3GKK

Insights into the Alkyl Peroxide Reduction Activity of Xanthomonas campestris Bacterioferritin Comigratory Protein from the Trapped Intermediate/Ligand Complex Structures


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into the alkyl peroxide reduction pathway of Xanthomonas campestris bacterioferritin comigratory protein from the trapped intermediate-ligand complex structures

Liao, S.-J.Yang, C.-Y.Chin, K.-H.Wang, A.H.-J.Chou, S.-H.

(2009) J Mol Biol 390: 951-966

  • DOI: 10.1016/j.jmb.2009.05.030
  • Primary Citation of Related Structures:  
    3GKK, 3GKM, 3GKN

  • PubMed Abstract: 
  • Considerable insights into the oxidoreduction activity of the Xanthomonas campestris bacterioferritin comigratory protein (XcBCP) have been obtained from trapped intermediate/ligand complex structures determined by X-ray crystallography. Multiple sequence alignment and enzyme assay indicate that XcBCP belongs to a subfamily of atypical 2-Cys peroxiredoxins (Prxs), containing a strictly conserved peroxidatic cysteine (C(P)48) and an unconserved resolving cysteine (C(R)84) ...

    Considerable insights into the oxidoreduction activity of the Xanthomonas campestris bacterioferritin comigratory protein (XcBCP) have been obtained from trapped intermediate/ligand complex structures determined by X-ray crystallography. Multiple sequence alignment and enzyme assay indicate that XcBCP belongs to a subfamily of atypical 2-Cys peroxiredoxins (Prxs), containing a strictly conserved peroxidatic cysteine (C(P)48) and an unconserved resolving cysteine (C(R)84). Crystals at different states, i.e. Free_SH state, Intra_SS state, and Inter_SS state, were obtained by screening the XcBCP proteins from a double C48S/C84S mutant, a wild type, and a C48A mutant, respectively. A formate or an alkyl analog with two water molecules that mimic an alkyl peroxide substrate was found close to the active site of the Free_SH or Inter_SS state, respectively. Their global structures were found to contain a novel substrate-binding pocket capable of accommodating an alkyl chain of no less than 16 carbons. In addition, in the Intra_SS or Inter_SS state, substantial local unfolding or complete unfolding of the C(R)-helix was detected, with the C(P)-helix remaining essentially unchanged. This is in contrast to the earlier observation that the C(P)-helix exhibits local unfolding during disulfide bond formation in typical 2-Cys Prxs. These rich experimental data have enabled us to propose a pathway by which XcBCP carries out its oxidoreduction activity through the alternate opening and closing of the substrate entry channel and the disulfide-bond pocket.


    Organizational Affiliation

    Institute of Biochemistry, National Chung-Hsing University, Taichung, Taiwan, ROC.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bacterioferritin comigratory proteinA163Xanthomonas campestris pv. campestrisMutation(s): 0 
Gene Names: bcp
EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
Find proteins for Q8P9V9 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25))
Explore Q8P9V9 
Go to UniProtKB:  Q8P9V9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.835α = 90
b = 54.646β = 108.23
c = 36.645γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-03-11 
  • Released Date: 2009-06-16 
  • Deposition Author(s): Liao, S.-J.

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: 2017-11-01
    Changes: Refinement description