7WNK | pdb_00007wnk

Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase K38R and A121E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.194 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.178 (Depositor) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7WNK

This is version 1.4 of the entry. See complete history

Literature

Introducing Intermolecular Interaction to Strengthen the Stability of MnSOD Dimer.

Retnoningrum, D.S.Yoshida, H.Pajatiwi, I.Muliadi, R.Utami, R.A.Artarini, A.Ismaya, W.T.

(2023) Appl Biochem Biotechnol 195: 4537-4551

  • DOI: https://doi.org/10.1007/s12010-023-04347-7
  • Primary Citation Related Structures: 
    7W6W, 7WNK, 7WNL

  • PubMed Abstract: 

    Manganese superoxide dismutase from Staphylococcus equorum (MnSODSeq) maintains its activity upon treatments like a wide range of pH, addition of detergent and denaturing agent, exposure to ultraviolet light, and heating up to 50 °C. The enzyme dimer dissociates at 52-55 °C, while its monomer unfolds at 63-67 °C. MnSOD dimeric form is indispensable for the enzyme activity; therefore, strengthening the interactions between the monomers is the most preferred strategy to improve the enzyme stability. However, to date, modification of MnSODSeq at the dimer interface has been unfruitful despite excluding the inner and outer sphere regions that are important to the enzyme activity. Here, a new strategy was developed and K38R-A121E/Y double substitutions were proposed. These mutants displayed similar enzyme activity to the wild type. K38R-A121E dimer was thermally more stable and its monomer stability was similar to the wild type. The thermal stability of K38R-A121Y dimer was similar to the wild type but its monomer was thermally less stable. In addition, the structure of the previously reported L169W mutant was also elucidated. The L169W mutant structure showed that intramolecular modification can decrease flexibility of the MnSODSeq monomer and leads to a less stable enzyme with similar activity to the wild type. Thus, while the enzyme activity depends on arrangement of residues in the dimer interface, the stability appears to depend more on its monomeric architecture. Furthermore, in the L169W structure in complex with azide, which is a specific inhibitor for MnSOD, one of the azide molecules was present in the dimer interface region that previously has been identified to involve in the enzymatic reaction. Nevertheless, the present results show that an MnSODSeq mutant with better thermal stability has been obtained.


  • Organizational Affiliation
    • Laboratory of Pharmaceutical Biotechnology, Pharmaceutics Research Group, School of Pharmacy, Institut Teknologi Bandung, Ganesha 10, Bandung, 40132, West Java, Indonesia.

Macromolecule Content 

  • Total Structure Weight: 95.07 kDa 
  • Atom Count: 7,411 
  • Modeled Residue Count: 798 
  • Deposited Residue Count: 820 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase
A, B, C, D
205Staphylococcus equorumMutation(s): 3 
Gene Names: AST02_02815
EC: 1.15.1.1
UniProt
Find proteins for A0A1E5TT85 (Staphylococcus equorum)
Explore A0A1E5TT85 
Go to UniProtKB:  A0A1E5TT85
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1E5TT85
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
F [auth A],
P [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
BR

Query on BR



Download:Ideal Coordinates CCD File
O [auth D]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
MN

Query on MN



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
K [auth C],
M [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
AZI

Query on AZI



Download:Ideal Coordinates CCD File
G [auth B],
I [auth B],
J [auth B],
L [auth C],
N [auth D]
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.194 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.178 (Depositor) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.765α = 90
b = 113.174β = 90
c = 119.908γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentIndonesia079/E4.1/AK.04.PT/2021

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2023-02-08
    Changes: Database references
  • Version 1.3: 2023-07-12
    Changes: Database references
  • Version 1.4: 2023-11-29
    Changes: Data collection, Refinement description