3BB0

Crystal Structure of a Trapped Phosphate-Intermediate in Vanadium Apochloroperoxidase Catalyzing a Dephosphorylation Reaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a trapped phosphate intermediate in vanadium apochloroperoxidase catalyzing a dephosphorylation reaction

Macedo-Ribeiro, S.Renirie, R.Wever, R.Messerschmidt, A.

(2008) Biochemistry 47: 929-934

  • DOI: 10.1021/bi7018628
  • Primary Citation of Related Structures:  
    3BB0

  • PubMed Abstract: 
  • The crystal structure of the apo form of vanadium chloroperoxidase from Curvularia inaequalis reacted with para-nitrophenylphosphate was determined at a resolution of 1.5 A. The aim of this study was to solve structural details of the dephosphorylation reaction catalyzed by this enzyme ...

    The crystal structure of the apo form of vanadium chloroperoxidase from Curvularia inaequalis reacted with para-nitrophenylphosphate was determined at a resolution of 1.5 A. The aim of this study was to solve structural details of the dephosphorylation reaction catalyzed by this enzyme. Since the chloroperoxidase is functionally and evolutionary related to several acid phosphatases including human glucose-6-phosphatase and a group of membrane-bound lipid phosphatases, the structure sheds light on the details of the dephosphorylation catalyzed by these enzymes as well. The trapped intermediate found is bound to the active site as a metaphosphate anion PO3-, with its phosphorus atom covalently attached to the Nepsilon2 atom of His496. An apical water molecule is within hydrogen-bonding distance to the phosphorus atom of the metaphosphate, and it is in a perfect position for a nucleophilic attack on the metaphosphate-histidine intermediate to form the inorganic phosphate. This is, to our knowledge, the first structural characterization of a real reaction intermediate of the inorganic phosphate group release in a dephosphorylation reaction.


    Related Citations: 
    • X-ray structure of a vanadium-containing enzyme: chloroperoxidase from the fungus Curvularia inaequalis
      Messerschmidt, A., Wever, R.
      (1996) Proc Natl Acad Sci U S A 93: 392
    • X-ray crystal structures of active site mutants of the vanadium-containing chloroperoxidase from the fungus Curvularia inaequalis
      Macedo-Ribeiro, S., Hemrika, W., Renirie, R., Wever, R., Messerschmidt, A.
      (1999) J Biol Inorg Chem 4: 209

    Organizational Affiliation

    Abteilung Proteomics und Signaltransduktion, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, 82152 Martinsried, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vanadium chloroperoxidaseA609Curvularia inaequalisMutation(s): 0 
Gene Names: CPO
EC: 1.11.1.10
Find proteins for P49053 (Curvularia inaequalis)
Explore P49053 
Go to UniProtKB:  P49053
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PO3
Query on PO3

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHITE ION
O3 P
AQSJGOWTSHOLKH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.06α = 90
b = 128.06β = 90
c = 103.31γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description