Crystal structure of a phosphonate monoester hydrolase from rhizobium leguminosarum: a new member of the alkaline phosphatase superfamily

Experimental Data Snapshot

  • Resolution: 1.42 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

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A New Member of the Alkaline Phosphatase Superfamily with a Formylglycine Nucleophile: Structural and Kinetic Characterisation of a Phosphonate Monoester Hydrolase/Phosphodiesterase from Rhizobium Leguminosarum.

Jonas, S.Van Loo, B.Hyvonen, M.Hollfelder, F.

(2008) J Mol Biol 384: 120

  • DOI: https://doi.org/10.1016/j.jmb.2008.08.072
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The alkaline phosphatase superfamily comprises a large number of hydrolytic metalloenzymes such as phosphatases and sulfatases. We have characterised a new member of this superfamily, a phosphonate monoester hydrolase/phosphodiesterase from Rhizobium leguminosarum (R/PMH) both structurally and kinetically. The 1.42 A crystal structure shows structural homology to arylsulfatases with conservation of the core alpha/beta-fold, the mononuclear active site and most of the active-site residues. Sulfatases use a unique formylglycine nucleophile, formed by posttranslational modification of a cysteine/serine embedded in a signature sequence (C/S)XPXR. We provide mass spectrometric and mutational evidence that R/PMH is the first non-sulfatase enzyme shown to use a formylglycine as the catalytic nucleophile. R/PMH hydrolyses phosphonate monoesters and phosphate diesters with similar efficiency. Burst kinetics suggest that substrate hydrolysis proceeds via a double-displacement mechanism. Kinetic characterisation of active-site mutations establishes the catalytic contributions of individual residues. A mechanism for substrate hydrolysis is proposed on the basis of the kinetic data and structural comparisons with E. coli alkaline phosphatase and Pseudomonas aeruginosa arylsulfatase. R/PMH represents a further example of conservation of the overall structure and mechanism within the alkaline phosphatase superfamily.

  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB21GA, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE SULFATASE543Rhizobium johnstonii 3841Mutation(s): 1 
Gene Names: pRL90232
EC: 3.1.4 (UniProt), 3.1.3 (UniProt)
Find proteins for Q1M964 (Rhizobium leguminosarum bv. viciae (strain 3841))
Explore Q1M964 
Go to UniProtKB:  Q1M964
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1M964
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.42 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.7α = 90
b = 96.6β = 90
c = 178.5γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-04-24
    Changes: Data collection, Derived calculations, Other, Polymer sequence