1U26 | pdb_00001u26

Crystal structure of Selenomonas ruminantium phytase complexed with persulfated phytate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.260 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.215 (DCC) 

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This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 79.15 kDa 
  • Atom Count: 5,889 
  • Modeled Residue Count: 627 
  • Deposited Residue Count: 674 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
myo-inositol hexaphosphate phosphohydrolase
A, B
337Selenomonas ruminantiumMutation(s): 0 
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.260 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.215 (DCC) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.301α = 90
b = 101.923β = 90
c = 46.06γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
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
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations