Crystal structure of the conserved hypothetical protein Rv2074 from Mycobacterium tuberculosis 1.6 A

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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The molecular structure of Rv2074, a probable pyridoxine 5'-phosphate oxidase from Mycobacterium tuberculosis, at 1.6 angstroms resolution.

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

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 735-742

  • DOI: https://doi.org/10.1107/S1744309106025012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of a conserved hypothetical protein corresponding to open reading frame Rv2074 from Mycobacterium tuberculosis (Mtb) has been solved by the two-wavelength anomalous dispersion method. Refinement of the molecular structure at 1.6 angstroms resolution resulted in an R(work) of 0.178 and an R(free) of 0.204. The crystal asymmetric unit contains an Rv2074 monomer; however, the crystallographic twofold symmetry operation of space group P4(3)2(1)2 generates dimeric Rv2074. Each monomer folds into a six-stranded antiparallel beta-barrel flanked by two alpha-helices. The three-dimensional structure of Rv2074 is very similar to that of Mtb Rv1155, a probable pyridoxine 5'-phosphate oxidase (PNPOx), which corroborates well with the relatively high sequence similarity (52%) between the two. A structural comparison between Rv2074 and Rv1155 revealed that the core structure (a six-stranded beta-barrel) is also well conserved; the major differences between the two lie in the N- and C-termini and in the small helical domain. Two citric acid molecules were observed in the active site of Rv2074, the crystals of which were grown in 0.2 M sodium citrate buffer pH 5.0. The citric acid molecules are bound to Rv2074 by hydrogen-bonding interactions with Thr55, Gln60 and Lys61. One of the two citric acid molecules occupies the same spatial position that corresponds to the position of the phosphate and ribose sugar moieties of the flavin mononucleotide (FMN) in the Mtb Rv1155-FMN, Escherichia coli PNPOx-FMN and human PNPOx-FMN complex structures. Owing to its extensive structural similarity with Mtb Rv1155 and to the E. coli and human PNPOx enzymes, Rv2074 may be involved in the final step in the biosynthesis of pyridoxal 5'-phosphate (PLP; a vitamin B6).

  • Organizational Affiliation

    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
Hypothetical protein Rv2074137Mycobacterium tuberculosisMutation(s): 2 
Find proteins for P9WLL7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WLL7 
Go to UniProtKB:  P9WLL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WLL7
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.395α = 90
b = 73.395β = 90
c = 44.794γ = 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: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance