4H02 | pdb_00004h02

Crystal structure of P. falciparum Lysyl-tRNA synthetase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
H	d4h02h1	All beta proteins	OB-fold	Nucleic acid-binding proteins	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
H	d4h02h2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
G	d4h02g1	All beta proteins	OB-fold	Nucleic acid-binding proteins	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
G	d4h02g2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
F	d4h02f1	All beta proteins	OB-fold	Nucleic acid-binding proteins	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
F	d4h02f2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
E	d4h02e1	All beta proteins	OB-fold	Nucleic acid-binding proteins	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
E	d4h02e2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
D	d4h02d1	All beta proteins	OB-fold	Nucleic acid-binding proteins	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
D	d4h02d2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
C	d4h02c1	All beta proteins	OB-fold	Nucleic acid-binding proteins	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
C	d4h02c2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
B	d4h02b1	All beta proteins	OB-fold	Nucleic acid-binding proteins	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
B	d4h02b2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
A	d4h02a1	All beta proteins	OB-fold	Nucleic acid-binding proteins	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
A	d4h02a2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	RPA43_OB	e4h02H5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: RPA43_OB	ECOD (v294.1)
G	RPA43_OB	e4h02G5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: RPA43_OB	ECOD (v294.1)
F	RPA43_OB	e4h02F5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: RPA43_OB	ECOD (v294.1)
E	RPA43_OB	e4h02E5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: RPA43_OB	ECOD (v294.1)
D	RPA43_OB	e4h02D5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: RPA43_OB	ECOD (v294.1)
C	RPA43_OB	e4h02C5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: RPA43_OB	ECOD (v294.1)
B	RPA43_OB	e4h02B3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: RPA43_OB	ECOD (v294.1)
A	RPA43_OB	e4h02A5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: RPA43_OB	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
H	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
G	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
G	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
F	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
F	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
E	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
E	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
D	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
D	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	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, G, H	PF00152	tRNA synthetases class II (D, K and N) (tRNA-synt_2)	tRNA synthetases class II (D, K and N)		Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF01336	OB-fold nucleic acid binding domain (tRNA_anti-codon)	OB-fold nucleic acid binding domain	This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an am ...	This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family [2,3]. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.	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, G, H	Lysyl-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 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 lysine-tRNA ligase activity catalytic activity ligase activity RNA binding tRNA binding nucleic acid binding	nucleoside phosphate metabolic process nucleotide biosynthetic process primary metabolic process diadenosine polyphosphate metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process diadenosine polyphosphate biosynthetic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process nucleotide biosynthetic process primary metabolic process diadenosine polyphosphate metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process diadenosine polyphosphate biosynthetic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process diadenosine tetraphosphate biosynthetic process lysyl-tRNA aminoacylation amino acid activation tRNA aminoacylation RNA 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 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, G, H	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, G, H	IPR034762	Bacterial/eukaryotic lysine-tRNA ligase, class II	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR004365	OB-fold nucleic acid binding domain, AA-tRNA synthetase-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018149	Lysyl-tRNA synthetase, class II, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR004364	Aminoacyl-tRNA synthetase, class II (D/K/N)	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR002313	Lysine-tRNA ligase, class II	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR044136	Lysine-tRNA ligase, class II, N-terminal	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.