7NE9

A single sensor controls large variations in zinc quotas in a marine cyanobacterium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A single sensor controls large variations in zinc quotas in a marine cyanobacterium.

Mikhaylina, A.Ksibe, A.Z.Wilkinson, R.C.Smith, D.Marks, E.Coverdale, J.P.C.Fulop, V.Scanlan, D.J.Blindauer, C.A.

(2022) Nat Chem Biol 18: 869-877

  • DOI: https://doi.org/10.1038/s41589-022-01051-1
  • Primary Citation of Related Structures:  
    7NE9

  • PubMed Abstract: 

    Marine cyanobacteria are critical players in global nutrient cycles that crucially depend on trace metals in metalloenzymes, including zinc for CO 2 fixation and phosphorus acquisition. How strains proliferating in the vast oligotrophic ocean gyres thrive at ultra-low zinc concentrations is currently unknown. Using Synechococcus sp. WH8102 as a model we show that its zinc-sensor protein Zur differs from all other known bacterial Zur proteins in overall structure and the location of its sensory zinc site. Uniquely, Synechococcus Zur activates metallothionein gene expression, which supports cellular zinc quotas spanning two orders of magnitude. Thus, a single zinc sensor facilitates growth across pico- to micromolar zinc concentrations with the bonus of banking this precious resource. The resultant ability to grow well at both ultra-low and excess zinc, together with overall lower zinc requirements, likely contribute to the broad ecological distribution of Synechococcus across the global oceans.


  • Organizational Affiliation

    Department of Chemistry, University of Warwick, Coventry, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferric uptake regulator familyA [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
134Parasynechococcus marenigrum WH 8102Mutation(s): 0 
Gene Names: SYNW2401
UniProt
Find proteins for Q7U3N0 (Parasynechococcus marenigrum (strain WH8102))
Explore Q7U3N0 
Go to UniProtKB:  Q7U3N0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7U3N0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth AAA]
F [auth AAA]
G [auth BBB]
H [auth BBB]
I [auth BBB]
E [auth AAA],
F [auth AAA],
G [auth BBB],
H [auth BBB],
I [auth BBB],
K [auth CCC],
L [auth CCC],
M [auth DDD],
N [auth DDD]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)
Query on ACT

Download Ideal Coordinates CCD File 
J [auth BBB]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.25α = 90
b = 129.25β = 90
c = 77.28γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2022-03-02 
  • Deposition Author(s): Fulop, V.

Funding OrganizationLocationGrant Number
University of WarwickUnited Kingdom--
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M003523/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-06-22
    Changes: Database references, Derived calculations
  • Version 1.2: 2022-08-10
    Changes: Database references
  • Version 1.3: 2024-06-19
    Changes: Data collection