3NTD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 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 r ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FAD-dependent pyridine nucleotide-disulphide oxidoreductaseAB565Shewanella loihica PV-4Mutation(s): 1 
Gene Names: Shew_0729
EC: 1.8.1.14
Find proteins for A3QAV3 (Shewanella loihica (strain ATCC BAA-1088 / PV-4))
Explore A3QAV3 
Go to UniProtKB:  A3QAV3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
COA
Query on COA

Download CCD File 
A, B
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.737α = 90
b = 133.737β = 90
c = 79.713γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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