2H6B

Crystal structure of oxidized CprK in complex with o-chlorophenolacetic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

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This is version 1.2 of the entry. See complete history


Literature

CprK Crystal Structures Reveal Mechanism for Transcriptional Control of Halorespiration.

Joyce, M.G.Levy, C.Pop, S.M.Biehl, B.D.Doukov, T.I.Ryter, J.M.Mazon, H.Smidt, H.van den Heuvel, R.H.Ragsdale, S.W.van der Oost, J.Leys, D.

(2006) J Biol Chem 281: 28318-28325

  • DOI: 10.1074/jbc.M602654200
  • Primary Citation of Related Structures:  
    2H6B, 2H6C

  • PubMed Abstract: 
  • Halorespiration is a bacterial respiratory process in which haloorganic compounds act as terminal electron acceptors. This process is controlled at transcriptional level by CprK, a member of the ubiquitous CRP-FNR family. Here we present the crystal structures of oxidized CprK in presence of the ligand ortho-chlorophenolacetic acid and of reduced CprK in absence of this ligand ...

    Halorespiration is a bacterial respiratory process in which haloorganic compounds act as terminal electron acceptors. This process is controlled at transcriptional level by CprK, a member of the ubiquitous CRP-FNR family. Here we present the crystal structures of oxidized CprK in presence of the ligand ortho-chlorophenolacetic acid and of reduced CprK in absence of this ligand. These structures reveal that highly specific binding of chlorinated, rather than the corresponding non-chlorinated, phenolic compounds in the NH(2)-terminal beta-barrels causes reorientation of these domains with respect to the central alpha-helix at the dimer interface. Unexpectedly, the COOH-terminal DNA-binding domains dimerize in the non-DNA binding state. We postulate the ligand-induced conformational change allows formation of interdomain contacts that disrupt the DNA domain dimer interface and leads to repositioning of the helix-turn-helix motifs. These structures provide a structural framework for further studies on transcriptional control by CRP-FNR homologs in general and of halorespiration regulation by CprK in particular.


    Organizational Affiliation

    Manchester Interdisciplinary Biocentre, P. O. Box 88, Manchester, M60 1QD, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ChloroPhenol Reduction gene KA, B250Desulfitobacterium hafnienseMutation(s): 0 
UniProt
Find proteins for Q8RPJ2 (Desulfitobacterium hafniense)
Explore Q8RPJ2 
Go to UniProtKB:  Q8RPJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RPJ2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3C4
Query on 3C4

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
(3-CHLORO-4-HYDROXYPHENYL)ACETIC ACID
C8 H7 Cl O3
IYTUKSIOQKTZEG-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3C4 PDBBind:  2H6B Kd: 4100 (nM) from 1 assay(s)
Binding MOAD:  2H6B Kd: 4100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.437α = 90
b = 112.185β = 90
c = 119.495γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance