Structural and Functional Characterization of a Novel Archaeal Phosphodiesterase

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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Structural and functional characterization of a novel phosphodiesterase from Methanococcus jannaschii

Chen, S.Yakunin, A.F.Kuznetsova, E.Busso, D.Pufan, R.Proudfoot, M.Kim, R.Kim, S.-H.

(2004) J Biol Chem 279: 31854-31862

  • DOI: https://doi.org/10.1074/jbc.M401059200
  • Primary Citation of Related Structures:  
    1S3L, 1S3M, 1S3N

  • PubMed Abstract: 

    Methanococcus jannaschii MJ0936 is a hypothetical protein of unknown function with over 50 homologs found in many bacteria and Archaea. To help define the molecular (biochemical and biophysical) function of MJ0936, we determined its crystal structure at 2.4-A resolution and performed a series of biochemical screens for catalytic activity. The overall fold of this single domain protein consists of a four-layered structure formed by two beta-sheets flanked by alpha-helices on both sides. The crystal structure suggested its biochemical function to be a nuclease, phosphatase, or nucleotidase, with a requirement for some metal ions. Crystallization in the presence of Ni(2+) or Mn(2+) produced a protein containing a binuclear metal center in the putative active site formed by a cluster of conserved residues. Analysis of MJ0936 against a panel of general enzymatic assays revealed catalytic activity toward bis-p-nitrophenyl phosphate, an indicator substrate for phosphodiesterases and nucleases. Significant activity was also found with two other phosphodiesterase substrates, thymidine 5'-monophosphate p-nitrophenyl ester and p-nitrophenylphosphorylcholine, but no activity was found for cAMP or cGMP. Phosphodiesterase activity of MJ0936 had an absolute requirement for divalent metal ions with Ni(2+) and Mn(2+) being most effective. Thus, our structural and enzymatic studies have identified the biochemical function of MJ0936 as that of a novel phosphodiesterase.

  • Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, California 94720, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical protein MJ0936
A, B
190Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: MJ0936
Find proteins for Q58346 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58346 
Go to UniProtKB:  Q58346
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58346
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.106α = 90
b = 70.106β = 90
c = 196.173γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations