4WWZ

UndA complexed with 2,3-dodecenoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Microbial biosynthesis of medium-chain 1-alkenes by a nonheme iron oxidase.

Rui, Z.Li, X.Zhu, X.Liu, J.Domigan, B.Barr, I.Cate, J.H.Zhang, W.

(2014) Proc.Natl.Acad.Sci.USA 111: 18237-18242

  • DOI: 10.1073/pnas.1419701112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aliphatic medium-chain 1-alkenes (MCAEs, ∼10 carbons) are "drop-in" compatible next-generation fuels and precursors to commodity chemicals. Mass production of MCAEs from renewable resources holds promise for mitigating dependence on fossil hydrocarbo ...

    Aliphatic medium-chain 1-alkenes (MCAEs, ∼10 carbons) are "drop-in" compatible next-generation fuels and precursors to commodity chemicals. Mass production of MCAEs from renewable resources holds promise for mitigating dependence on fossil hydrocarbons. An MCAE, such as 1-undecene, is naturally produced by Pseudomonas as a semivolatile metabolite through an unknown biosynthetic pathway. We describe here the discovery of a single gene conserved in Pseudomonas responsible for 1-undecene biosynthesis. The encoded enzyme is able to convert medium-chain fatty acids (C10-C14) into their corresponding terminal olefins using an oxygen-activating, nonheme iron-dependent mechanism. Both biochemical and X-ray crystal structural analyses suggest an unusual mechanism of β-hydrogen abstraction during fatty acid substrate activation. Our discovery unveils previously unidentified chemistry in the nonheme Fe(II) enzyme family, provides an opportunity to explore the biology of 1-undecene in Pseudomonas, and paves the way for tailored bioconversion of renewable raw materials to MCAE-based biofuels and chemical commodities.


    Organizational Affiliation

    Energy Biosciences Institute, Departments of Chemical and Biomolecular Engineering.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TENA/THI-4 family protein
A, B
263Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)Mutation(s): 0 
Find proteins for Q4K8M0 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5))
Go to UniProtKB:  Q4K8M0
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
B
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
3X1
Query on 3X1

Download SDF File 
Download CCD File 
A, B
(2E)-dodec-2-enoic acid
C12 H22 O2
PAWGRNGPMLVJQH-ZHACJKMWSA-N
 Ligand Interaction
PSL
Query on PSL

Download SDF File 
Download CCD File 
A, B
PYROSULFATE
O7 S2
VFNGKCDDZUSWLR-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.158 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 67.480α = 90.00
b = 74.160β = 90.00
c = 142.500γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-11-13 
  • Released Date: 2014-12-24 
  • Deposition Author(s): Li, X., Cate, J.D.H.

Funding OrganizationLocationGrant Number
Energy Biosciences Institute and National Cancer InstituteUnited States--

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-01-07
    Type: Database references