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 

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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 asymmetric unit contained two homologous subunits and a dimer was generated by twofold symmetry ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein TM_0416A, B290Thermotoga maritimaMutation(s): 0 
Gene Names: TM_0416
EC: 5.1.3 (UniProt), 5.3.1 (UniProt)
UniProt
Find proteins for Q9WYP7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WYP7 
Go to UniProtKB:  Q9WYP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WYP7
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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