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: 2.10 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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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: https://doi.org/10.1074/jbc.M805643200
  • Primary Citation of Related Structures:  
    2V4J

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT ALPHA
A, D
437Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 0 
EC: 1.8.99.3
UniProt
Find proteins for P45574 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P45574 
Go to UniProtKB:  P45574
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45574
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT BETA
B, E
381Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 0 
EC: 1.8.99.3
UniProt
Find proteins for P45575 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P45575 
Go to UniProtKB:  P45575
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45575
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT GAMMA
C, F
105Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 0 
EC: 1.8.99.3
UniProt
Find proteins for P45573 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P45573 
Go to UniProtKB:  P45573
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45573
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SRM
Query on SRM

Download Ideal Coordinates CCD File 
L [auth B],
S [auth E]
SIROHEME
C42 H44 Fe N4 O16
DLKSSIHHLYNIKN-MWBYXLBFSA-L
SH0
Query on SH0

Download Ideal Coordinates CCD File 
I [auth A],
P [auth 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
C42 H52 N4 O16
PTDGOSZHGZMQAZ-IIRIWOCESA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
J [auth B]
K [auth B]
N [auth D]
G [auth A],
H [auth A],
J [auth B],
K [auth B],
N [auth D],
O [auth D],
Q [auth E],
R [auth E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
SO3
Query on SO3

Download Ideal Coordinates CCD File 
M [auth B],
T [auth E]
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.41α = 90
b = 118.9β = 104.13
c = 132.24γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2014-07-16
    Changes: Atomic model, Derived calculations, Non-polymer description, Version format compliance
  • Version 2.0: 2023-12-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary