3WQY | pdb_00003wqy

Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with wild-type tRNA(Ala) having G3.U70

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)
B	tRNA-synt_2c_3rd	e3wqyB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: tRNA-synt_2c_3rd	ECOD (1.6)
B	A-tRNA_syn_arch	e3wqyB2	A: alpha bundles	X: C-terminal helical domain of alanine-tRNA ligase (From Homology)	H: C-terminal helical domain of alanine-tRNA ligase	T: Archaeal C-Ala helical domain	F: A-tRNA_syn_arch	ECOD (1.6)
B	tRNA-synt_2c_2nd	e3wqyB4	A: alpha complex topology	X: Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) (From Topology)	H: Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) (From Topology)	T: Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	F: tRNA-synt_2c_2nd	ECOD (1.6)
B	tRNA_SAD	e3wqyB3	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-synt_2c_1st	e3wqyB6	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2c_1st	ECOD (1.6)
B	DHHA1_1	e3wqyB5	A: a+b three layers	X: C-terminal domain in DHH phosphoesterases (From Topology)	H: C-terminal domain in DHH phosphoesterases (From Topology)	T: C-terminal domain in DHH phosphoesterases	F: DHHA1_1	ECOD (1.6)
A	tRNA-synt_2c_3rd	e3wqyA3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: tRNA-synt_2c_3rd	ECOD (1.6)
A	A-tRNA_syn_arch	e3wqyA6	A: alpha bundles	X: C-terminal helical domain of alanine-tRNA ligase (From Homology)	H: C-terminal helical domain of alanine-tRNA ligase	T: Archaeal C-Ala helical domain	F: A-tRNA_syn_arch	ECOD (1.6)
A	tRNA-synt_2c_2nd	e3wqyA2	A: alpha complex topology	X: Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) (From Topology)	H: Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) (From Topology)	T: Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	F: tRNA-synt_2c_2nd	ECOD (1.6)
A	tRNA_SAD	e3wqyA4	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-synt_2c_1st	e3wqyA1	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2c_1st	ECOD (1.6)
A	DHHA1_1	e3wqyA5	A: a+b three layers	X: C-terminal domain in DHH phosphoesterases (From Topology)	H: C-terminal domain in DHH phosphoesterases (From Topology)	T: C-terminal domain in DHH phosphoesterases	F: DHHA1_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (utative)
B	2.40.30.130	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (utative)
B	3.30.980.10	Alpha Beta	2-Layer Sandwich	Threonyl-tRNA Synthetase	Chain A, domain 2	CATH (utative)
B	3.30.54.20	Alpha Beta	2-Layer Sandwich	Replication Terminator Protein	Chain A, domain 2	CATH (utative)
B	3.10.310.40	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (utative)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (utative)
A	2.40.30.130	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (utative)
A	3.30.980.10	Alpha Beta	2-Layer Sandwich	Threonyl-tRNA Synthetase	Chain A, domain 2	CATH (utative)
A	3.30.54.20	Alpha Beta	2-Layer Sandwich	Replication Terminator Protein	Chain A, domain 2	CATH (utative)
A	3.10.310.40	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02272	DHHA1 domain (DHHA1)	DHHA1 domain	This domain is often found adjacent to the DHH domain Pfam:PF01368 and is called DHHA1 for DHH associated domain. This domain is diagnostic of DHH subfamily 1 members [1]. This domain is also found in alanyl tRNA synthetase e.g. Swiss:P00957, suggest ...	This domain is often found adjacent to the DHH domain Pfam:PF01368 and is called DHHA1 for DHH associated domain. This domain is diagnostic of DHH subfamily 1 members [1]. This domain is also found in alanyl tRNA synthetase e.g. Swiss:P00957, suggesting that this domain may have an RNA binding function. The domain is about 60 residues long and contains a conserved GG motif.	Domain
A, B	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, B	PF01411	tRNA synthetases class II (A) (tRNA-synt_2c)	tRNA synthetases class II (A)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	RNA (75-MER)	-	-	-
A, B	Alanine--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 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 alanine-tRNA ligase activity aminoacyl-tRNA ligase activity ligase activity cation binding transition metal ion binding zinc ion binding metal ion binding RNA binding tRNA binding nucleic acid binding identical protein binding protein 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 alanyl-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 alanyl-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	IPR022429	Alanine-tRNA ligase, archaea	Family
A, B	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B	IPR018164	Alanyl-tRNA synthetase, class IIc, N-terminal	Domain
A, B	IPR018162	Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily	Homologous Superfamily
A, B	IPR003156	DHHA1 domain	Domain
A, B	IPR012947	Threonyl/alanyl tRNA synthetase, SAD	Domain
A, B	IPR002318	Alanine-tRNA ligase, class IIc	Family
A, B	IPR050058	Alanine--tRNA ligase	Family
A, B	IPR018163	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily	Homologous Superfamily
A, B	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A, B	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 R01GM157729.