5WYB

Structure of Pseudomonas aeruginosa DspI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural and functional studies on Pseudomonas aeruginosa DspI: implications for its role in DSF biosynthesis.

Liu, L.Li, T.Cheng, X.J.Peng, C.T.Li, C.C.He, L.H.Ju, S.M.Wang, N.Y.Ye, T.H.Lian, M.Xiao, Q.J.Song, Y.J.Zhu, Y.B.Yu, L.T.Wang, Z.L.Bao, R.

(2018) Sci Rep 8: 3928-3928

  • DOI: https://doi.org/10.1038/s41598-018-22300-1
  • Primary Citation of Related Structures:  
    5WYB, 5WYD

  • PubMed Abstract: 

    DspI, a putative enoyl-coenzyme A (CoA) hydratase/isomerase, was proposed to be involved in the synthesis of cis-2-decenoic acid (CDA), a quorum sensing (QS) signal molecule in the pathogen Pseudomonas aeruginosa (P. aeruginosa). The present study provided a structural basis for the dehydration reaction mechanism of DspI during CDA synthesis. Structural analysis reveals that Glu126, Glu146, Cys127, Cys131 and Cys154 are important for its enzymatic function. Moreover, we show that the deletion of dspI results in a remarkable decreased in the pyoverdine production, flagella-dependent swarming motility, and biofilm dispersion as well as attenuated virulence in P. aeruginosa PA14. This study thus unravels the mechanism of DspI in diffusible signal factor (DSF) CDA biosynthesis, providing vital information for developing inhibitors that interfere with DSF associated pathogenicity in P. aeruginosa.


  • Organizational Affiliation

    Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable enoyl-CoA hydratase/isomeraseA [auth B]280Pseudomonas aeruginosa PA14Mutation(s): 1 
Gene Names: PA0745
UniProt
Find proteins for Q9I5I4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I5I4 
Go to UniProtKB:  Q9I5I4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I5I4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download Ideal Coordinates CCD File 
B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.234 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.262α = 90
b = 125.262β = 90
c = 72.651γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.3: 2019-08-14
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 1.4: 2023-11-22
    Changes: Data collection, Database references, Refinement description