4MCM

Human SOD1 C57S Mutant, As-isolated


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

    From the Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, the Department of Wine Studies, Santa Rosa Junior College, Santa Rosa, California 95401, kevinsea@yahoo.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
153Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00441
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth E]
EA [auth F]
HA [auth G]
KA [auth H]
LA [auth H]
BA [auth E],
EA [auth F],
HA [auth G],
KA [auth H],
LA [auth H],
O [auth A],
OA [auth I],
R [auth B],
RA [auth J],
S [auth B],
UA [auth K],
V [auth C],
XA [auth L],
Y [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth E]
CA [auth F]
DA [auth F]
FA [auth G]
GA [auth G]
AA [auth E],
CA [auth F],
DA [auth F],
FA [auth G],
GA [auth G],
IA [auth H],
JA [auth H],
M [auth A],
MA [auth I],
N [auth A],
NA [auth I],
P [auth B],
PA [auth J],
Q [auth B],
QA [auth J],
SA [auth K],
T [auth C],
TA [auth K],
U [auth C],
VA [auth L],
W [auth D],
WA [auth L],
X [auth D],
Z [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.53α = 90
b = 163.883β = 90
c = 174.14γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description