7DDW

Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase S126C

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The role of S126 in the Staphylococcus equorum MnSOD activity and stability.

Soefie Retnoningrum, D., Yoshida, H., Dzaky Razani, M., Muliadi, R., Felix Meidianto, V., Artarini, A., Tirta Ismaya, W.

(2021) J Struct Biol : 107731-107731

  • DOI: 10.1016/j.jsb.2021.107731
  • Primary Citation of Related Structures:  
    7DDW

  • PubMed Abstract: 

    • The dimeric form of manganese superoxide dismutase is instrumental for activity because each of the monomers provides amino acid residues participating in the enzymatic reaction. Hence, preventing dissociation of the dimer would maintain the enzymatic activity in detrimental conditions e ...

    The dimeric form of manganese superoxide dismutase is instrumental for activity because each of the monomers provides amino acid residues participating in the enzymatic reaction. Hence, preventing dissociation of the dimer would maintain the enzymatic activity in detrimental conditions e.g. high temperature. To prevent dissociation of the dimer, a disulphide (S-S) bond was introduced at the dimer interface. In the wild type structure, S126 interacts with S126 of the other monomer. In the presented work, a mutant was designed with an S126C substitution. The crystal structure of the S126C mutant showed that only 50-70% of monomers formed the S-S bond. This observed imperfect S-S bonding was likely caused by photolytic S-S bond breakage mediated by the neighbouring tryptophan residue. In the wild type, S126 is located facing W163 and forms a water-mediated hydrogen bond with E164; W163 and E164 are crucial in the enzyme's activity. The replacement of S126 by a cysteine residue lowered the activity of the enzyme by ~70%. S126 has never been considered to play a role in the enzyme's activity or stability, thus the finding showed the importance of this residue.

    Related Citations: 
    • The first crystal structure of manganese superoxide dismutase from the genus Staphylococcus.
      Retnoningrum, D.S., Yoshida, H., Arumsari, S., Kamitori, S., Ismaya, W.T.
      (2018) Acta Crystallogr F Struct Biol Commun 74: 135
    Organizational Affiliation: 

    Dexa Laboratories of Biomolecular Sciences, Dexa Medica, Industri Selatan V Blok PP-7, Cikarang 17750, West Java, Indonesia.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Superoxide dismutase A, B, C, D, E, F205Staphylococcus equorumMutation(s): 2 
Gene Names: AST02_02815
EC: 1.15.1.1
Find proteins for A0A1E5TT85 (Staphylococcus equorum)
Explore A0A1E5TT85 
Go to UniProtKB:  A0A1E5TT85
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.287α = 90
b = 131.732β = 110.35
c = 80.188γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references