5VXH | pdb_00005vxh

Crystal structure of Xanthomonas campestris OleA E117D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.198 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5VXH

This is version 1.3 of the entry. See complete history

Literature

OleA Glu117 is key to condensation of two fatty-acyl coenzyme A substrates in long-chain olefin biosynthesis.

Jensen, M.R.Goblirsch, B.R.Christenson, J.K.Esler, M.A.Mohamed, F.A.Wackett, L.P.Wilmot, C.M.

(2017) Biochem J 474: 3871-3886

  • DOI: https://doi.org/10.1042/BCJ20170642
  • Primary Citation Related Structures: 
    5VXD, 5VXE, 5VXF, 5VXG, 5VXH, 5VXI

  • PubMed Abstract: 

    In the interest of decreasing dependence on fossil fuels, microbial hydrocarbon biosynthesis pathways are being studied for renewable, tailored production of specialty chemicals and biofuels. One candidate is long-chain olefin biosynthesis, a widespread bacterial pathway that produces waxy hydrocarbons. Found in three- and four-gene clusters, oleABCD encodes the enzymes necessary to produce cis -olefins that differ by alkyl chain length, degree of unsaturation, and alkyl chain branching. The first enzyme in the pathway, OleA, catalyzes the Claisen condensation of two fatty acyl-coenzyme A (CoA) molecules to form a β-keto acid. In this report, the mechanistic role of Xanthomonas campestris OleA Glu117 is investigated through mutant enzymes. Crystal structures were determined for each mutant as well as their complex with the inhibitor cerulenin. Complemented by substrate modeling, these structures suggest that Glu117 aids in substrate positioning for productive carbon-carbon bond formation. Analysis of acyl-CoA substrate hydrolysis shows diminished activity in all mutants. When the active site lacks an acidic residue in the 117 position, OleA cannot form condensed product, demonstrating that Glu117 has a critical role upstream of the essential condensation reaction. Profiling of pH dependence shows that the apparent p K a for Glu117 is affected by mutagenesis. Taken together, we propose that Glu117 is the general base needed to prime condensation via deprotonation of the second, non-covalently bound substrate during turnover. This is the first example of a member of the thiolase superfamily of condensing enzymes to contain an active site base originating from the second monomer of the dimer.


  • Organizational Affiliation
    • Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, U.S.A.

Macromolecule Content 

  • Total Structure Weight: 78.12 kDa 
  • Atom Count: 5,419 
  • Modeled Residue Count: 671 
  • Deposited Residue Count: 716 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3-oxoacyl-[ACP] synthase III
A, B
358Xanthomonas campestris pv. campestris str. ATCC 33913Mutation(s): 1 
Gene Names: fabHXCC0212
EC: 2.3.1.41 (PDB Primary Data), 2.3.3.20 (UniProt)
UniProt
Find proteins for Q8PDX2 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25))
Explore Q8PDX2 
Go to UniProtKB:  Q8PDX2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PDX2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.198 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.876α = 90
b = 85.409β = 90
c = 102.794γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing
HKLdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-008700

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description