4RNI | pdb_00004rni

PaMorA dimeric phosphodiesterase. apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.238 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4RNI

This is version 1.2 of the entry. See complete history

Literature

Formation and dimerization of the phosphodiesterase active site of the Pseudomonas aeruginosa MorA, a bi-functional c-di-GMP regulator.

Phippen, C.W.Mikolajek, H.Schlaefli, H.G.Keevil, C.W.Webb, J.S.Tews, I.

(2014) FEBS Lett 588: 4631-4636

  • DOI: https://doi.org/10.1016/j.febslet.2014.11.002
  • Primary Citation Related Structures: 
    4RNF, 4RNH, 4RNI, 4RNJ

  • PubMed Abstract: 

    Diguanylate cyclases (DGC) and phosphodiesterases (PDE), respectively synthesise and hydrolyse the secondary messenger cyclic dimeric GMP (c-di-GMP), and both activities are often found in a single protein. Intracellular c-di-GMP levels in turn regulate bacterial motility, virulence and biofilm formation. We report the first structure of a tandem DGC-PDE fragment, in which the catalytic domains are shown to be active. Two phosphodiesterase states are distinguished by active site formation. The structures, in the presence or absence of c-di-GMP, suggest that dimerisation and binding pocket formation are linked, with dimerisation being required for catalytic activity. An understanding of PDE activation is important, as biofilm dispersal via c-di-GMP hydrolysis has therapeutic effects on chronic infections.


  • Organizational Affiliation
    • Centre for Biological Sciences and Institute for Life Sciences, Life Sciences Building B85, The University of Southampton, University Rd, Southampton, Hampshire, SO17 1BJ, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 63.45 kDa 
  • Atom Count: 4,167 
  • Modeled Residue Count: 507 
  • Deposited Residue Count: 572 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Motility regulator
A, B
286Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: morAPA4601
EC: 3.1.4.52
UniProt
Find proteins for Q9HVI8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HVI8 
Go to UniProtKB:  Q9HVI8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HVI8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.238 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.754α = 90
b = 94.466β = 90
c = 154.703γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
xia2data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references