5Y3Z

Structure of the periplasmic domain of the MotB L119P mutant from Salmonella (crystal form 1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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
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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ARG
Query on ARG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B]
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
MPD
Query on MPD

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.13α = 90
b = 84.8β = 90
c = 86.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan--

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