Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.83 kDa 
• Atom Count: 6539 
• Modelled Residue Count: 728 
• Deposited Residue Count: 744 
• Unique protein chains: 1

2A9D

Crystal structure of recombinant chicken sulfite oxidase with Arg at residue 161

• PDB DOI: 10.2210/pdb2A9D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-07-11 Released: 2005-08-02 
• Deposition Author(s): Karakas, E., Wilson, H.L., Graf, T.N., Xiang, S., Jaramillo-Busquets, S., Rajagopalan, K.V., Kisker, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.187 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

Literature

Structural insights into sulfite oxidase deficiency

Karakas, E., Wilson, H.L., Graf, T.N., Xiang, S., Jaramillo-Busquets, S., Rajagopalan, K.V., Kisker, C.

(2005) J Biol Chem 280: 33506-33515

• PubMed: 16048997 
• DOI: 10.1074/jbc.M505035200
• Primary Citation of Related Structures:  
  2A99, 2A9A, 2A9B, 2A9C, 2A9D


• PubMed Abstract: 
  

Sulfite oxidase deficiency is a lethal genetic disease that results from defects either in the genes encoding proteins involved in molybdenum cofactor biosynthesis or in the sulfite oxidase gene itself. Several point mutations in the sulfite oxidase gene have been identified from patients suffering from this disease worldwide. Although detailed biochemical analyses have been carried out on these mutations, no structural data could be obtained because of problems in crystallizing recombinant human and rat sulfite oxidases and the failure to clone the chicken sulfite oxidase gene. We synthesized the gene for chicken sulfite oxidase de novo, working backward from the amino acid sequence of the native chicken liver enzyme by PCR amplification of a series of 72 overlapping primers. The recombinant protein displayed the characteristic absorption spectrum of sulfite oxidase and exhibited steady state and rapid kinetic parameters comparable with those of the tissue-derived enzyme. We solved the crystal structures of the wild type and the sulfite oxidase deficiency-causing R138Q (R160Q in humans) variant of recombinant chicken sulfite oxidase in the resting and sulfate-bound forms. Significant alterations in the substrate-binding pocket were detected in the structure of the mutant, and a comparison between the wild type and mutant protein revealed that the active site residue Arg-450 adopts different conformations in the presence and absence of bound sulfate. The size of the binding pocket is thereby considerably reduced, and its position relative to the cofactor is shifted, causing an increase in the distance of the sulfur atom of the bound sulfate to the molybdenum.

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Organizational Affiliation: 

Department of Pharmacological Sciences, State University of New York, Stony Brook, New York 11794-5115, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfite Oxidase	A, B	372	Gallus gallus	Mutation(s): 1  Gene Names: SUOX EC: 1.8.3.1
UniProt
Find proteins for P07850 (Gallus gallus) Explore P07850  Go to UniProtKB:  P07850

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTE	E [auth A], I [auth B]	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
SO4	C [auth A], D [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MO	F [auth A], J [auth B]	MOLYBDENUM ATOM Mo ZOKXTWBITQBERF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.187 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.137	α = 90
b = 123.102	β = 94.31
c = 55.129	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing
REFMAC	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-07-11 
• Released Date: 2005-08-02 
Deposition Author(s): Karakas, E., Wilson, H.L., Graf, T.N., Xiang, S., Jaramillo-Busquets, S., Rajagopalan, K.V., Kisker, C.

Revision History  

• Version 1.0: 2005-08-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations