6ELK

C.elegans MnSOD-3 mutant - Q142H

• PDB DOI: https://doi.org/10.2210/pdb6ELK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-09-29 Released: 2017-12-06 
• Deposition Author(s): Hunter, G.J., Trinh, C.H., Hunter, T.
• Funding Organization(s): UoM

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.210 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

A Single Mutation is Sufficient to Modify the Metal Selectivity and Specificity of a Eukaryotic Manganese Superoxide Dismutase to Encompass Iron.

Hunter, T., Bonetta, R., Sacco, A., Vella, M., Sultana, P.M., Trinh, C.H., Fadia, H.B.R., Borowski, T., Garcia-Fandino, R., Stockner, T., Hunter, G.J.

(2018) Chemistry 24: 5303-5308

• PubMed: 29178484 
• DOI: https://doi.org/10.1002/chem.201704655
• Primary Citation of Related Structures:  
  6ELK


• PubMed Abstract: 
  

  We have generated a site-directed mutant of the manganese superoxide dismutase SOD-3 of C.elegans (MnSOD-3) which modifies the metal specificity of the enzyme. While wild-type MnSOD-3 functions with manganese in the active site (3600 U mg ^-1 of protein) it has little or no activity when iron is incorporated. However, when histidine replaces glutamine 142 in the active site, the enzyme retains 50 % of its activity and becomes cambialistic for its metal cofactor exhibiting very similar specific activity with either manganese or iron.

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Organizational Affiliation: 

Department of Physiology and Biochemistry, University of Malta, Msida, MSD2080, Malta.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.52 kDa 
• Atom Count: 3,513 
• Modelled Residue Count: 388 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Mn] 2, mitochondrial	A, B [auth C]	195	Caenorhabditis elegans	Mutation(s): 1  Gene Names: sod-3, C08A9.1 EC: 1.15.1.1
UniProt
Find proteins for P41977 (Caenorhabditis elegans) Explore P41977  Go to UniProtKB:  P41977

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], H [auth C], I [auth C], J [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	K [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	C [auth A], G [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.210 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.53	α = 90
b = 81.53	β = 90
c = 137.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Hunter, G.J., Trinh, C.H., Hunter, T.

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Funding Organization	Location	Grant Number
UoM	Malta	MDS-BP

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description