2C1H

The X-ray Structure of Chlorobium vibrioforme 5-Aminolaevulinic Acid Dehydratase Complexed with a Diacid Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.263 

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This is version 1.2 of the entry. See complete history


Literature

Structure of Chlorobium Vibrioforme 5-Aminolaevulinic Acid Dehydratase Complexed with a Diacid Inhibitor.

Coates, L.Beaven, G.Erskine, P.T.Beale, S.Wood, S.P.Shoolingin-Jordan, P.M.Cooper, J.B.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1594

  • DOI: 10.1107/S0907444905030350
  • Primary Citation of Related Structures:  
    2C1H

  • PubMed Abstract: 
  • The structure of Chlorobium vibrioforme 5-aminolaevulinic acid dehydratase (ALAD) complexed with the irreversible inhibitor 4,7-dioxosebacic acid has been solved. The inhibitor binds by forming Schiff-base linkages with lysines 200 and 253 at the active site ...

    The structure of Chlorobium vibrioforme 5-aminolaevulinic acid dehydratase (ALAD) complexed with the irreversible inhibitor 4,7-dioxosebacic acid has been solved. The inhibitor binds by forming Schiff-base linkages with lysines 200 and 253 at the active site. The structure reported here provides a definition of the interactions made by both of the substrate molecules (A-side and P-side substrates) with the C. vibrioforme ALAD and is compared and contrasted with structures of the same inhibitor bound to Escherichia coli and yeast ALAD. The structure suggests why 4,7-dioxosebacic acid is a better inhibitor of the zinc-dependent ALADs than of the zinc-independent ALADs.


    Organizational Affiliation

    Bioscience Division, Los Alamos National Laboratory, NM 87545, USA. lcoates@lanl.gov



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DELTA-AMINOLEVULINIC ACID DEHYDRATASEA, B328Prosthecochloris vibrioformisMutation(s): 0 
EC: 4.2.1.24
UniProt
Find proteins for Q59334 (Chlorobaculum parvum (strain DSM 263 / NCIMB 8327))
Explore Q59334 
Go to UniProtKB:  Q59334
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59334
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DSB
Query on DSB

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
4,7-DIOXOSEBACIC ACID
C10 H14 O6
DUAWJQCMZICMIK-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.263 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.48α = 90
b = 126.48β = 90
c = 81.85γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance