7B4O

A Bacteroidetes bacterium CuZn-superoxide dismutase with ZnZn metalation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Bacterial Evolutionary Precursors of Eukaryotic Copper-Zinc Superoxide Dismutases.

Wright, G.S.A.

(2021) Mol Biol Evol 38: 3789-3803

  • DOI: https://doi.org/10.1093/molbev/msab157
  • Primary Citation of Related Structures:  
    7B4O, 7B4P

  • PubMed Abstract: 

    Internalization of a bacteria by an archaeal cell expedited eukaryotic evolution. An important feature of the species that diversified into the great variety of eukaryotic life visible today was the ability to combat oxidative stress with a copper-zinc superoxide dismutase (CuZnSOD) enzyme activated by a specific, high-affinity copper chaperone. Adoption of a single protein interface that facilitates homodimerization and heterodimerization was essential; however, its evolution has been difficult to rationalize given the structural differences between bacterial and eukaryotic enzymes. In contrast, no consistent strategy for the maturation of periplasmic bacterial CuZnSODs has emerged. Here, 34 CuZnSODs are described that closely resemble the eukaryotic form but originate predominantly from aquatic bacteria. Crystal structures of a Bacteroidetes bacterium CuZnSOD portray both prokaryotic and eukaryotic characteristics and propose a mechanism for self-catalyzed disulfide maturation. Unification of a bacterial but eukaryotic-like CuZnSOD along with a ferredoxin-fold MXCXXC copper-binding domain within a single polypeptide created the advanced copper delivery system for CuZnSODs exemplified by the human copper chaperone for superoxide dismutase-1. The development of this system facilitated evolution of large and compartmentalized cells following endosymbiotic eukaryogenesis.


  • Organizational Affiliation

    Department of Biochemistry & Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]A [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
153Bacteroidetes bacterium GWA2_30_7Mutation(s): 0 
Gene Names: A2046_17220
EC: 1.15.1.1
UniProt
Find proteins for A0A1F3DVA5 (Bacteroidetes bacterium GWA2_30_7)
Explore A0A1F3DVA5 
Go to UniProtKB:  A0A1F3DVA5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1F3DVA5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth AAA]
F [auth AAA]
G [auth AAA]
H [auth AAA]
I [auth BBB]
E [auth AAA],
F [auth AAA],
G [auth AAA],
H [auth AAA],
I [auth BBB],
J [auth BBB],
K [auth BBB],
L [auth BBB],
M [auth CCC],
N [auth CCC],
O [auth CCC],
P [auth CCC],
Q [auth DDD],
R [auth DDD],
S [auth DDD]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.469α = 90
b = 96.637β = 90
c = 136.118γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited KingdomWright/Oct18/969-799

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 2.0: 2021-09-29
    Changes: Atomic model, Data collection, Database references
  • Version 2.1: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description