8VHW

Neutron Structure of Peroxide-Soaked Trp161Phe MnSOD


Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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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) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.01.26.577433
  • 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 O 2 ●- to O 2 and H 2 O 2 with proton-coupled electron transfers (PCETs). Since changes in mitochondrial H 2 O 2 concentrations are capable of stimulating apoptotic signaling pathways, human MnSOD has evolutionarily gained the ability to be highly inhibited by its own product, H 2 O 2 . A separate set of PCETs is thought to regulate product inhibition, though mechanisms of PCETs are typically unknown 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 underlying mechanism, we combined neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states to reveal the all-atom structures and electronic configuration of the metal. The data identifies the product-inhibited complex for the first time and a PCET mechanism of inhibition is constructed.


Macromolecules
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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 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • 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