Active Site Structure of E. coli pyridoxine 5'-phosphate Oxidase

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

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Active site structure and stereospecificity of Escherichia coli pyridoxine-5'-phosphate oxidase.

di Salvo, M.L.Ko, T.P.Musayev, F.N.Raboni, S.Schirch, V.Safo, M.K.

(2002) J Mol Biol 315: 385-397

  • DOI: https://doi.org/10.1006/jmbi.2001.5254
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Pyridoxine-5'-phosphate oxidase catalyzes the oxidation of either the C4' alcohol group or amino group of the two substrates pyridoxine 5'-phosphate and pyridoxamine 5'-phosphate to an aldehyde, forming pyridoxal 5'-phosphate. A hydrogen atom is removed from C4' during the oxidation and a pair of electrons is transferred to tightly bound FMN. A new crystal form of the enzyme in complex with pyridoxal 5'-phosphate shows that the N-terminal segment of the protein folds over the active site to sequester the ligand from solvent during the catalytic cycle. Using (4'R)-[(3)H]PMP as substrate, nearly 100 % of the radiolabel appears in water after oxidation to pyridoxal 5'-phosphate. Thus, the enzyme is specific for removal of the proR hydrogen atom from the prochiral C4' carbon atom of pyridoxamine 5'-phosphate. Site mutants were made of all residues at the active site that interact with the oxygen atom or amine group on C4' of the substrates. Other residues that make interactions with the phosphate moiety of the substrate were mutated. The mutants showed a decrease in affinity, but exhibited considerable catalytic activity, showing that these residues are important for binding, but play a lesser role in catalysis. The exception is Arg197, which is important for both binding and catalysis. The R197 M mutant enzyme catalyzed removal of the proS hydrogen atom from (4'R)-[(3)H]PMP, showing that the guanidinium side-chain plays an important role in determining stereospecificity. The crystal structure and the stereospecificity studies suggests that the pair of electrons on C4' of the substrate are transferred to FMN as a hydride ion.

  • Organizational Affiliation

    A. Rossi Fanelli Dipartimento di Scienze Biochimiche, Centro di Biologia Molecolare del Consiglio Nazionale delle Ricerche, Università La Sapienza, Rome, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxine 5'-phosphate oxidase218Escherichia coliMutation(s): 5 
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
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.358α = 90
b = 52.238β = 101.45
c = 53.913γ = 90
Software Package:
Software NamePurpose
bioteXdata reduction
bioteXdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection