5CPG

R-Hydratase PhaJ1 from Pseudomonas aeruginosa in the unliganded form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.694 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Contribution of the Distal Pocket Residue to the Acyl-Chain-Length Specificity of (R)-Specific Enoyl-Coenzyme A Hydratases from Pseudomonas spp.

Tsuge, T.Sato, S.Hiroe, A.Ishizuka, K.Kanazawa, H.Shiro, Y.Hisano, T.

(2015) Appl.Environ.Microbiol. 81: 8076-8083

  • DOI: 10.1128/AEM.02412-15

  • PubMed Abstract: 
  • (R)-Specific enoyl-coenzyme A (enoyl-CoA) hydratases (PhaJs) are capable of supplying monomers from fatty acid β-oxidation to polyhydroxyalkanoate (PHA) biosynthesis. PhaJ1Pp from Pseudomonas putida showed broader substrate specificity than did PhaJ1 ...

    (R)-Specific enoyl-coenzyme A (enoyl-CoA) hydratases (PhaJs) are capable of supplying monomers from fatty acid β-oxidation to polyhydroxyalkanoate (PHA) biosynthesis. PhaJ1Pp from Pseudomonas putida showed broader substrate specificity than did PhaJ1Pa from Pseudomonas aeruginosa, despite sharing 67% amino acid sequence identity. In this study, the substrate specificity characteristics of two Pseudomonas PhaJ1 enzymes were investigated by site-directed mutagenesis, chimeragenesis, X-ray crystallographic analysis, and homology modeling. In PhaJ1Pp, the replacement of valine with isoleucine at position 72 resulted in an increased preference for enoyl-coenzyme A (CoA) elements with shorter chain lengths. Conversely, at the same position in PhaJ1Pa, the replacement of isoleucine with valine resulted in an increased preference for enoyl-CoAs with longer chain lengths. These changes suggest a narrowing and broadening in the substrate specificity range of the PhaJ1Pp and PhaJ1Pa mutants, respectively. However, the substrate specificity remains broader in PhaJ1Pp than in PhaJ1Pa. Additionally, three chimeric PhaJ1 enzymes, composed from PhaJ1Pp and PhaJ1Pa, all showed significant hydratase activity, and their substrate preferences were within the range exhibited by the parental PhaJ1 enzymes. The crystal structure of PhaJ1Pa was determined at a resolution of 1.7 Å, and subsequent homology modeling of PhaJ1Pp revealed that in the acyl-chain binding pocket, the amino acid at position 72 was the only difference between the two structures. These results indicate that the chain-length specificity of PhaJ1 is determined mainly by the bulkiness of the amino acid residue at position 72, but that other factors, such as structural fluctuations, also affect specificity.


    Organizational Affiliation

    Department of Innovative and Engineered Materials, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan tsuge.t.aa@m.titech.ac.jp hisano@riken.jp.,Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.,Graduate School of Life Science, University of Hyogo, Hyogo, Japan RIKEN SPring-8 Center, Hyogo, Japan.,Department of Innovative and Engineered Materials, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan.,RIKEN SPring-8 Center, Hyogo, Japan tsuge.t.aa@m.titech.ac.jp hisano@riken.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
(R)-specific enoyl-CoA hydratase
A, B
155Pseudomonas aeruginosaMutation(s): 0 
Gene Names: phaJ1 (phaJ)
EC: 4.2.1.119
Find proteins for Q9LBK2 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q9LBK2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.694 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.530α = 90.00
b = 65.721β = 90.00
c = 77.453γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan--

Revision History 

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-11-11
    Type: Database references