2I4M

Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with ProAMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Two Bacterial Prolyl-tRNA Synthetases with and without a cis-Editing Domain.

Crepin, T.Yaremchuk, A.Tukalo, M.Cusack, S.

(2006) Structure 14: 1511-1525

  • DOI: 10.1016/j.str.2006.08.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Prolyl-tRNA synthetases (ProRSs) are unique among synthetases in that they have diverse architectures, notably the variable presence of a cis-editing domain homologous to the freestanding deacylase proteins YbaK and ProX. Here, we describe crystal st ...

    Prolyl-tRNA synthetases (ProRSs) are unique among synthetases in that they have diverse architectures, notably the variable presence of a cis-editing domain homologous to the freestanding deacylase proteins YbaK and ProX. Here, we describe crystal structures of two bacterial ProRSs from the pathogen Enterococcus faecalis, which possesses an editing domain, and from Rhodopseudomonas palustris, which does not. We compare the overall structure and binding mode of ATP and prolyl-adenylate with those of the archael/eukaryote-type ProRS from Thermus thermophilus. Although structurally more homologous to YbaK, which preferentially hydrolyzes Cys-tRNA(Pro), the editing domain of E. faecalis ProRS possesses key elements similar to ProX, with which it shares the activity of hydrolyzing Ala-tRNA(Pro). The structures give insight into the complex evolution of ProRSs, the mechanism of editing, and structural differences between prokaryotic- and eukaryotic-type ProRSs that can be exploited for antibiotic design.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proline-tRNA ligase
A, B, C
458Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)Mutation(s): 0 
Gene Names: proS
EC: 6.1.1.15
Find proteins for Q6N5P6 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Go to UniProtKB:  Q6N5P6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PSD
Query on PSD

Download SDF File 
Download CCD File 
B, C
5'-O-[N-(PROLYL)-SULFAMOYL]ADENOSINE
C15 H22 N7 O7 P
BIVNOVXAWQKFMF-JVEUSOJLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 110.360α = 90.00
b = 211.900β = 90.00
c = 150.200γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
REFMACrefinement
XSCALEdata scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2008-05-05
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance