2CA3

Sulfite dehydrogenase from Starkeya Novella r55m mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Basis for Enzymatic Sulfite Oxidation: How Three Conserved Active Site Residues Shape Enzyme Activity.

Bailey, S.Rapson, T.Johnson-Winters, K.Astashkin, A.V.Enemark, J.H.Kappler, U.

(2009) J.Biol.Chem. 284: 2053

  • DOI: 10.1074/jbc.M807718200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sulfite dehydrogenases (SDHs) catalyze the oxidation and detoxification of sulfite to sulfate, a reaction critical to all forms of life. Sulfite-oxidizing enzymes contain three conserved active site amino acids (Arg-55, His-57, and Tyr-236) that are ...

    Sulfite dehydrogenases (SDHs) catalyze the oxidation and detoxification of sulfite to sulfate, a reaction critical to all forms of life. Sulfite-oxidizing enzymes contain three conserved active site amino acids (Arg-55, His-57, and Tyr-236) that are crucial for catalytic competency. Here we have studied the kinetic and structural effects of two novel and one previously reported substitution (R55M, H57A, Y236F) in these residues on SDH catalysis. Both Arg-55 and His-57 were found to have key roles in substrate binding. An R55M substitution increased Km(sulfite)(app) by 2-3 orders of magnitude, whereas His-57 was required for maintaining a high substrate affinity at low pH when the imidazole ring is fully protonated. This effect may be mediated by interactions of His-57 with Arg-55 that stabilize the position of the Arg-55 side chain or, alternatively, may reflect changes in the protonation state of sulfite. Unlike what is seen for SDHWT and SDHY236F, the catalytic turnover rates of SDH R55M and SDHH57A are relatively insensitive to pH (approximately 60 and 200 s(-1), respectively). On the structural level, striking kinetic effects appeared to correlate with disorder (in SDHH57A and SDHY236F) or absence of Arg-55 (SDHR55M), suggesting that Arg-55 and the hydrogen bonding interactions it engages in are crucial for substrate binding and catalysis. The structure of SDHR55M has sulfate bound at the active site, a fact that coincides with a significant increase in the inhibitory effect of sulfate in SDHR55M. Thus, Arg-55 also appears to be involved in enabling discrimination between the substrate and product in SDH.


    Related Citations: 
    • 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


    Organizational Affiliation

    Molecular Biophysics Group, Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SULFITE\:CYTOCHROME C OXIDOREDUCTASE SUBUNIT A
A
373Starkeya novellaMutation(s): 1 
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: 2 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 97.654α = 90.00
b = 93.321β = 90.00
c = 56.035γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance