2WNI

Crystal Structure Analysis of Klebsiella sp ASR1 Phytase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Klebsiella Sp. Asr1 Phytase Suggests Substrate Binding to a Preformed Active Site that Meets the Requirements of a Plant Rhizosphere Enzyme.

Bohm, K.Herter, T.Mueller, J.J.Borriss, R.Heinemann, U.

(2010) FEBS J. 277: 1284

  • DOI: 10.1111/j.1742-4658.2010.07559.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The extracellular phytase of the plant-associated Klebsiella sp. ASR1 is a member of the histidine-acid-phosphatase family and acts primarily as a scavenger of phosphate groups locked in the phytic acid molecule. The Klebsiella enzyme is distinguishe ...

    The extracellular phytase of the plant-associated Klebsiella sp. ASR1 is a member of the histidine-acid-phosphatase family and acts primarily as a scavenger of phosphate groups locked in the phytic acid molecule. The Klebsiella enzyme is distinguished from the Escherichia coli phytase AppA by its sequence and phytate degradation pathway. The crystal structure of the phytase from Klebsiella sp. ASR1 has been determined to 1.7 A resolution using single-wavelength anomalous-diffraction phasing. Despite low sequence similarity, the overall structure of Klebsiella phytase bears similarity to other histidine-acid phosphatases, such as E. coli phytase, glucose-1-phosphatase and human prostatic-acid phosphatase. The polypeptide chain is organized into an alpha and an alpha/beta domain, and the active site is located in a positively charged cleft between the domains. Three sulfate ions bound to the catalytic pocket of an inactive mutant suggest a unique binding mode for its substrate phytate. Even in the absence of substrate, the Klebsiella phytase is closer in structure to the E. coli phytase AppA in its substrate-bound form than to phytate-free AppA. This is taken to suggest a preformed substrate-binding site in Klebsiella phytase. Differences in habitat and substrate availability thus gave rise to enzymes with different substrate-binding modes, specificities and kinetics.


    Organizational Affiliation

    Kristallographie, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-PHYTASE
A, B, C, D
418Klebsiella pneumoniaeMutation(s): 4 
Gene Names: phyK
EC: 3.1.3.8
Find proteins for Q84CN9 (Klebsiella pneumoniae)
Go to UniProtKB:  Q84CN9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.713α = 90.00
b = 122.929β = 90.00
c = 205.402γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-24
    Type: Source and taxonomy