2ZVR

Crystal structure of a D-tagatose 3-epimerase-related protein from Thermotoga maritima


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a D-tagatose 3-epimerase-related protein from the hyperthermophilic bacterium Thermotoga maritima

Sakuraba, H.Yoneda, K.Satomura, T.Kawakami, R.Ohshima, T.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 199-203

  • DOI: 10.1107/S1744309109002115
  • Primary Citation of Related Structures:  
    2ZVR

  • PubMed Abstract: 
  • The crystal structure of a D-tagatose 3-epimerase-related protein (TM0416p) encoded by the hypothetical open reading frame TM0416 in the genome of the hyperthermophilic bacterium Thermotoga maritima was determined at a resolution of 2.2 A. The asymme ...

    The crystal structure of a D-tagatose 3-epimerase-related protein (TM0416p) encoded by the hypothetical open reading frame TM0416 in the genome of the hyperthermophilic bacterium Thermotoga maritima was determined at a resolution of 2.2 A. The asymmetric unit contained two homologous subunits and a dimer was generated by twofold symmetry. The main-chain coordinates of the enzyme monomer proved to be similar to those of D-tagatose 3-epimerase from Pseudomonas cichorii and D-psicose 3-epimerase from Agrobacterium tumefaciens; however, TM0416p exhibited a unique solvent-accessible substrate-binding pocket that reflected the absence of an alpha-helix that covers the active-site cleft in the two aforementioned ketohexose 3-epimerases. In addition, the residues responsible for creating a hydrophobic environment around the substrate in TM0416p differ entirely from those in the other two enzymes. Collectively, these findings suggest that the substrate specificity of TM0416p is likely to differ substantially from those of other D-tagatose 3-epimerase family enzymes.


    Organizational Affiliation

    Department of Applied Biological Science, Kagawa University, Ikenobe, Miki-cho, Kita-gun, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein TM_0416AB290Thermotoga maritimaMutation(s): 0 
Gene Names: TM_0416
EC: 5.1.3 (UniProt), 5.3.1 (UniProt)
Find proteins for Q9WYP7 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Explore Q9WYP7 
Go to UniProtKB:  Q9WYP7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.245α = 107.14
b = 55.211β = 102.71
c = 58.714γ = 91.54
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-25
    Changes: Database references