1U26

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 
  • R-Value Work: 0.207 

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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:  
    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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
myo-inositol hexaphosphate phosphohydrolaseA, B337Selenomonas ruminantiumMutation(s): 0 
Gene Names: phyA
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHS
Query on IHS
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth B]		D-MYO-INOSITOL-HEXASULPHATE
C6 H12 O24 S6
NBTMNFYXJYCQHQ-GPIVLXJGSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • 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