2V4J

THE CRYSTAL STRUCTURE OF Desulfovibrio vulgaris DISSIMILATORY SULFITE REDUCTASE BOUND TO DsrC PROVIDES NOVEL INSIGHTS INTO THE MECHANISM OF SULFATE RESPIRATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration.

Oliveira, T.F.Vonrhein, C.Matias, P.M.Venceslau, S.S.Pereira, I.A.C.Archer, M.

(2008) J.Biol.Chem. 283: 34141

  • DOI: 10.1074/jbc.M805643200

  • PubMed Abstract: 
  • Sulfate reduction is one of the earliest types of energy metabolism used by ancestral organisms to sustain life. Despite extensive studies, many questions remain about the way respiratory sulfate reduction is associated with energy conservation. A cr ...

    Sulfate reduction is one of the earliest types of energy metabolism used by ancestral organisms to sustain life. Despite extensive studies, many questions remain about the way respiratory sulfate reduction is associated with energy conservation. A crucial enzyme in this process is the dissimilatory sulfite reductase (dSiR), which contains a unique siroheme-[4Fe4S] coupled cofactor. Here, we report the structure of desulfoviridin from Desulfovibrio vulgaris, in which the dSiR DsrAB (sulfite reductase) subunits are bound to the DsrC protein. The alpha(2)beta(2)gamma(2) assembly contains two siroheme-[4Fe4S] cofactors bound by DsrB, two sirohydrochlorins and two [4Fe4S] centers bound by DsrA, and another four [4Fe4S] centers in the ferredoxin domains. A sulfite molecule, coordinating the siroheme, is found at the active site. The DsrC protein is bound in a cleft between DsrA and DsrB with its conserved C-terminal cysteine reaching the distal side of the siroheme. We propose a novel mechanism for the process of sulfite reduction involving DsrAB, DsrC, and the DsrMKJOP membrane complex (a membrane complex with putative disulfide/thiol reductase activity), in which two of the six electrons for reduction of sulfite derive from the membrane quinone pool. These results show that DsrC is involved in sulfite reduction, which changes the mechanism of sulfate respiration. This has important implications for models used to date ancient sulfur metabolism based on sulfur isotope fractionations.


    Related Citations: 
    • Purification, Crystallization and Preliminary Crystallographic Analysis of a Dissimilatory Dsrab Sulfite Reductase in Complex with Dsrc.
      Oliveira, T.F.,Vonrhein, C.,Matias, P.M.,Venceslau, S.S.,Pereira, I.A.,Archer, M.
      (2008) J.Struct.Biol. 164: 236


    Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa (ITQB-UNL), Av. da República - EAN, 2780-157 Oeiras, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT ALPHA
A, D
437Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 0 
Gene Names: dsvA (dsrA)
Find proteins for P45574 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  P45574
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT BETA
B, E
381Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 0 
Gene Names: dsvB (dsrB)
EC: 1.8.99.5
Find proteins for P45575 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  P45575
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT GAMMA
C, F
105Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 0 
Gene Names: dsvC
EC: 1.8.99.5
Find proteins for P45573 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  P45573
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

Download SDF File 
Download CCD File 
B, E
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
SH0
Query on SH0

Download SDF File 
Download CCD File 
A, D
3,3',3'',3'''-[(1R,2S,3S,4S,7S,8S,11S,12S,13S,16S,19S)-3,8,13,17-tetrakis(carboxylatomethyl)-8,13-dimethyl-1,2,3,4,7,8,11,12,13,16,19,20,22,24-tetradecahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoate
Sirohydrochlorin
C42 H52 N4 O16
PTDGOSZHGZMQAZ-IIRIWOCESA-N
 Ligand Interaction
SRM
Query on SRM

Download SDF File 
Download CCD File 
B, E
SIROHEME
C42 H42 Fe N4 O16
PGYXHNRRBJLFEV-NBUGCWMUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.410α = 90.00
b = 118.900β = 104.13
c = 132.240γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTER-TNTrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2014-07-16
    Type: Atomic model, Derived calculations, Non-polymer description, Version format compliance