9BWQ | pdb_00009bwq

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

• PDB DOI: https://doi.org/10.2210/pdb9BWQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-05-21 Released: 2025-03-12 
• Deposition Author(s): Azadmanesh, J., Slobodnik, K., Struble, L.R., 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.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Aeronautics and Space Administration (NASA, United States), Department of Energy (DOE, United States)

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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

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

• PubMed: 39987263 
• DOI: https://doi.org/10.1038/s41467-025-57180-3
• Primary Citation 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.

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Organizational Affiliation: 
• Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, USA.
Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, USA.
Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, USA.
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.16 kDa 
• Atom Count: 3,760 
• Modeled Residue Count: 398 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Mn], mitochondrial	A, B	199	Homo sapiens	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN	C [auth A], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
K	G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
PEO (Subject of Investigation/LOI)	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 = 78.221	α = 90
b = 78.221	β = 90
c = 239.501	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Azadmanesh, J., Slobodnik, K., Struble, L.R., 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.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM145647
National Aeronautics and Space Administration (NASA, United States)	United States	44-0307-1021-201
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release