5VX6

Structure of Bacillus subtilis Inhibitor of motility (MotI/DgrA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

MotI (DgrA) acts as a molecular clutch on the flagellar stator protein MotA inBacillus subtilis.

Subramanian, S.Gao, X.Dann 3rd., C.E.Kearns, D.B.

(2017) Proc Natl Acad Sci U S A 114: 13537-13542

  • DOI: https://doi.org/10.1073/pnas.1716231114
  • Primary Citation of Related Structures:  
    5VX6

  • PubMed Abstract: 

    Stator elements consisting of MotA 4 MotB 2 complexes are anchored to the cell wall, extend through the cell membrane, and interact with FliG in the cytoplasmic C ring rotor of the flagellum. The cytoplasmic loop of MotA undergoes proton-driven conformational changes that drive flagellar rotation. Functional regulators inhibit motility by either disengaging or jamming the stator-rotor interaction. Here we show that the YcgR homolog MotI (formerly DgrA) of Bacillus subtilis inhibits motility like a molecular clutch that disengages MotA. MotI-inhibited flagella rotated freely by Brownian motion, and suppressor mutations in MotA that were immune to MotI inhibition were located two residues downstream of the critical force generation site. The 3D structure of MotI bound to c-di-GMP was solved, and MotI-fluorescent fusions localized as transient MotA-dependent puncta at the membrane when induced at subinhibitory levels. Finally, subinhibitory levels of MotI expression resulted in incomplete inhibition and proportional decreases in swimming speed. We propose a model in which flagellar stators are disengaged and sequestered from the flagellar rotor when bound by MotI.


  • Organizational Affiliation

    Department of Chemistry, Indiana University, Bloomington, IN 47405.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein YpfA
A, B
216Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: ypfAjofABSU22910
UniProt
Find proteins for P38491 (Bacillus subtilis (strain 168))
Explore P38491 
Go to UniProtKB:  P38491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38491
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2E
Query on C2E

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth B],
F [auth B]
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.240 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.41α = 90
b = 75.41β = 90
c = 402.47γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM093030

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.2: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence, Structure summary
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references