Structure of a NAD-Dependent Persulfide Reductase from A. fulgidus

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

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Structural and Kinetic Characterization of Hyperthermophilic NADH-Dependent Persulfide Reductase from Archaeoglobus fulgidus .

Shabdar, S.Anaclet, B.Castineiras, A.G.Desir, N.Choe, N.Crane 3rd, E.J.Sazinsky, M.H.

(2021) Archaea 2021: 8817136-8817136

  • DOI: https://doi.org/10.1155/2021/8817136
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    NADH-dependent persulfide reductase (Npsr) has been proposed to facilitate dissimilatory sulfur respiration by reducing persulfide or sulfane sulfur-containing substrates to H 2 S. The presence of this gene in the sulfate and thiosulfate-reducing Archaeoglobus fulgidus DSM 4304 and other hyperthermophilic Archaeoglobales appears anomalous, as A. fulgidus is unable to respire S 0 and grow in the presence of elemental sulfur. To assess the role of Npsr in the sulfur metabolism of A. fulgidus DSM 4304, the Npsr from A. fulgidus was characterized. AfNpsr is specific for persulfide and polysulfide as substrates in the oxidative half-reaction, exhibiting k cat / K m on the order of 10 4 M -1 s -1 , which is similar to the kinetic parameters observed for hyperthermophilic CoA persulfide reductases. In contrast to the bacterial Npsr, AfNpsr exhibits low disulfide reductase activity with DTNB; however, similar to the bacterial enzymes, it does not show detectable activity with CoA-disulfide, oxidized glutathione, or cystine. The 3.1 Å X-ray structure of AfNpsr reveals access to the tightly bound catalytic CoA, and the active site Cys 42 is restricted by a flexible loop (residues 60-66) that is not seen in the bacterial homologs from Shewanella loihica PV-4 and Bacillus anthracis . Unlike the bacterial enzymes, AfNpsr exhibits NADH oxidase activity and also shows no detectable activity with NADPH. Models suggest steric and electrostatic repulsions of the NADPH 2'-phosphate account for the strong preference for NADH. The presence of Npsr in the nonsulfur-reducing A. fulgidus suggests that the enzyme may offer some protection against S 0 or serve in another metabolic role that has yet to be identified.

  • Organizational Affiliation

    Department of Biology, Pomona College, 175 West 6th Street, Claremont, CA 91711, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH oxidase (NoxA-3)A [auth D],
B [auth A],
C [auth B],
D [auth C]
551Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: AF_0400
Find proteins for O29847 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29847 
Go to UniProtKB:  O29847
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO29847
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

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E [auth D],
G [auth A],
J [auth B],
M [auth C]
C27 H33 N9 O15 P2
Query on COA

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F [auth D],
H [auth A],
K [auth B],
N [auth C]
C21 H36 N7 O16 P3 S
Query on CA

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I [auth A],
L [auth B],
O [auth C],
P [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.976α = 90
b = 100.355β = 91.894
c = 136.196γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1518306

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description