Structure of the Shewanella loihica PV-4 NADH-dependent persulfide reductase C43S/C531S Double Mutant

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.124 

Starting Model: experimental
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Characterization of an NADH-Dependent Persulfide Reductase from Shewanella loihica PV-4: Implications for the Mechanism of Sulfur Respiration via FAD-Dependent Enzymes .

Warner, M.D.Lukose, V.Lee, K.H.Lopez, K.H Sazinsky, M.Crane, E.J.

(2010) Biochemistry 50: 194-206

  • DOI: https://doi.org/10.1021/bi101232y
  • Primary Citation of Related Structures:  
    3NT6, 3NTA, 3NTD

  • PubMed Abstract: 

    The NADH-dependent persulfide reductase (Npsr), a recently discovered member of the PNDOR family of flavoproteins that contains both the canonical flavoprotein reductase domain and a rhodanese domain, is proposed to be involved in the dissimilatory reduction of S(0) for Shewanella loihica PV-4. We have previously shown that polysulfide is a substrate for this enzyme, and a recently determined structure of a closely related enzyme (CoADR-Rhod from Bacillus anthracis) suggested the importance of a bound coenzyme A in the mechanism. The work described here shows that the in vivo oxidizing substrates of Npsr are the persulfides of small thiols such as CoA and glutathione. C43S, C531S, and C43,531S mutants were created to determine the role of the flavoprotein domain cysteine (C43) and the rhodanese domain cysteine (C531) in the mechanism. The absolute requirement for C43 in persulfide or DTNB reductase activity shows that this residue is involved in S-S bond breakage. C531 contributes to, but is not required for, catalysis of DTNB reduction, while it is absolutely required for reduction of any persulfide substrates. Titrations of the enzyme with NADH, dithionite, titanium(III), or TCEP demonstrate the presence of a mixed-disulfide between C43 and a tightly bound CoA, and structures of the C43 and C43,531S mutants confirm that this coenzyme A remains tightly bound to the enzyme in the absence of a C43-CoA S-S bond. The structure of Npsr suggests a likely site for binding and reaction with the persulfide substrate on the rhodanese domain. On the basis of kinetic, titration, and structural data, a mechanism for the reduction of persulfides by Npsr is proposed.

  • Organizational Affiliation

    Pomona College Department of Chemistry, Claremont, California 91711, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FAD-dependent pyridine nucleotide-disulphide oxidoreductase
A, B
574Shewanella loihica PV-4Mutation(s): 2 
Gene Names: Shew_0729
Find proteins for A3QAV3 (Shewanella loihica (strain ATCC BAA-1088 / PV-4))
Explore A3QAV3 
Go to UniProtKB:  A3QAV3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3QAV3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.124 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.705α = 90
b = 133.705β = 90
c = 79.238γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-22
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-22
    Changes: Data collection