9M58 | pdb_00009m58

Cu/Zn-superoxide dismutase from Deinococcus radiodurans (Calcium-free)

• PDB DOI: https://doi.org/10.2210/pdb9M58/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-03-05 Released: 2025-09-24 
• Deposition Author(s): Akutsu, M., Muraki, N., Megata, M., Furukawa, Y.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: in silico

Literature

Cu/Zn-superoxide dismutase naturally fused with a beta-propeller lactonase in Deinococcus radiodurans.

Furukawa, Y., Megata, M., Shintani, A., Sue, K., Morohoshi, T., Akutsu, M., Muraki, N.

(2025) J Biological Chem 301: 110499-110499

• PubMed: 40684944 
• DOI: https://doi.org/10.1016/j.jbc.2025.110499
• Primary Citation of Related Structures:  
  9M58, 9M59


• PubMed Abstract: 
  

  Cu/Zn-superoxide dismutase (Cu/Zn-SOD) is an antioxidant enzyme widely present across species; however, the structural diversity and physiological roles of Cu/Zn-SOD are yet to be fully uncovered. Here, we show a unique type of Cu/Zn-SOD from Deinococcus radiodurans (DrSOD) with an additional β-propeller domain. Our structural analysis of DrSOD revealed a typical bacterial Cu/Zn-SOD domain, binding both a copper and zinc ion, alongside a six-bladed β-propeller domain coordinating a calcium ion. DrSOD was indeed expressed in D. radiodurans, but its deletion did not lead to any noticeable changes in resistance to DNA-damaging stresses, a characteristic trait of D. radiodurans. Despite this, the Cu/Zn-SOD domain retained superoxide dismutase activity, and the β-propeller domain was found to exhibit a lactonase activity specifically for hydrolyzing 2-coumaranone. Taken together, while the precise physiological role of DrSOD needs to be further investigated, our findings here reveal a unique multi-functional enzyme architecture, expanding the known structural diversity of Cu/Zn-SODs.

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Organizational Affiliation: 
• Department of Chemistry, Keio University, Yokohama, Kanagawa, Japan. Electronic address: [e-mail].
Department of Chemistry, Keio University, Yokohama, Kanagawa, Japan.
Graduate School of Regional Development and Creativity, Utsunomiya University, Utsunomiya, Tochigi, Japan.
Department of Chemistry, Keio University, Yokohama, Kanagawa, Japan; Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.72 kDa 
• Atom Count: 6,448 
• Modeled Residue Count: 792 
• Deposited Residue Count: 882 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase (SodC), Cu-Zn family	A, B	441	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: DR_A0202 EC: 1.15.1.1
UniProt
Find proteins for Q9RYV4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RYV4  Go to UniProtKB:  Q9RYV4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	C [auth A], E [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.067	α = 90
b = 83.067	β = 90
c = 119.525	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Akutsu, M., Muraki, N., Megata, M., Furukawa, Y.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	19H05765
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	22H02768
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	22K19389

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release