1TAZ

Catalytic Domain Of Human Phosphodiesterase 1B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Glutamine Switch Mechanism for Nucleotide Selectivity by Phosphodiesterases

Zhang, K.Y.J.Card, G.L.Suzuki, Y.Artis, D.R.Fong, D.Gillette, S.Hsieh, D.Neiman, J.West, B.L.Zhang, C.Milburn, M.V.Kim, S.-H.Schlessinger, J.Bollag, G.

(2004) Mol Cell 15: 279-286

  • DOI: https://doi.org/10.1016/j.molcel.2004.07.005
  • Primary Citation of Related Structures:  
    1T9R, 1T9S, 1TAZ, 1TB5, 1TB7, 1TBB, 1TBF

  • PubMed Abstract: 

    Phosphodiesterases (PDEs) comprise a family of enzymes that modulate the immune response, inflammation, and memory, among many other functions. There are three types of PDEs: cAMP-specific, cGMP-specific, and dual-specific. Here we describe the mechanism of nucleotide selectivity on the basis of high-resolution co-crystal structures of the cAMP-specific PDE4B and PDE4D with AMP, the cGMP-specific PDE5A with GMP, and the apo-structure of the dual-specific PDE1B. These structures show that an invariant glutamine functions as the key specificity determinant by a "glutamine switch" mechanism for recognizing the purine moiety in cAMP or cGMP. The surrounding residues anchor the glutamine residue in different orientations for cAMP and for cGMP. The PDE1B structure shows that in dual-specific PDEs a key histidine residue may enable the invariant glutamine to toggle between cAMP and cGMP. The structural understanding of nucleotide binding enables the design of new PDE inhibitors that may treat diseases in which cyclic nucleotides play a critical role.


  • Organizational Affiliation

    Plexxikon Inc., 91 Bolivar Drive, Berkeley, CA 94710, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B365Homo sapiensMutation(s): 0 
Gene Names: PDE1BPDE1B1
EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q01064 (Homo sapiens)
Explore Q01064 
Go to UniProtKB:  Q01064
PHAROS:  Q01064
GTEx:  ENSG00000123360 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01064
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.232α = 90
b = 87.232β = 90
c = 134.151γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance