Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 43.99 kDa 
• Atom Count: 3220 
• Residue Count: 392 
• Unique protein chains: 1

2QKC

Structural and Kinetic Study of the Differences between Human and E.coli Manganese Superoxide Dismutases

• DOI: 10.2210/pdb2QKC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-07-10 Released: 2008-07-29 
• Deposition Author(s): Zheng, J., Domsic, J.F., Cabelli, D., McKenna, R., Silverman, D.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.206 
• R-Value Work: 0.199 

Literature

Structural and kinetic study of differences between human and Escherichia coli manganese superoxide dismutases.

Zheng, J., Domsic, J.F., Cabelli, D., McKenna, R., Silverman, D.N.

(2007) Biochemistry 46: 14830-14837

• PubMed: 18044968 
• DOI: 10.1021/bi7014103
• Primary Citation of Related Structures:  
  2QKC, 2QKA


• PubMed Abstract: 
  

Human manganese superoxide dismutase (MnSOD) is characterized by a product inhibition stronger than that observed in bacterial forms of MnSOD. Previous studies show that the conserved, active-site residue Tyr34 mediates product inhibition; however, the protein environment of Tyr34 is different in human and Escherichia coli MnSOD. We have prepared two site-specific mutants of human MnSOD with replacements of Phe66 with Ala and Leu (F66A and F66L, respectively), altering the surroundings of Tyr34. Pulse radiolysis was used to generate superoxide, and measurements of catalysis were taken in single-turnover experiments by observing the visible absorbance of species of MnSOD and under catalytic conditions observing the absorbance of superoxide. The mutation of Phe66 to Leu resulted in a mutant of human MnSOD with weakened product inhibition resembling that of E. coli MnSOD. Moreover, the mechanism of this weakened product inhibition was similar to that in E. coli MnSOD, specifically a decrease in the rate constant for the oxidative addition of superoxide to Mn2+MnSOD leading to the formation of the peroxide-inhibited enzyme. In addition, the crystal structures of both mutants have been determined and compared to those of wild-type human and E. coli MnSOD. The crystallographic data suggest that the solvent structure and its mobility as well as side chain conformations may affect the extent of product inhibition. These data emphasize the role of residue 66 in catalysis and inhibition and provide a structural explanation for differences in catalytic properties between human and certain bacterial forms of MnSOD.

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Organizational Affiliation: 

Department of Pharmacology and Therapeutics, University of Florida, Gainesville, Florida 32610, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Mn]	A, C	196	Homo sapiens	Mutation(s): 1  Gene Names: SOD2 EC: 1.15.1.1
Find proteins for P04179 (Homo sapiens) Explore P04179  Go to UniProtKB:  P04179
NIH Common Fund Data Resources
PHAROS:  P04179 GTEx:  ENSG00000112096

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	A, C	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.206 
• R-Value Work: 0.199 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.108	α = 90
b = 81.108	β = 90
c = 242.545	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-07-10 
• Released Date: 2008-07-29 
Deposition Author(s): Zheng, J., Domsic, J.F., Cabelli, D., McKenna, R., Silverman, D.N.

Revision History 

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description