8VHW | pdb_00008vhw

Neutron Structure of Peroxide-Soaked Trp161Phe MnSOD


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.277 (Depositor) 
  • R-Value Work: 
    0.248 (Depositor) 
  • R-Value Observed: 
    0.250 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition.

Azadmanesh, J.Slobodnik, K.Struble, L.R.Lutz, W.E.Coates, L.Weiss, K.L.Myles, D.A.A.Kroll, T.Borgstahl, G.E.O.

(2024) Nat Commun 15: 5973-5973

  • DOI: https://doi.org/10.1038/s41467-024-50260-w
  • Primary Citation of Related Structures:  
    8VHW, 8VHY, 8VJ0, 8VJ4, 8VJ5, 8VJ8

  • PubMed Abstract: 

    Human manganese superoxide dismutase (MnSOD) is a crucial oxidoreductase that maintains the vitality of mitochondria by converting superoxide (O 2 ●- ) to molecular oxygen (O 2 ) and hydrogen peroxide (H 2 O 2 ) with proton-coupled electron transfers (PCETs). Human MnSOD has evolved to be highly product inhibited to limit the formation of H 2 O 2 , a freely diffusible oxidant and signaling molecule. The product-inhibited complex is thought to be composed of a peroxide (O 2 2- ) or hydroperoxide (HO 2 - ) species bound to Mn ion and formed from an unknown PCET mechanism. PCET mechanisms of proteins are typically not known due to difficulties in detecting the protonation states of specific residues that coincide with the electronic state of the redox center. To shed light on the mechanism, we combine neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states of the enzyme to reveal the positions of all the atoms, including hydrogen, and the electronic configuration of the metal ion. The data identifies the product-inhibited complex, and a PCET mechanism of inhibition is constructed.


  • Organizational Affiliation
    • Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, 68198-6805, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Mn], mitochondrial
A, B
199Homo sapiensMutation(s): 1 
Gene Names: SOD2
EC: 1.15.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04179 (Homo sapiens)
Explore P04179 
Go to UniProtKB:  P04179
PHAROS:  P04179
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04179
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.277 (Depositor) 
  • R-Value Work:  0.248 (Depositor) 
  • R-Value Observed: 0.250 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.8α = 90
b = 77.8β = 90
c = 236.8γ = 120

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM145647
National Aeronautics and Space Administration (NASA, United States)United States44-0307-1021-201
Department of Energy (DOE, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references, Structure summary