3MMA

Dissimilatory sulfite reductase phosphate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

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This is version 1.2 of the entry. See complete history


Literature

Reaction cycle of the dissimilatory sulfite reductase from Archaeoglobus fulgidus.

Parey, K.Warkentin, E.Kroneck, P.M.Ermler, U.

(2010) Biochemistry 49: 8912-8921

  • DOI: 10.1021/bi100781f
  • Primary Citation of Related Structures:  
    3MM5, 3MM6, 3MM7, 3MM8, 3MM9, 3MMA, 3MMB

  • PubMed Abstract: 
  • A vital process in the biogeochemical sulfur cycle is the dissimilatory sulfate reduction pathway in which sulfate (SO₄⁻²) is converted to hydrogen sulfide (H₂S). Dissimilatory sulfite reductase (dSir), its key enzyme, hosts a unique siroheme-[4Fe-4S] cofactor and catalyzes the six-electron reduction of sulfite (SO₃²⁻) to H₂S ...

    A vital process in the biogeochemical sulfur cycle is the dissimilatory sulfate reduction pathway in which sulfate (SO₄⁻²) is converted to hydrogen sulfide (H₂S). Dissimilatory sulfite reductase (dSir), its key enzyme, hosts a unique siroheme-[4Fe-4S] cofactor and catalyzes the six-electron reduction of sulfite (SO₃²⁻) to H₂S. To explore this reaction, we determined the X-ray structures of dSir from the archaeon Archaeoglobus fulgidus in complex with sulfite, sulfide (S²⁻) carbon monoxide (CO), cyanide (CN⁻), nitrite (NO₂⁻), nitrate (NO₃⁻), and phosphate (PO₄³⁻). Activity measurements indicated that dSir of A. fulgidus reduces, besides sulfite and nitrite, thiosulfate (S₂O₃²⁻) and trithionate (S₃O₆²⁻) and produces the latter two compounds besides sulfide. On this basis, a three-step mechanism was proposed, each step consisting of a two-electron transfer, a two-proton uptake, and a dehydration event. In comparison, the related active site structures of the assimilatory sulfite reductase (aSir)- and dSir-SO₃²⁻complexes reveal different conformations of Argα170 and Lysα211 both interacting with the sulfite oxygens (its sulfur atom coordinates the siroheme iron), a sulfite rotation of ~60° relative to each other, and different access of solvent molecules to the sulfite oxygens from the active site cleft. Therefore, solely in dSir a further sulfite molecule can be placed in van der Waals contact with the siroheme-ligated sulfite or sulfur-oxygen intermediates necessary for forming thiosulfate and trithionate. Although reported for dSir from several sulfate-reducing bacteria, the in vivo relevance of their formation is questionable.


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Max-von-Laue-Strasse 3, Frankfurt, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sulfite reductase, dissimilatory-type subunit alphaA, C [auth D]418Archaeoglobus fulgidusMutation(s): 0 
EC: 1.8.99.3 (PDB Primary Data), 1.8.99.5 (UniProt)
UniProt
Find proteins for Q59109 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore Q59109 
Go to UniProtKB:  Q59109
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sulfite reductase, dissimilatory-type subunit betaB, D [auth E]366Archaeoglobus fulgidusMutation(s): 0 
EC: 1.8.99.3 (PDB Primary Data), 1.8.99.5 (UniProt)
UniProt
Find proteins for Q59110 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore Q59110 
Go to UniProtKB:  Q59110
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.6α = 90
b = 68.9β = 107.5
c = 145.1γ = 90
Software Package:
Software NamePurpose
MAR345data collection
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description