4WX0 | pdb_00004wx0

UndA complexed with beta-hydroxydodecanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.185 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.137 (Depositor) 
  • R-Value Observed: 
    0.139 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4WX0

Ligand Structure Quality Assessment 


This is version 1.2 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 U S A 111: 18237-18242

  • DOI: https://doi.org/10.1073/pnas.1419701112

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 62.08 kDa 
  • Atom Count: 4,821 
  • Modeled Residue Count: 511 
  • Deposited Residue Count: 526 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TENA/THI-4 family protein
A, B
263Pseudomonas protegens Pf-5Mutation(s): 0 
Gene Names: PFL_4321
UniProt
Find proteins for Q4K8M0 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5))
Explore Q4K8M0 
Go to UniProtKB:  Q4K8M0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4K8M0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HXD

Query on HXD



Download:Ideal Coordinates CCD File
D [auth A],
K [auth B]
(3R)-3-HYDROXYDODECANOIC ACID
C12 H24 O3
MUCMKTPAZLSKTL-LLVKDONJSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
M [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE

Query on FE



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
PER

Query on PER



Download:Ideal Coordinates CCD File
E [auth A],
L [auth B]
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.185 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.137 (Depositor) 
  • R-Value Observed: 0.139 (Depositor) 
Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.41α = 90
b = 73.99β = 90
c = 142.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-01-07
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy