9BWQ | pdb_00009bwq

X-ray Counterpart to the Neutron Structure of Peroxide-Soaked Tyr34Phe MnSOD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.205 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

The role of Tyr34 in proton coupled electron transfer and product inhibition of manganese superoxide dismutase.

Azadmanesh, J.Slobodnik, K.Struble, L.R.Lovelace, J.J.Cone, E.A.Dasgupta, M.Lutz, W.E.Kumar, S.Natarajan, A.Coates, L.Weiss, K.L.Myles, D.A.A.Kroll, T.Borgstahl, G.E.O.

(2025) Nat Commun 16: 1887-1887

  • DOI: https://doi.org/10.1038/s41467-025-57180-3
  • Primary Citation of Related Structures:  
    9BVY, 9BW2, 9BWM, 9BWQ, 9BWR

  • PubMed Abstract: 

    Human manganese superoxide dismutase (MnSOD) plays a crucial role in controlling levels of reactive oxygen species (ROS) by converting superoxide ( O 2 - ) to molecular oxygen (O 2 ) and hydrogen peroxide (H 2 O 2 ) with proton-coupled electron transfers (PCETs). A key catalytic residue, Tyr34, determines the activity of human MnSOD and also becomes post-translationally inactivated by nitration in various diseases associated with mitochondrial dysfunction. Tyr34 has an unusual pK a due to its proximity to the Mn metal and undergoes cyclic deprotonation and protonation events to promote the electron transfers of MnSOD. Neutron diffraction, X-ray spectroscopy, and quantum chemistry calculations in oxidized, reduced and product inhibited enzymatic states shed light on the role of Tyr34 in MnSOD catalysis. The data identify the contributions of Tyr34 in MnSOD activity that support mitochondrial function and give a thorough characterization of how a single tyrosine modulates PCET catalysis. Product inhibition occurs by an associative displacement mechanism.


  • Organizational Affiliation

    Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, 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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
G [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
PEO (Subject of Investigation/LOI)
Query on PEO

Download Ideal Coordinates CCD File 
D [auth A]HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.205 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.221α = 90
b = 78.221β = 90
c = 239.501γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



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: 2025-03-12
    Type: Initial release