3T02

Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoacetate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural and mechanistic insights into C-p bond hydrolysis by phosphonoacetate hydrolase.

Agarwal, V.Borisova, S.A.Metcalf, W.W.van der Donk, W.A.Nair, S.K.

(2011) Chem Biol 18: 1230-1240

  • DOI: https://doi.org/10.1016/j.chembiol.2011.07.019
  • Primary Citation of Related Structures:  
    3SZY, 3SZZ, 3T00, 3T01, 3T02

  • PubMed Abstract: 

    Bacteria have evolved pathways to metabolize phosphonates as a nutrient source for phosphorus. In Sinorhizobium meliloti 1021, 2-aminoethylphosphonate is catabolized to phosphonoacetate, which is converted to acetate and inorganic phosphate by phosphonoacetate hydrolase (PhnA). Here we present detailed biochemical and structural characterization of PhnA that provides insights into the mechanism of C-P bond cleavage. The 1.35 Å resolution crystal structure reveals a catalytic core similar to those of alkaline phosphatases and nucleotide pyrophosphatases but with notable differences, such as a longer metal-metal distance. Detailed structure-guided analysis of active site residues and four additional cocrystal structures with phosphonoacetate substrate, acetate, phosphonoformate inhibitor, and a covalently bound transition state mimic provide insight into active site features that may facilitate cleavage of the C-P bond. These studies expand upon the array of reactions that can be catalyzed by enzymes of the alkaline phosphatase superfamily.


  • Organizational Affiliation

    Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
phosphonoacetate hydrolase427Sinorhizobium meliloti 1021Mutation(s): 1 
Gene Names: phnARB0978SM_b21538
EC: 3.6.1.9
UniProt
Find proteins for Q92UV8 (Rhizobium meliloti (strain 1021))
Explore Q92UV8 
Go to UniProtKB:  Q92UV8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92UV8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.354α = 90
b = 111.354β = 90
c = 72.77γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MD2data collection
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2011-11-09
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description