Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.35 kDa 
• Atom Count: 4381 
• Residue Count: 521 
• Unique protein chains: 1

2ZVR

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

• DOI: 10.2210/pdb2ZVR/pdb

• Classification: ISOMERASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-14 Released: 2009-03-10 
• Deposition Author(s): Sakuraba, H., Ohshima, T.

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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 

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

• PubMed: 19255464 
• DOI: 10.1107/S1744309109002115
• Structures With Same Primary Citation


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Uncharacterized protein TM_0416	A, B	290	Thermotoga maritima	Mutation(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)) Go to UniProtKB:  Q9WYP7

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 = 50.245	α = 107.14
b = 55.211	β = 102.71
c = 58.714	γ = 91.54

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-11-14 
• Released Date: 2009-03-10 
Deposition Author(s): Sakuraba, H., Ohshima, T.

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