5WID

Structure of a flavodoxin from the domain Archaea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structure and function of an unusual flavodoxin from the domainArchaea.

Prakash, D.Iyer, P.R.Suharti, S.Walters, K.A.Santiago-Martinez, M.G.Golbeck, J.H.Murakami, K.S.Ferry, J.G.

(2019) Proc Natl Acad Sci U S A 116: 25917-25922

  • DOI: https://doi.org/10.1073/pnas.1908578116
  • Primary Citation of Related Structures:  
    5WID

  • PubMed Abstract: 

    Flavodoxins, electron transfer proteins essential for diverse metabolisms in microbes from the domain Bacteria , are extensively characterized. Remarkably, although genomic annotations of flavodoxins are widespread in microbes from the domain Archaea , none have been isolated and characterized. Herein is described the structural, biochemical, and physiological characterization of an unusual flavodoxin (FldA) from Methanosarcina acetivorans , an acetate-utilizing methane-producing microbe of the domain Archaea In contrast to all flavodoxins, FldA is homodimeric, markedly less acidic, and stabilizes an anionic semiquinone. The crystal structure reveals an flavin mononucleotide (FMN) binding site unique from all other flavodoxins that provides a rationale for stabilization of the anionic semiquinone and a remarkably low reduction potentials for both the oxidized/semiquinone (-301 mV) and semiquinone/hydroquinone couples (-464 mV). FldA is up-regulated in acetate-grown versus methanol-grown cells and shown here to substitute for ferredoxin in mediating the transfer of low potential electrons from the carbonyl of acetate to the membrane-bound electron transport chain that generates ion gradients driving ATP synthesis. FldA offers potential advantages over ferredoxin by ( i ) sparing iron for abundant iron-sulfur proteins essential for acetotrophic growth and ( ii ) resilience to oxidative damage.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavodoxin
A, B, C
149Methanosarcina acetivorans C2AMutation(s): 0 
Gene Names: MA_1799
UniProt
Find proteins for Q8TPV5 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A))
Explore Q8TPV5 
Go to UniProtKB:  Q8TPV5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TPV5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.773α = 90
b = 112.773β = 90
c = 173.724γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM087350
Department of Energy (DOE, United States)United StatesDE-FG02-95ER20198 MOD16

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2020-02-19
    Changes: Database references
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description