3HBP

The crystal structure of C185S mutant of recombinant sulfite oxidase with bound substrate, sulfite, at the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structures of the C185S and C185A mutants of sulfite oxidase reveal rearrangement of the active site.

Qiu, J.A.Wilson, H.L.Pushie, M.J.Kisker, C.George, G.N.Rajagopalan, K.V.

(2010) Biochemistry 49: 3989-4000

  • DOI: 10.1021/bi1001954
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sulfite oxidase (SO) catalyzes the physiologically critical conversion of sulfite to sulfate. Enzymatic activity is dependent on the presence of the metal molybdenum complexed with a pyranopterin-dithiolene cofactor termed molybdopterin. Comparison o ...

    Sulfite oxidase (SO) catalyzes the physiologically critical conversion of sulfite to sulfate. Enzymatic activity is dependent on the presence of the metal molybdenum complexed with a pyranopterin-dithiolene cofactor termed molybdopterin. Comparison of the amino acid sequences of SOs from a variety of sources has identified a single conserved Cys residue essential for catalytic activity. The crystal structure of chicken liver sulfite oxidase indicated that this residue, Cys185 in chicken SO, coordinates the Mo atom in the active site. To improve our understanding of the role of this residue in the catalytic mechanism of sulfite oxidase, serine and alanine variants at position 185 of recombinant chicken SO were generated. Spectroscopic and kinetic studies indicate that neither variant is capable of sulfite oxidation. The crystal structure of the C185S variant was determined to 1.9 A resolution and to 2.4 A resolution in the presence of sulfite, and the C185A variant to 2.8 A resolution. The structures of the C185S and C185A variants revealed that neither the Ser or Ala side chains appeared to closely interact with the Mo atom and that a third oxo group replaced the usual cysteine sulfur ligand at the Mo center, confirming earlier extended X-ray absorption fine structure spectroscopy (EXAFS) work on the human C207S mutant. An unexpected result was that in the C185S variant, in the absence of sulfite, the active site residue Tyr322 became disordered as did the loop region flanking it. In the C185S variant crystallized in the presence of sulfite, the Tyr322 residue relocalized to the active site. The C185A variant structure also indicated the presence of a third oxygen ligand; however, Tyr322 remained in the active site. EXAFS studies of the Mo coordination environment indicate the Mo atom is in the oxidized Mo(VI) state in both the C185S and C185A variants of chicken SO and show the expected trioxodithiolene active site. Density functional theory calculations of the trioxo form of the cofactor reasonably reproducd the Mo horizontal lineO distances of the complex; however, the calculated Mo-S distances were slightly longer than either crystallographic or EXAFS measurements. Taken together, these results indicate that the active sites of the C185S and C185A variants are essentially catalytically inactive, the crystal structures of C185S and C185A variants contain a fully oxidized, trioxo form of the cofactor, and Tyr322 can undergo a conformational change that is relevant to the reaction mechanism. Additional DFT calculations demonstrated that such methods can reasonably reproduce the geometry and bond lengths of the active site.


    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sulfite Oxidase mutant C185S
A
466Gallus gallusMutation(s): 0 
Gene Names: SUOX
EC: 1.8.3.1
Find proteins for P07850 (Gallus gallus)
Go to Gene View: SUOX
Go to UniProtKB:  P07850
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO3
Query on SO3

Download SDF File 
Download CCD File 
A
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
MTE
Query on MTE

Download SDF File 
Download CCD File 
A
PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C10 H14 N5 O6 P S2
HPEUEJRPDGMIMY-IFQPEPLCSA-N
 Ligand Interaction
MOM
Query on MOM

Download SDF File 
Download CCD File 
A
HYDROXY(DIOXO)MOLYBDENUM
H Mo O3
WEHYDZQUOLJPRX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.179 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 86.284α = 90.00
b = 86.284β = 90.00
c = 152.339γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-05-04 
  • Released Date: 2010-04-14 
  • Deposition Author(s): Qiu, J.A.

Revision History 

  • Version 1.0: 2010-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description