3E0O | pdb_00003e0o

Crystal structure of MsrB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.294 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3E0O

This is version 1.2 of the entry. See complete history

Literature

Structural and Kinetic Analysis of an MsrA-MsrB Fusion Protein from Streptococcus pneumoniae

Kim, Y.K.Shin, Y.J.Lee, W.-H.Kim, H.-Y.Hwang, K.Y.

(2009) Mol Microbiol 72: 699-709

  • DOI: https://doi.org/10.1111/j.1365-2958.2009.06680.x
  • Primary Citation Related Structures: 
    3E0M, 3E0O

  • PubMed Abstract: 

    Methionine sulphoxide reductases (Msr) catalyse the reduction of oxidized methionine to methionine. These enzymes are divided into two classes, MsrA and MsrB, according to substrate specificity. Although most MsrA and MsrB exist as separate enzymes, in some bacteria these two enzymes are fused to form a single polypeptide (MsrAB). Here, we report the first crystal structure of MsrAB from Streptococcus pneumoniae (SpMsrAB) at 2.4 A resolution. SpMsrAB consists of an N-terminal MsrA domain, a C-terminal MsrB domain and a linker. The linker is composed of 13 residues and contains one 3(10)-helix and several hydrogen bonds interacting with both MsrA and MsrB domains. Interestingly, our structure includes the MsrB domain complexed with an SHMAEI hexa-peptide that is the N-terminal region of neighbouring MsrA domain. A kinetic analysis showed that the apparent K(m) of SpMsrAB for the R-form-substrate was 20-fold lower than that for the S-form substrate, indicating that the MsrB domain had a much higher affinity for the substrate than the MsrA domain. Our study reveals the first structure of the MsrAB by providing insights into the formation of a disulphide bridge in the MsrB, the structure of the linker region, and the distinct structural nature of active site of each MsrA and MsrB domain.


  • Organizational Affiliation
    • Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea.

Macromolecule Content 

  • Total Structure Weight: 100.55 kDa 
  • Atom Count: 7,294 
  • Modeled Residue Count: 844 
  • Deposited Residue Count: 864 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptide methionine sulfoxide reductase msrB
A, B, C, D, E
A, B, C, D, E, F
144Bacillus subtilisMutation(s): 0 
Gene Names: msrByppQBSU21680
EC: 1.8.4.12
UniProt
Find proteins for P54155 (Bacillus subtilis (strain 168))
Explore P54155 
Go to UniProtKB:  P54155
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54155
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.294 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.114α = 90
b = 136.114β = 90
c = 61.925γ = 120
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references