1WV4

X-ray Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in tetragonal crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 

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This is version 1.4 of the entry. See complete history


Literature

Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme.

Safo, M.K.Musayev, F.N.Schirch, V.

(2005) Acta Crystallogr D Biol Crystallogr 61: 599-604

  • DOI: https://doi.org/10.1107/S0907444905005512
  • Primary Citation of Related Structures:  
    1WV4

  • PubMed Abstract: 

    Escherichia coli pyridoxine 5'-phosphate oxidase (ePNPOx) catalyzes the terminal step in the biosynthesis of pyridoxal 5'-phosphate (PLP) by the FMN oxidation of pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP), forming FMNH(2) and H(2)O(2). The crystal structure of ePNPOx is reported in a tetragonal unit cell at 2.6 A resolution. The three-dimensional fold of this structure is very similar to those of the E. coli and human enzymes that crystallized in trigonal and monoclinic unit cells. However, unlike the previous structures, the tetragonal structure shows major disorder in one of the two subunit domains that has opened up both the active site and a putative tunnel. Comparison of these structures gives an insight into the mechanistic pathway of PNPOx: from the resting enzyme with no substrate bound, to the initial binding of the substrate at the active site, to the catalytic stage and to the release of the catalytic product from the active site.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23219, USA. msafo@mail2.vcu.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxamine 5'-phosphate oxidase
A, B
218Escherichia coliMutation(s): 0 
EC: 1.4.3.5
UniProt
Find proteins for P0AFI7 (Escherichia coli (strain K12))
Explore P0AFI7 
Go to UniProtKB:  P0AFI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFI7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.42α = 90
b = 54.42β = 90
c = 164.42γ = 90
Software Package:
Software NamePurpose
CNSrefinement
bioteXdata reduction
bioteXdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description