3MM5

Dissimilatory sulfite reductase in complex with the substrate sulfite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.188 
  • 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

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
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sulfite reductase, dissimilatory-type subunit alphaA, D418Archaeoglobus fulgidusMutation(s): 0 
EC: 1.8.99.3 (PDB Primary Data), 1.8.99.5 (UniProt)
Find proteins for Q59109 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Explore Q59109 
Go to UniProtKB:  Q59109
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sulfite reductase, dissimilatory-type subunit betaB, E366Archaeoglobus fulgidusMutation(s): 0 
EC: 1.8.99.3 (PDB Primary Data), 1.8.99.5 (UniProt)
Find proteins for Q59110 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Explore Q59110 
Go to UniProtKB:  Q59110
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRM
Query on SRM

Download CCD File 
A, B, D, E
SIROHEME
C42 H42 Fe N4 O16
PGYXHNRRBJLFEV-NBUGCWMUSA-N
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
A, B, D, E
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SO3
Query on SO3

Download CCD File 
A, D
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • 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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Entry History 

Deposition Data

Revision History 

  • 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: Advisory, Refinement description