3HCH

Structure of the C-terminal domain (MsrB) of Neisseria meningitidis PilB (complex with substrate)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1016/j.jmb.2009.08.073
  • Primary Citation of Related Structures:  
    3HCG, 3HCH, 3HCI, 3HCJ

  • 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 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide methionine sulfoxide reductase msrA/msrB
A, B
146Neisseria meningitidis serogroup AMutation(s): 2 
Gene Names: msrABNMA0290pilB
EC: 1.8.4.12
UniProt
Find proteins for Q9JWM8 (Neisseria meningitidis serogroup A / serotype 4A (strain DSM 15465 / Z2491))
Explore Q9JWM8 
Go to UniProtKB:  Q9JWM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JWM8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
RSM
Query on RSM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B]
(2S)-2-(acetylamino)-N-methyl-4-[(R)-methylsulfinyl]butanamide
C8 H16 N2 O3 S
HOKSMYPIXLKSMM-JKYUHCHBSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
E [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
H [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.879α = 90
b = 154.879β = 90
c = 154.879γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-04-09
    Changes: Database references
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description