5YLO | pdb_00005ylo

Structural of Pseudomonas aeruginosa PA4980

• PDB DOI: https://doi.org/10.2210/pdb5YLO/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-10-18 Released: 2018-08-22 
• Deposition Author(s): Liu, L., Li, T., Peng, C.T., Li, C.C., Xiao, Q.J., He, L.H., Wang, N.Y., Bao, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.270 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.238 (Depositor) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

Structural characterization of a Delta3, Delta2-enoyl-CoA isomerase from Pseudomonas aeruginosa: implications for its involvement in unsaturated fatty acid metabolism.

Liu, L., Li, T., Peng, C.T., Sun, C.Z., Li, C.C., Xiao, Q.J., He, L.H., Wang, N.Y., Song, Y.J., Zhu, Y.B., Li, H., Kang, M., Tang, H., Xiong, X., Bao, R.

(2019) J Biomol Struct Dyn 37: 2695-2702

• PubMed: 30052139 
• DOI: https://doi.org/10.1080/07391102.2018.1495102
• Primary Citation Related Structures: 
  5YLO


• PubMed Abstract: 
  

  Gene PA4980 from Pseudomonas aeruginosa encodes a putative enoyl-coenzyme A hydratase/isomerase that is associated with the function of the biofilm dispersion-inducing signal molecule cis-2-decenoic acid. To elucidate the role of PA4980 in cis-2-decenoic acid biosynthesis, we reported the crystal structure of its protein product at 2.39 Å. The structural analysis and substrate binding prediction suggest that it acts as a monofunctional enoyl-coenzyme A isomerase, implicating an alternative pathway of the cis-2-decenoic acid synthesis.

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Organizational Affiliation: 
• a Department of Dermatology , Affiliated Hospital, Southwest Medical University , Luzhou , China.
b Center of Infectious Diseases, West China Hospital , Sichuan University , Chengdu , P.R. China.
e Drug Research Center of Integrated Traditional Chinese and Western Medicine, Affiliated Traditional Chinese Medicine Hospital , Southwest Medical University , Luzhou , China.
c School of Life Science and Engineering , Southwest Jiaotong University , Chengdu , P.R. China.
d State Key Laboratory of Biotherapy and Cancer Center and Healthy Food Evaluation Research Center , Sichuan University , Chengdu , P.R. China.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.05 kDa 
• Atom Count: 1,834 
• Modeled Residue Count: 235 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable enoyl-CoA hydratase/isomerase	A	271	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA4980
UniProt
Find proteins for Q9HUI5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HUI5  Go to UniProtKB:  Q9HUI5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.270 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.238 (Depositor) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.958	α = 90
b = 124.958	β = 90
c = 111.468	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: 2018-08-22 
Deposition Author(s): Liu, L., Li, T., Peng, C.T., Li, C.C., Xiao, Q.J., He, L.H., Wang, N.Y., Bao, R.

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2018-12-05
  Changes: Data collection, Database references
• Version 1.2: 2019-05-22
  Changes: Data collection, Database references
• Version 1.3: 2024-03-27
  Changes: Data collection, Database references