1U24

Crystal structure of Selenomonas ruminantium phytase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of Selenomonas ruminantium Phytase in Complex with Persulfated Phytate; DSP Phytase Fold and Mechanism for Sequential Substrate Hydrolysis

Chu, H.M.Guo, R.T.Lin, T.W.Chou, C.C.Shr, H.L.Lai, H.L.Tang, T.Y.Cheng, K.J.Selinger, B.L.Wang, A.H.-J.

(2004) Structure 12: 2015-2024

  • DOI: https://doi.org/10.1016/j.str.2004.08.010
  • Primary Citation of Related Structures:  
    1U24, 1U25, 1U26

  • PubMed Abstract: 

    Various inositide phosphatases participate in the regulation of inositol polyphosphate signaling molecules. Plant phytases are phosphatases that hydrolyze phytate to less-phosphorylated myo-inositol derivatives and phosphate. The phytase from Selenomonas ruminantium shares no sequence homology with other microbial phytases. Its crystal structure revealed a phytase fold of the dual-specificity phosphatase type. The active site is located near a conserved cysteine-containing (Cys241) P loop. We also solved two other crystal forms in which an inhibitor, myo-inositol hexasulfate, is cocrystallized with the enzyme. In the "standby" and the "inhibited" crystal forms, the inhibitor is bound, respectively, in a pocket slightly away from Cys241 and at the substrate binding site where the phosphate group to be hydrolyzed is held close to the -SH group of Cys241. Our structural and mutagenesis studies allow us to visualize the way in which the P loop-containing phytase attracts and hydrolyzes the substrate (phytate) sequentially.


  • Organizational Affiliation

    Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
myo-inositol hexaphosphate phosphohydrolase
A, B
337Selenomonas ruminantiumMutation(s): 6 
EC: 3.1.3.72
UniProt
Find proteins for Q7WUJ1 (Selenomonas ruminantium)
Explore Q7WUJ1 
Go to UniProtKB:  Q7WUJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7WUJ1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.469α = 90
b = 140.378β = 102.85
c = 80.68γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance