6SV1

Crystal structure of Rhodospirillum rubrum Rru_A0973 E34A variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Dissecting the structural and functional roles of a putative metal entry site in encapsulated ferritins.

Piergentili, C.Ross, J.He, D.Gallagher, K.J.Stanley, W.A.Adam, L.Mackay, C.L.Basle, A.Waldron, K.J.Clarke, D.J.Marles-Wright, J.

(2020) J Biol Chem 295: 15511-15526

  • DOI: https://doi.org/10.1074/jbc.RA120.014502
  • Primary Citation of Related Structures:  
    6SUW, 6SV1

  • PubMed Abstract: 

    Encapsulated ferritins belong to the universally distributed ferritin superfamily, whose members function as iron detoxification and storage systems. Encapsulated ferritins have a distinct annular structure and must associate with an encapsulin nanocage to form a competent iron store that is capable of holding significantly more iron than classical ferritins. The catalytic mechanism of iron oxidation in the ferritin family is still an open question because of the differences in organization of the ferroxidase catalytic site and neighboring secondary metal-binding sites. We have previously identified a putative metal-binding site on the inner surface of the Rhodospirillum rubrum encapsulated ferritin at the interface between the two-helix subunits and proximal to the ferroxidase center. Here we present a comprehensive structural and functional study to investigate the functional relevance of this putative iron-entry site by means of enzymatic assays, MS, and X-ray crystallography. We show that catalysis occurs in the ferroxidase center and suggest a dual role for the secondary site, which both serves to attract metal ions to the ferroxidase center and acts as a flow-restricting valve to limit the activity of the ferroxidase center. Moreover, confinement of encapsulated ferritins within the encapsulin nanocage, although enhancing the ability of the encapsulated ferritin to undergo catalysis, does not influence the function of the secondary site. Our study demonstrates a novel molecular mechanism by which substrate flux to the ferroxidase center is controlled, potentially to ensure that iron oxidation is productively coupled to mineralization.


  • Organizational Affiliation

    School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Encapsulated Ferritin116Rhodospirillum rubrumMutation(s): 1 
Gene Names: Rru_A0973
UniProt
Find proteins for Q2RVS1 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
Explore Q2RVS1 
Go to UniProtKB:  Q2RVS1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2RVS1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
AB [auth M]
BB [auth N]
CB [auth O]
DB [auth P]
EA [auth A]
AB [auth M],
BB [auth N],
CB [auth O],
DB [auth P],
EA [auth A],
EB [auth Q],
FA [auth B],
GB [auth R],
HA [auth C],
HB [auth S],
JA [auth D],
JB [auth T],
LA [auth E],
LB [auth U],
MA [auth F],
MB [auth V],
NA [auth G],
OA [auth H],
OB [auth W],
PB [auth X],
RA [auth I],
RB [auth Y],
SB [auth Z],
TA [auth J],
UB [auth a],
VB [auth b],
WA [auth K],
XB [auth c],
YA [auth L],
ZB [auth d]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
FB [auth Q]
GA [auth B]
IA [auth C]
IB [auth S]
KA [auth D]
FB [auth Q],
GA [auth B],
IA [auth C],
IB [auth S],
KA [auth D],
KB [auth T],
NB [auth V],
PA [auth H],
QA [auth H],
QB [auth X],
SA [auth I],
TB [auth Z],
UA [auth J],
VA [auth J],
WB [auth b],
XA [auth K],
YB [auth c],
ZA [auth L]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.794α = 90
b = 120.136β = 95.202
c = 139.335γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N005570/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description