3HCG

Structure of the C-terminal domain (MsrB) of Neisseria meningitidis PilB (reduced form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Methionine sulfoxide reductase B displays a high level of flexibility.

Ranaivoson, F.M.Neiers, F.Kauffmann, B.Boschi-Muller, S.Branlant, G.Favier, F.

(2009) J.Mol.Biol. 394: 83-93

  • DOI: 10.1016/j.jmb.2009.08.073
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Methionine sulfoxide reductases (Msrs) are enzymes that catalyze the reduction of methionine sulfoxide back to methionine. In vivo, Msrs are essential in the protection of cells against oxidative damage to proteins and in the virulence of some bacter ...

    Methionine sulfoxide reductases (Msrs) are enzymes that catalyze the reduction of methionine sulfoxide back to methionine. In vivo, Msrs are essential in the protection of cells against oxidative damage to proteins and in the virulence of some bacteria. Two structurally unrelated classes of Msrs, named MsrA and MsrB, exist. MsrB are stereospecific to R epimer on the sulfur of sulfoxide. All MsrB share a common reductase step with the formation of a sulfenic acid intermediate. For the subclass of MsrB whose recycling process passes through the formation of an intradisulfide bond, the recycling reducer is thioredoxin. In the present study, X-ray structures of Neisseria meningitidis MsrB have been determined. The structures have a fold based on two beta-sheets, similar to the fold already described for other MsrB, with the recycling Cys63 located in a position favorable for disulfide bond formation with the catalytic Cys117. X-ray structures of Xanthomonas campestris MsrB have also been determined. In the C117S MsrB structure with a bound substrate, the recycling Cys31 is far from Ser117, with Trp65 being essential in the reductase step located in between. This positioning prevents the formation of the Cys31-Cys117 disulfide bond. In the oxidized structure, a drastic conformational reorganization of the two beta-sheets due to withdrawal of the Trp65 region from the active site, which remains compatible with an efficient thioredoxin-recycling process, is observed. The results highlight the remarkable structural malleability of the MsrB fold.


    Related Citations: 
    • Crystallization and preliminary X-ray diffraction studies of the peptide methionine sulfoxide reductase B domain of Neisseria meningitidis PILB.
      Kauffmann, B.,Favier, F.,Olry, A.,Boschi-Muller, S.,Carpentier, P.,Branlant, G.,Aubry, A.
      (2002) Acta Crystallogr.,Sect.D 58: 1467


    Organizational Affiliation

    CRM2, Equipe Biocristallographie, UMR 7036 CNRS-UHP, Institut Jean Barriol, Nancy Université, Faculté des Sciences et Techniques, BP 70239, 54506 Vandoeuvre-les-Nancy, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide methionine sulfoxide reductase msrA/msrB
A, B, C, D
146Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)Gene Names: msrAB (pilB)
EC: 1.8.4.11, 1.8.4.12
Find proteins for Q9JWM8 (Neisseria meningitidis serogroup A / serotype 4A (strain Z2491))
Go to UniProtKB:  Q9JWM8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.663α = 90.00
b = 117.232β = 90.00
c = 137.686γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
Xnemodata collection
SnBphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-04-09
    Type: Database references