5WYD | pdb_00005wyd

Structural of Pseudomonas aeruginosa DspI

• PDB DOI: https://doi.org/10.2210/pdb5WYD/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-01-12 Released: 2018-01-31 
• Deposition Author(s): Liu, L., Peng, C., Li, T., Li, C., He, L., Song, Y., Zhu, Y., Shen, Y., Bao, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.276 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

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

• PubMed: 29500457 
• DOI: https://doi.org/10.1038/s41598-018-22300-1
• Primary Citation 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.

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Organizational Affiliation: 
• Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.
Department of Dermatology, Southwest Medical University, affiliated hospital, Luzhou, China.
School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China. [e-mail].
Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China. [e-mail].
Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 187.05 kDa 
• Atom Count: 12,387 
• Modeled Residue Count: 1,572 
• Deposited Residue Count: 1,680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable enoyl-CoA hydratase/isomerase	A, B, C, D, E, F	280	Pseudomonas aeruginosa PAO1	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	R [auth F]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD	K [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PTD	G [auth A], L [auth D], N [auth E]	PENTANEDIAL C5 H8 O2 SXRSQZLOMIGNAQ-UHFFFAOYSA-N
IPA	H [auth B], I [auth C], J [auth C], M [auth E], O [auth F], P [auth F], Q [auth F]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.276 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.309	α = 90
b = 83.309	β = 90
c = 207.547	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Liu, L., Peng, C., Li, T., Li, C., He, L., Song, Y., Zhu, Y., Shen, Y., Bao, R.

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Database references
• Version 1.2: 2019-08-14
  Changes: Data collection, Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description