1U25

Crystal structure of Selenomonas ruminantium phytase complexed with persulfated phytate in the C2221 crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.179 

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: 10.1016/j.str.2004.08.010
  • Primary Citation of Related Structures:  

  • 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 Selenom ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
myo-inositol hexaphosphate phosphohydrolase
A, B, C
337Selenomonas ruminantiumMutation(s): 0 
Gene Names: phyA
Find proteins for Q7WUJ1 (Selenomonas ruminantium)
Go to UniProtKB:  Q7WUJ1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHS
Query on IHS

Download SDF File 
Download CCD File 
A, C
D-MYO-INOSITOL-HEXASULPHATE
C6 H12 O24 S6
NBTMNFYXJYCQHQ-GPIVLXJGSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 128.376α = 90.00
b = 228.745β = 90.00
c = 91.778γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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