4OJX

crystal structure of yeast phosphodiesterase-1 in complex with GMP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

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: 10.1021/bi500406h
  • Primary Citation of Related Structures:  
    4OJX, 4OJV

  • 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 ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3',5'-cyclic-nucleotide phosphodiesterase 1 A369Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PDE1, YGL248W, NRB369
EC: 3.1.4.17
Find proteins for P22434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22434 
Go to UniProtKB:  P22434
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G
Query on G
Download Ideal Coordinates CCD File 
A
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N		 Ligand Interaction
MPD
Query on MPD
Download Ideal Coordinates CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.674α = 90
b = 85.162β = 90
c = 130.836γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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