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: 31.72 kDa 
• Atom Count: 1878 
• Modelled Residue Count: 254 
• Deposited Residue Count: 306 
• Unique protein chains: 1

4MCN

Human SOD1 C57S Mutant, Metal-free

• PDB DOI: 10.2210/pdb4MCN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2013-08-21 Released: 2014-08-27 
• Deposition Author(s): Sea, K., Sohn, S.H., Durazo, A., Sheng, Y., Shaw, B., Cao, X., Taylor, A.B., Whitson, L.J., Holloway, S.P., Hart, P.J., Cabelli, D.E., Gralla, E.B., Valentine, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.245 
• R-Value Work: 0.189 
• R-Value Observed: 0.194 

Literature

Insights into the role of the unusual disulfide bond in copper-zinc superoxide dismutase.

Sea, K., Sohn, S.H., Durazo, A., Sheng, Y., Shaw, B.F., Cao, X., Taylor, A.B., Whitson, L.J., Holloway, S.P., Hart, P.J., Cabelli, D.E., Gralla, E.B., Valentine, J.S.

(2015) J Biol Chem 290: 2405-2418

• PubMed: 25433341 
• DOI: 10.1074/jbc.M114.588798
• Primary Citation of Related Structures:  
  4MCM, 4MCN


• PubMed Abstract: 
  

The functional and structural significance of the intrasubunit disulfide bond in copper-zinc superoxide dismutase (SOD1) was studied by characterizing mutant forms of human SOD1 (hSOD) and yeast SOD1 lacking the disulfide bond. We determined x-ray crystal structures of metal-bound and metal-deficient hC57S SOD1. C57S hSOD1 isolated from yeast contained four zinc ions per protein dimer and was structurally very similar to wild type. The addition of copper to this four-zinc protein gave properly reconstituted 2Cu,2Zn C57S hSOD, and its spectroscopic properties indicated that the coordination geometry of the copper was remarkably similar to that of holo wild type hSOD1. In contrast, the addition of copper and zinc ions to apo C57S human SOD1 failed to give proper reconstitution. Using pulse radiolysis, we determined SOD activities of yeast and human SOD1s lacking disulfide bonds and found that they were enzymatically active at ∼10% of the wild type rate. These results are contrary to earlier reports that the intrasubunit disulfide bonds in SOD1 are essential for SOD activity. Kinetic studies revealed further that the yeast mutant SOD1 had less ionic attraction for superoxide, possibly explaining the lower rates. Saccharomyces cerevisiae cells lacking the sod1 gene do not grow aerobically in the absence of lysine, but expression of C57S SOD1 increased growth to 30-50% of the growth of cells expressing wild type SOD1, supporting that C57S SOD1 retained a significant amount of activity.

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Organizational Affiliation: 

From the Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, the Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, Korea [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, B	153	Homo sapiens	Mutation(s): 1  Gene Names: SOD1 EC: 1.15.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens) Explore P00441  Go to UniProtKB:  P00441
PHAROS:  P00441 GTEx:  ENSG00000142168

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.245 
• R-Value Work: 0.189 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.926	α = 90
b = 56.048	β = 90
c = 105.539	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-21 
• Released Date: 2014-08-27 
Deposition Author(s): Sea, K., Sohn, S.H., Durazo, A., Sheng, Y., Shaw, B., Cao, X., Taylor, A.B., Whitson, L.J., Holloway, S.P., Hart, P.J., Cabelli, D.E., Gralla, E.B., Valentine, J.S.

Revision History  

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Database references
• Version 1.2: 2015-02-11
  Changes: Database references