5Y40

Structure of the periplasmic domain of the MotB L119P mutant from Salmonella (crystal form 2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Helix Rearrangement in the Periplasmic Domain of the Flagellar Stator B Subunit Activates Peptidoglycan Binding and Ion Influx.

Kojima, S.Takao, M.Almira, G.Kawahara, I.Sakuma, M.Homma, M.Kojima, C.Imada, K.

(2018) Structure 26: 590-598.e5

  • DOI: https://doi.org/10.1016/j.str.2018.02.016
  • Primary Citation of Related Structures:  
    5Y3Z, 5Y40

  • PubMed Abstract: 

    The stator of the bacterial flagellar motor couples ion flow with torque generation. The ion-conducting stator channel opens only when incorporated into and anchored around the rotor via the peptidoglycan (PG) binding domain of the B subunit (MotB C ). However, no direct evidence of PG binding coupled with channel activation has been presented. Here, we report the structural rearrangements of MotB C responsible for this coupling process. A MotB C fragment with the L119P replacement, which is known to cause channel activation, was able to bind PG. Nuclear magnetic resonance analysis of MotB C and the crystal structure of the MotB C -L119P dimer revealed major structural changes in helix α1. In vivo crosslinking results confirm that a major rearrangement occurs. Our results suggest that, upon stator incorporation into the motor, helix α1 of MotB C changes into an extended non-helical structure. We propose that this change allows the stator both to bind PG and to open its proton channel.


  • Organizational Affiliation

    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan. Electronic address: z47616a@cc.nagoya-u.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Motility protein B
A, B, C, D
183Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 1 
Gene Names: motBSTM1922
UniProt
Find proteins for P55892 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P55892 
Go to UniProtKB:  P55892
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55892
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.95α = 90
b = 150.95β = 90
c = 91.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description