabolic process cellular metabolic process primary metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process biosynthetic process ncRNA metabolic process metabolic process cellular process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR018164	Alanyl-tRNA synthetase, class IIc, N-terminal	Domain
A	IPR018163	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily	Homologous Superfamily
A	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A	IPR012947	Threonyl/alanyl tRNA synthetase, SAD	Domain
A	IPR018165	Alanyl-tRNA synthetase, class IIc, core domain	Domain

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 R01GM133198.