Crystal structure of unliganded yeast PDE1

Experimental Data Snapshot

  • Resolution: 1.31 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-monophosphate.

Tian, Y.Cui, W.Huang, M.Robinson, H.Wan, Y.Wang, Y.Ke, H.

(2014) Biochemistry 53: 4938-4945

  • DOI: https://doi.org/10.1021/bi500406h
  • Primary Citation of Related Structures:  
    4OJV, 4OJX

  • PubMed Abstract: 

    Cyclic nucleotide phosphodiesterases (PDEs) decompose second messengers cAMP and cGMP that play critical roles in many physiological processes. PDE1 of Saccharomyces cerevisiae has been subcloned and expressed in Escherichia coli. Recombinant yPDE1 has a KM of 110 μM and a kcat of 16.9 s(-1) for cAMP and a KM of 105 μM and a kcat of 11.8 s(-1) for cGMP. Thus, the specificity constant (kcat/KM(cAMP))/(kcat/KM(cGMP)) of 1.4 indicates a dual specificity of yPDE1 for hydrolysis of both cAMP and cGMP. The crystal structures of unliganded yPDE1 and its complex with GMP at 1.31 Å resolution reveal a new structural folding that is different from those of human PDEs but is partially similar to that of some other metalloenzymes such as metallo-β-lactamase. In spite of their different structures and divalent metals, yPDE1 and human PDEs may share a common mechanism for hydrolysis of cAMP and cGMP.

  • Organizational Affiliation

    Beijing Laboratory for Food Quality and Safety and Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University , Beijing 100048, P. R. China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3',5'-cyclic-nucleotide phosphodiesterase 1369Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PDE1YGL248WNRB369
Find proteins for P22434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22434 
Go to UniProtKB:  P22434
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22434
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.31 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.478α = 90
b = 85.151β = 90
c = 130.565γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2015-07-01
    Changes: Database references