6P5Q

X-ray structure of Fe(II)-soaked UndA bound to lauric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

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This is version 1.2 of the entry. See complete history


Literature

Substrate-Triggered Formation of a Peroxo-Fe2(III/III) Intermediate during Fatty Acid Decarboxylation by UndA.

Zhang, B.Rajakovich, L.J.Van Cura, D.Blaesi, E.J.Mitchell, A.J.Tysoe, C.R.Zhu, X.Streit, B.R.Rui, Z.Zhang, W.Boal, A.K.Krebs, C.Bollinger Jr., J.M.

(2019) J Am Chem Soc 141: 14510-14514

  • DOI: 10.1021/jacs.9b06093
  • Primary Citation of Related Structures:  
    6P5Q

  • PubMed Abstract: 
  • The iron-dependent oxidase UndA cleaves one C3-H bond and the C1-C2 bond of dodecanoic acid to produce 1-undecene and CO 2 . A published X-ray crystal structure showed that UndA has a heme-oxygenase-like fold, thus associating it with a structural superfamily that includes known and postulated non-heme diiron proteins, but revealed only a single iron ion in the active site ...

    The iron-dependent oxidase UndA cleaves one C3-H bond and the C1-C2 bond of dodecanoic acid to produce 1-undecene and CO 2 . A published X-ray crystal structure showed that UndA has a heme-oxygenase-like fold, thus associating it with a structural superfamily that includes known and postulated non-heme diiron proteins, but revealed only a single iron ion in the active site. Mechanisms proposed for initiation of decarboxylation by cleavage of the C3-H bond using a monoiron cofactor to activate O 2 necessarily invoked unusual or potentially unfeasible steps. Here we present spectroscopic, crystallographic, and biochemical evidence that the cofactor of Pseudomonas fluorescens Pf-5 UndA is actually a diiron cluster and show that binding of the substrate triggers rapid addition of O 2 to the Fe 2 (II/II) cofactor to produce a transient peroxo-Fe 2 (III/III) intermediate. The observations of a diiron cofactor and substrate-triggered formation of a peroxo-Fe 2 (III/III) intermediate suggest a small set of possible mechanisms for O 2 , C3-H and C1-C2 activation by UndA; these routes obviate the problematic steps of the earlier hypotheses that invoked a single iron.


    Organizational Affiliation

    Department of Chemical and Biomolecular Engineering , University of California Berkeley , Berkeley , California 94720 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UndAA, B308Pseudomonas fluorescensMutation(s): 0 
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
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.009α = 90
b = 74.148β = 90
c = 142.563γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence