2XSJ

Structure of desulforubidin from Desulfomicrobium norvegicum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insights Into Dissimilatory Sulfite Reductases: Structure of Desulforubidin from Desulfomicrobium Norvegicum

Oliveira, T.F.Franklin, E.Afonso, J.P.Khan, A.R.Oldham, N.J.Pereira, I.A.C.Archer, M.

(2011) Front.Microbiol. 2: 71

  • DOI: 10.3389/fmicb.2011.00071

  • PubMed Abstract: 
  • Dissimilatory sulfite reductases (dSiRs) are crucial enzymes in bacterial sulfur-based energy metabolism, which are likely to have been present in some of the earliest life forms on Earth. Several classes of dSiRs have been proposed on the basis of d ...

    Dissimilatory sulfite reductases (dSiRs) are crucial enzymes in bacterial sulfur-based energy metabolism, which are likely to have been present in some of the earliest life forms on Earth. Several classes of dSiRs have been proposed on the basis of different biochemical and spectroscopic properties, but it is not clear whether this corresponds to actual physiological or structural differences. Here, we describe the first structure of a dSiR from the desulforubidin class isolated from Desulfomicrobium norvegicum. The desulforubidin (Drub) structure is assembled as α(2)β(2)γ(2), in which two DsrC proteins are bound to the core [DsrA](2)[DsrB](2) unit, as reported for the desulfoviridin (Dvir) structure from Desulfovibrio vulgaris. Unlike Dvir, four sirohemes and eight [4Fe-4S] clusters are present in Drub. However, the structure indicates that only two of the Drub coupled siroheme-[4Fe-4S] cofactors are catalytically active. Mass spectrometry studies of purified Drub and Dvir show that both proteins present different oligomeric complex forms that bind two, one, or no DsrC proteins, providing an explanation for conflicting spectroscopic and biochemical results in the literature, and further indicating that DsrC is not a subunit of dSiR, but rather a protein with which it interacts.


    Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SULFITE REDUCTASE ALPHA SUBUNIT
A, D
437Desulfomicrobium norvegicum (strain DSM 1741 / NCIMB 8310)Mutation(s): 0 
Gene Names: dsrA
Find proteins for Q93UT1 (Desulfomicrobium norvegicum (strain DSM 1741 / NCIMB 8310))
Go to UniProtKB:  Q93UT1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SULFITE REDUCTASE BETA SUBUNIT
B, E
386Desulfomicrobium norvegicum (strain DSM 1741 / NCIMB 8310)Mutation(s): 0 
Gene Names: dsrB
Find proteins for Q93UT0 (Desulfomicrobium norvegicum (strain DSM 1741 / NCIMB 8310))
Go to UniProtKB:  Q93UT0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SULFUR RELAY PROTEIN, TUSE/DSRC/DSVC FAMILY
C, F
105Desulfomicrobium baculatum (strain DSM 4028 / VKM B-1378)Mutation(s): 0 
Find proteins for C7LV29 (Desulfomicrobium baculatum (strain DSM 4028 / VKM B-1378))
Go to UniProtKB:  C7LV29
Small Molecules
Ligands 3 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
SRM
Query on SRM

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 99.340α = 90.00
b = 135.090β = 90.00
c = 178.030γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2011-09-14
    Type: Database references