6QFJ

MamB CTD magnetosome protein [Desulfamplus magnetovallimortis BW-1]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

From conservation to structure, studies of magnetosome associated cation diffusion facilitators (CDF) proteins in Proteobacteria.

Keren-Khadmy, N.Zeytuni, N.Kutnowski, N.Perriere, G.Monteil, C.Zarivach, R.

(2020) PLoS One 15: e0231839-e0231839

  • DOI: 10.1371/journal.pone.0231839
  • Primary Citation of Related Structures:  
    6QFJ

  • PubMed Abstract: 
  • Magnetotactic bacteria (MTB) are prokaryotes that sense the geomagnetic field lines to geolocate and navigate in aquatic sediments. They are polyphyletically distributed in several bacterial divisions but are mainly represented in the Proteobacteria. In this phylum, magnetotactic Deltaproteobacteria represent the most ancestral class of MTB ...

    Magnetotactic bacteria (MTB) are prokaryotes that sense the geomagnetic field lines to geolocate and navigate in aquatic sediments. They are polyphyletically distributed in several bacterial divisions but are mainly represented in the Proteobacteria. In this phylum, magnetotactic Deltaproteobacteria represent the most ancestral class of MTB. Like all MTB, they synthesize membrane-enclosed magnetic nanoparticles, called magnetosomes, for magnetic sensing. Magnetosome biogenesis is a complex process involving a specific set of genes that are conserved across MTB. Two of the most conserved genes are mamB and mamM, that encode for the magnetosome-associated proteins and are homologous to the cation diffusion facilitator (CDF) protein family. In magnetotactic Alphaproteobacteria MTB species, MamB and MamM proteins have been well characterized and play a central role in iron-transport required for biomineralization. However, their structural conservation and their role in more ancestral groups of MTB like the Deltaproteobacteria have not been established. Here we studied magnetite cluster MamB and MamM cytosolic C-terminal domain (CTD) structures from a phylogenetically distant magnetotactic Deltaproteobacteria species represented by BW-1 strain, which has the unique ability to biomineralize magnetite and greigite. We characterized them in solution, analyzed their crystal structures and compared them to those characterized in Alphaproteobacteria MTB species. We showed that despite the high phylogenetic distance, MamBBW-1 and MamMBW-1 CTDs share high structural similarity with known CDF-CTDs and will probably share a common function with the Alphaproteobacteria MamB and MamM.


    Organizational Affiliation

    Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family
A, B, C, D, E, F
A, B, C, D, E, F
84Desulfamplus magnetovallimortisMutation(s): 0 
Gene Names: mamB-1DEMABW1_80065MTBBW1_80065
UniProt
Find proteins for L0R6P9 (Desulfamplus magnetovallimortis)
Explore L0R6P9 
Go to UniProtKB:  L0R6P9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0R6P9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.973α = 74.19
b = 47.07β = 84.86
c = 74.626γ = 84.21
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael3-9248

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 2.0: 2019-10-02
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2020-08-19
    Changes: Database references