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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/s41598-018-22300-1
  • Primary Citation of Related Structures:  

  • 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 pr ...

    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.


    Related Citations: 
    • Author Correction: 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: 12632


    Organizational Affiliation

    Department of Dermatology, Southwest Medical University, affiliated hospital, Luzhou, China.,Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China. yuluot@scu.edu.cn.,Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China. baorui@scu.edu.cn.,Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China. wangzhenling@scu.edu.cn.,School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.,Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable enoyl-CoA hydratase/isomerase
B
280Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 1 
Find proteins for Q9I5I4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I5I4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MRD
Query on MRD

Download SDF File 
Download CCD File 
B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.230 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 125.262α = 90.00
b = 125.262β = 90.00
c = 72.651γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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