2AQ6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.,Sect.D 61: 1492-1499

  • DOI: 10.1107/S0907444905026673
  • Primary Citation of Related Structures:  

  • 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 refin ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRIDOXINE 5'-PHOSPHATE OXIDASE
A, B
147Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
EC: 1.-.-.-
Find proteins for O06553 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  O06553
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.870α = 90.00
b = 55.350β = 107.77
c = 54.520γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
SCALEPACKdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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