6KTY

Crystal structure of the flagellar cap protein FliD from Bdellovibrio bacteriovorus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of the flagellar cap protein FliD from Bdellovibrio bacteriovorus.

Cho, S.Y.Song, W.S.Yoon, S.I.

(2019) Biochem.Biophys.Res.Commun. --: --

  • DOI: 10.1016/j.bbrc.2019.09.024

  • PubMed Abstract: 
  • Bdellovibrio bacteriovorus is a predator bacterial species of the Deltaproteobacteria class that requires flagellum-mediated motility to initiate the parasitization of other gram-negative bacteria. The flagellum is capped by FliD, which polymerizes f ...

    Bdellovibrio bacteriovorus is a predator bacterial species of the Deltaproteobacteria class that requires flagellum-mediated motility to initiate the parasitization of other gram-negative bacteria. The flagellum is capped by FliD, which polymerizes flagellin into a flagellar filament. FliD has been reported to function as a species-specific oligomer, such as a tetramer, a pentamer, or a hexamer, in members of the Gammaproteobacteria class. However, the oligomeric state and structural features of FliD from bacterial species outside the Gammaproteobacteria class are unknown. Based on structural and biochemical analyses, we report here that B. bacteriovorus FliD (bbFliD) forms a tetramer. bbFliD tetramerizes in a circular head-to-tail arrangement by inserting the D2 domain of one subunit into the concave surface of the second subunit generated between the D2 and D3 domains as observed in Serratia marcescens FliD. However, bbFliD adopts a more compact and flat oligomeric structure, which exhibits a more extended tetramerization interface flanked by two additional surfaces due to different intersubunit and interdomain organizations as well as an elongated loop. In conclusion, FliD from B. bacteriovorus, which belongs to the Deltaproteobacteria class, also produces a tetramer similar to FliD from Gammaproteobacterial species but adopts a unique species-specific oligomeric structure.


    Organizational Affiliation

    Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.,Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea. Electronic address: sungil@kangwon.ac.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Flagellar hook-associated protein 2
A
196Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100)Mutation(s): 0 
Gene Names: fliD
Find proteins for Q6MQ71 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100))
Go to UniProtKB:  Q6MQ71
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 97.811α = 90.00
b = 97.811β = 90.00
c = 83.057γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-08-29 
  • Released Date: 2019-10-09 
  • Deposition Author(s): Cho, S.Y., Yoon, S.I.

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2019R1A2C1002100

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release