2XSJ

Structure of desulforubidin from Desulfomicrobium norvegicum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 

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This is version 2.1 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: https://doi.org/10.3389/fmicb.2011.00071
  • Primary Citation of Related Structures:  
    2XSJ

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SULFITE REDUCTASE ALPHA SUBUNIT
A, D
437Desulfomicrobium norvegicumMutation(s): 0 
EC: 1.8.99.3
UniProt
Find proteins for Q93UT1 (Desulfomicrobium norvegicum (strain DSM 1741 / NCIMB 8310))
Explore Q93UT1 
Go to UniProtKB:  Q93UT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93UT1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SULFITE REDUCTASE BETA SUBUNIT
B, E
386Desulfomicrobium norvegicumMutation(s): 0 
EC: 1.8.99.3
UniProt
Find proteins for Q93UT0 (Desulfomicrobium norvegicum (strain DSM 1741 / NCIMB 8310))
Explore Q93UT0 
Go to UniProtKB:  Q93UT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93UT0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SULFUR RELAY PROTEIN, TUSE/DSRC/DSVC FAMILY
C, F
105Desulfomicrobium norvegicumMutation(s): 0 
EC: 1.8.99.3
UniProt
Find proteins for C7LV29 (Desulfomicrobium baculatum (strain DSM 4028 / VKM B-1378 / X))
Explore C7LV29 
Go to UniProtKB:  C7LV29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7LV29
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SRM
Query on SRM

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
P [auth D],
S [auth E]
SIROHEME
C42 H44 Fe N4 O16
DLKSSIHHLYNIKN-MWBYXLBFSA-L
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: 2.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.34α = 90
b = 135.09β = 90
c = 178.03γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2011-09-14
    Changes: Database references
  • Version 2.0: 2023-12-06
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Refinement description