2BLF

Sulfite dehydrogenase from Starkeya Novella


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Molecular Basis of Intramolecular Electron Transfer in Sulfite-Oxidizing Enzymes is Revealed by High Resolution Structure of a Heterodimeric Complex of the Catalytic Molybdopterin Subunit and a C-Type Cytochrome Subunit.

Kappler, U.Bailey, S.

(2005) J.Biol.Chem. 280: 24999

  • DOI: 10.1074/jbc.M503237200
  • Primary Citation of Related Structures:  
  • Also Cited By: 2CA3, 2CA4, 2C9X

  • PubMed Abstract: 
  • Sulfite-oxidizing molybdoenzymes convert the highly reactive and therefore toxic sulfite to sulfate and have been identified in insects, animals, plants, and bacteria. Although the well studied enzymes from higher animals serve to detoxify sulfite th ...

    Sulfite-oxidizing molybdoenzymes convert the highly reactive and therefore toxic sulfite to sulfate and have been identified in insects, animals, plants, and bacteria. Although the well studied enzymes from higher animals serve to detoxify sulfite that arises from the catabolism of sulfur-containing amino acids, the bacterial enzymes have a central role in converting sulfite formed during dissimilatory oxidation of reduced sulfur compounds. Here we describe the structure of the Starkeya novella sulfite dehydrogenase, a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit, that reveals the molecular mechanism of intramolecular electron transfer in sulfite-oxidizing enzymes. The close approach of the two redox centers in the protein complex (Mo-Fe distance 16.6 A) allows for rapid electron transfer via tunnelling or aided by the protein environment. The high resolution structure of the complex has allowed the identification of potential through-bond pathways for electron transfer including a direct link via Arg-55A and/or an aromatic-mediated pathway. A potential site of electron transfer to an external acceptor cytochrome c was also identified on the SorB subunit on the opposite side to the interaction with the catalytic SorA subunit.


    Related Citations: 
    • Crystallisation and Preliminary X-Ray Analysis of Sulfite Dehydrogenase from Starkeya Novella.
      Kappler, U.,Bailey, S.
      (2004) Acta Crystallogr. 60: 2070


    Organizational Affiliation

    Centre for Metals in Biology, University of Queensland, St. Lucia, Queensland 4072, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sulfite:cytochrome c oxidoreductase subunit A
A
373Starkeya novellaMutation(s): 0 
Gene Names: sorA
Find proteins for Q9LA16 (Starkeya novella)
Go to UniProtKB:  Q9LA16
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sulfite:cytochrome c oxidoreductase subunit B
B
81Starkeya novellaMutation(s): 0 
Gene Names: sorB
Find proteins for Q9LA15 (Starkeya novella)
Go to UniProtKB:  Q9LA15
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MSS
Query on MSS

Download SDF File 
Download CCD File 
A
(MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM
C10 H12 Mo N5 O7 P S2
BDXDYZBRBRKVRM-MRZGRPIRSA-L
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.136 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 97.466α = 90.00
b = 92.513β = 90.00
c = 55.897γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
CCP4phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-28
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 2.0: 2018-02-07
    Type: Advisory, Atomic model, Database references, Derived calculations, Source and taxonomy, Structure summary