6B2S

Crystal structure of Xanthomonas campestris OleA H285N

• PDB DOI: https://doi.org/10.2210/pdb6B2S/pdb

• Classification: TRANSFERASE
• Organism(s): Xanthomonas campestris pv. campestris str. ATCC 33913
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-09-20 Released: 2018-02-28 
• Deposition Author(s): Jensen, M.R., Goblirsch, B.R., Esler, M.A., Christenson, J.K., Mohamed, F.A., Wackett, L.P., Wilmot, C.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), BioTechnology Institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

The role of OleA His285 in orchestration of long-chain acyl-coenzyme A substrates.

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

(2018) FEBS Lett 592: 987-998

• PubMed: 29430657 
• DOI: https://doi.org/10.1002/1873-3468.13004
• Primary Citation of Related Structures:  
  6B2R, 6B2S, 6B2T


• PubMed Abstract: 
  

  Renewable production of hydrocarbons is being pursued as a petroleum-independent source of commodity chemicals and replacement for biofuels. The bacterial biosynthesis of long-chain olefins represents one such platform. The process is initiated by OleA catalyzing the condensation of two fatty acyl-coenzyme A substrates to form a β-keto acid. Here, the mechanistic role of the conserved His285 is investigated through mutagenesis, activity assays, and X-ray crystallography. Our data demonstrate that His285 is required for product formation, influences the thiolase nucleophile Cys143 and the acyl-enzyme intermediate before and after transesterification, and orchestrates substrate coordination as a defining component of an oxyanion hole. As a consequence, His285 plays a key role in enabling a mechanistic strategy in OleA that is distinct from other thiolases.

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Organizational Affiliation: 

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St Paul, MN, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 78.51 kDa 
• Atom Count: 5,391 
• Modelled Residue Count: 684 
• Deposited Residue Count: 716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[ACP] synthase III	A, B	358	Xanthomonas campestris pv. campestris str. ATCC 33913	Mutation(s): 1  Gene Names: fabH, XCC0212 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth A], G [auth A], J [auth B], K [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A], D [auth A], E [auth A], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.517	α = 90
b = 85.077	β = 90
c = 103.28	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Jensen, M.R., Goblirsch, B.R., Esler, M.A., Christenson, J.K., Mohamed, F.A., Wackett, L.P., Wilmot, C.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008700
BioTechnology Institute	United States	1000014885 10866 MNT11

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection, 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
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-16
  Changes: Structure summary