X-ray crystal structure of mycobacterium tuberculosis pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 1.7 a resolution

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

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Structures of Mycobacterium tuberculosispyridoxine 5'-phosphate oxidase and its complexes with flavin mononucleotide and pyridoxal 5'-phosphate.

Biswal, B.K.Cherney, M.M.Wang, M.Garen, C.James, M.N.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1492-1499

  • DOI: https://doi.org/10.1107/S0907444905026673
  • Primary Citation of Related Structures:  
    1Y30, 2AQ6

  • PubMed Abstract: 

    The X-ray crystal structure of a conserved hypothetical protein of molecular weight 16.3 kDa from Mycobacterium tuberculosis corresponding to open reading frame (ORF) Rv1155 has been solved by the multiwavelength anomalous dispersion method and refined at 1.8 A resolution. The crystal structure revealed that Rv1155 is a dimer in the crystal and that each monomer folds into a large and a small domain; the large domain is a six-stranded antiparallel beta-barrel flanked by two small alpha-helices and the small domain is a helix-loop-helix motif. The dimer interface is formed by residues protruding primarily from five of the six beta-strands in each subunit. Based on structural similarity and on ligand binding, it has been established that Rv1155 is a pyridoxine 5'-phosphate oxidase, the Escherichia coli and human counterparts of which catalyse the terminal step in the biosynthesis of pyridoxal 5'-phosphate (PLP), a cofactor used by many enzymes involved in amino-acid metabolism. The structures of flavin mononucleotide (FMN) and pyridoxal 5'-phosphate (PLP) bound separately to Rv1155 have been determined at 2.2 and 1.7 A resolution, respectively. Only one monomer binds non-covalently to one FMN molecule or to one PLP molecule. Arg55 and Lys57 are the key residues making hydrogen bonds and ionic interactions with the phosphate and ribose groups of the FMN molecule, whereas Arg55 and Arg129 provide hydrogen bonds and ionic interactions with the phosphate group of the PLP. Structural comparisons of Rv1155 from M. tuberculosis with its E. coli and human counterparts demonstrate that the core structure is highly conserved and the FMN-binding site is similarly disposed in each of the structures.

  • Organizational Affiliation

    CIHR Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton T6G 2H7, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
147Mycobacterium tuberculosisMutation(s): 0 
Gene Names: Rv1155
EC: 1
Find proteins for O06553 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O06553 
Go to UniProtKB:  O06553
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06553
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PLP

Download Ideal Coordinates CCD File 
C8 H10 N O6 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.87α = 90
b = 55.35β = 107.77
c = 54.52γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance