1WV4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.,Sect.D 61: 599-604

  • DOI: 10.1107/S0907444905005512

  • 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( ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyridoxamine 5'-phosphate oxidase
A, B
218Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pdxH
EC: 1.4.3.5
Find proteins for P0AFI7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFI7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FMN
Query on FMN

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Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.242 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 54.420α = 90.00
b = 54.420β = 90.00
c = 164.420γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
bioteXdata reduction
bioteXdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description