ISDA

Deposition Date 2014-06-14

Release Date 2014-10-29

Last Version Date 2024-01-10

Entry Detail

PDB ID:

4UP7

Keywords:

LIGASE

Title:

Crystal structure of Entamoeba histolytica lysyl-tRNA synthetase in complex with lysyl-adenylate

Biological Source:

Source Organism:

ENTAMOEBA HISTOLYTICA (Taxon ID: 5759)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.79 Å

R-Value Free:

0.22

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

P 62

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:LYSINE--TRNA LIGASE
Gene (Uniprot):EHI_047810
Mutations:YES
Chain IDs:A
Chain Length:777
Number of Molecules:1
Biological Source:ENTAMOEBA HISTOLYTICA

UniProt ID:C4M7X2 Pfam ID:PF01336, PF00152, PF01588 EC:6.1.1.6

Ligand Molecules

LAD

Primary Citation

Crystal Structures of Entamoeba Histolytica Lysyl-tRNA Synthetase Reveal Conformational Changes Upon Lysine Binding and a Specific Helix Bundle Domain.

Bonnefond, L, Castro De Moura, M, Ribas De Pouplana, L, Nureki, O.Show

FEBS Lett. 588 4478 ? (2014)

PMID: 25448989 DOI: 10.1016/J.FEBSLET.2014.10.019

Abstact

The class II lysyl-tRNA synthetases (KRS) are conserved aminoacyl-tRNA synthetases that attach lysine to the cognate tRNA in a two-step mechanism. The enzyme from the parasitic protozoan Entamoeba histolytica was crystallized in the presence of small ligands to generate snapshots of the lysine-adenylate formation. The residues involved in lysine activation are highly conserved and the active site closes around the lysyl-adenylate, as observed in bacterial KRS. The Entamoeba EMAPII-like polypeptide is not resolved in the crystals, but another Entamoeba-specific insertion could be modeled as a small helix bundle that may contribute to tRNA binding through interaction with the tRNA hinge.

Legend

Protein

Chemical

Disease

Primary Citation of related structures