Literature summary for 6.1.1.6 extracted from

Bonnefond, L.; Castro de Moura, M.; Ribas de Pouplana, L.; Nureki, O.
Crystal structures of Entamoeba histolytica lysyl-tRNA synthetase reveal conformational changes upon lysine binding and a specific helix bundle domain (2014), FEBS Lett., 588, 4478-4486 .

Cloned(Commentary)

Cloned (Comment)	Organism
gene lysS, sequence comparisons, recombinant expression of N-terminally His6-tagged enzyme in Escherichia coli strain C41(DE3)	Entamoeba histolytica

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified enzyme free or in complex with ATP, Lys-AMP, or AMPPNP, hanging drop vapor diffusion method, mixing of 0.001 ml of protein solution with 0.001 ml of reservoir solution, the latter contains: for the free enzyme KRS 100 mM HEPES pH 7.5, 10% PEG 6000, and 5% 2-methyl-2,4-pentanediol, for the KRS-Lys-AMP crystals 50 mM HEPES, pH 8.0, 50 mM NaCl, 1 mM spermine, and 8% PEG 4000, for the KRS-ATP crystals 50 mM HEPES pH 8.0, 50 mM NaCl, 7.5% PEG 4000,and 1.2 mM spermine, and for the KRS-AMPPNP crystals 50 mM HEPES pH 8.0, 50 mM NaCl, 7.5% PEG 4000, and 1.2 mM spermine, 3 days, 20°C, X-ray diffraction structure determination and analysis at 2.80-3.05 A resolution, molecular replacement using HsKRS structure, PDB ID 3BJU, as the search model, modeling	Entamoeba histolytica

Crystallization (Comment)

Organism

purified enzyme free or in complex with ATP, Lys-AMP, or AMPPNP, hanging drop vapor diffusion method, mixing of 0.001 ml of protein solution with 0.001 ml of reservoir solution, the latter contains: for the free enzyme KRS 100 mM HEPES pH 7.5, 10% PEG 6000, and 5% 2-methyl-2,4-pentanediol, for the KRS-Lys-AMP crystals 50 mM HEPES, pH 8.0, 50 mM NaCl, 1 mM spermine, and 8% PEG 4000, for the KRS-ATP crystals 50 mM HEPES pH 8.0, 50 mM NaCl, 7.5% PEG 4000,and 1.2 mM spermine, and for the KRS-AMPPNP crystals 50 mM HEPES pH 8.0, 50 mM NaCl, 7.5% PEG 4000, and 1.2 mM spermine, 3 days, 20°C, X-ray diffraction structure determination and analysis at 2.80-3.05 A resolution, molecular replacement using HsKRS structure, PDB ID 3BJU, as the search model, modeling

Entamoeba histolytica

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Entamoeba histolytica

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
ATP + L-lysine + tRNALys	Entamoeba histolytica	-	AMP + diphosphate + L-lysyl-tRNALys	-	?

Organism

Organism	UniProt	Comment	Textmining
Entamoeba histolytica	C4M7X2	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged enzyme from Escherichia coli strain C41(DE3) by nickel affinity and heparin affinity chromatography, followed by gel filtration and ultrafiltration	Entamoeba histolytica

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
ATP + L-lysine + tRNALys	-	Entamoeba histolytica	AMP + diphosphate + L-lysyl-tRNALys	-	?
ATP + L-lysine + tRNALys	conformational changes in KRS structures upon lysine binding, structural basis of lysyl-adenylate formation, overview	Entamoeba histolytica	AMP + diphosphate + L-lysyl-tRNALys	-	?
additional information	binding strutcure analysis of enzyme KRS with ATP, AMP, Lys, and analogue AMPPNP	Entamoeba histolytica	?	-	?

Subunits

Subunits	Comment	Organism
homodimer	the enzyme consists of a N-terminal anticodon-binding domain (residues 1-137), a catalytic domain (residues 150-554), a linker (residues 563-580) and the C-terminal EELP (residues 603-769). The asymmetric unit contains one EhKRS monomer, and the active dimer is formed with the symmetric monomer in the 2fold axis	Entamoeba histolytica

Synonyms

Synonyms	Comment	Organism
class II lysyl-tRNA synthetase	-	Entamoeba histolytica
KRS	-	Entamoeba histolytica
Lysyl-tRNA synthetase	-	Entamoeba histolytica

Cofactor

Cofactor	Comment	Organism	Structure
ATP	binding structure analysis	Entamoeba histolytica

General Information

General Information	Comment	Organism
evolution	the enzyme belongs to the class II aminoacyl-tRNA synthetases	Entamoeba histolytica
additional information	the residues involved in lysine activation are highly conserved and the active site closes around the lysyl-adenylate. A small helix bundle may contribute to tRNA binding through interaction with the tRNA hinge, modeling, overview	Entamoeba histolytica
physiological function	class II lysyl-tRNA synthetases (KRS) attach lysine to the cognate tRNA in a two-step mechanism	Entamoeba histolytica