9P6I | pdb_00009p6i

Crystal Structure of the Histidine Kinase VC2136 from Vibrio cholerae serotype O1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.286 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The PAS domain of the polarly localized histidine kinase FlrB in Vibrio cholerae controls class III flagellar transcription and contributes to intestinal colonization.

Stanton, V.Himes, B.Mejia-Santana, A.Eppinger, M.Romo, J.Xing, J.Zhulin, I.B.Cai, H.Wang, Y.Inniss, N.l.Minasov, G.Satchell, K.J.F.Klose, K.E.

(2025) mBio 16: e0237925-e0237925

  • DOI: https://doi.org/10.1128/mbio.02379-25
  • Primary Citation of Related Structures:  
    9P6I

  • PubMed Abstract: 

    Vibrio cholerae motility is mediated by a single polar flagellum, composed of four flagellin subunits (FlaABCD) in the filament; however, only FlaA is required for motility. Class III flagellar genes, which include flaA , are controlled by the two-component FlrBC system. FlrB is a histidine kinase that phosphorylates FlrC, which activates Class III promoters. The signal(s) that control phosphotransfer between FlrB and FlrC are unknown. A V. cholerae strain lacking the "non-essential" flagellin genes (Δ flaCEDB ) is non-motile. Selection for spontaneous motile strains resulted in mutations localized to a Per-Arnt-Sim (PAS) domain in the FlrB N-terminus, including the mutation L36F. The X-ray crystal structure of FlrB revealed an asymmetric dimer with a unique fold of the PAS domain. Transcriptome analysis showed that class III transcription is increased with the addition of the L36F PAS mutation to FlrB, while class III gene transcription was eliminated with a mutation at the site of phosphorylation (H135N). H135N prevents phosphorylation of purified FlrB, whereas L36F increases phosphorylation, indicating these mutations represent "off" and "on" forms of FlrB. FlrB localizes to the V. cholerae cell pole, and localization is dependent on the flagellar polar targeting protein FlhF. V. cholerae strains containing either "off" or "on" forms of FlrB were defective for intestinal colonization in infant mice (10- to 40-fold defect). Our results demonstrate that the PAS domain controls FlrB activity and class III flagellar gene expression, and FlrB must switch between inactive and active forms in order for V. cholerae to successfully colonize the intestine. Vibrio cholerae causes the severe diarrheal disease cholera when it colonizes the human intestine. The bacteria are able to swim due to a polar flagellum, and motility is linked to disease, as well as environmental persistence. This study demonstrates that FlrB, a key regulatory protein, localizes to the cell pole and controls flagellar gene transcription via a PAS domain that regulates autophosphorylation. The ability of FlrB to switch between active and inactive forms is critical for motility, as well as intestinal colonization, emphasizing the importance of V. cholerae swimming for its ability to cause disease.


  • Organizational Affiliation
    • South Texas Center for Emerging Infectious Diseases and Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, Texas, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
histidine kinase
A, B, C, D, E
A, B, C, D, E, F, G, H
354Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: VC_2136
EC: 2.7.13.3
UniProt
Find proteins for H9L4P6 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore H9L4P6 
Go to UniProtKB:  H9L4P6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH9L4P6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
AB [auth H]
BA [auth D]
CA [auth D]
DA [auth D]
AA [auth D],
AB [auth H],
BA [auth D],
CA [auth D],
DA [auth D],
GA [auth E],
HA [auth E],
I [auth A],
IA [auth F],
J [auth A],
JA [auth F],
K [auth A],
KA [auth F],
L [auth A],
LA [auth F],
M [auth A],
MA [auth F],
N [auth A],
NA [auth F],
O [auth B],
OA [auth G],
P [auth B],
PA [auth G],
Q [auth B],
QA [auth G],
R [auth B],
RA [auth G],
S [auth B],
SA [auth G],
T [auth B],
TA [auth H],
U [auth B],
UA [auth H],
VA [auth H],
W [auth C],
WA [auth H],
X [auth C],
XA [auth H],
Y [auth D],
YA [auth H],
Z [auth D],
ZA [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
EA [auth E],
FA [auth E],
V [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.286 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.211α = 90
b = 86.211β = 90
c = 212.636γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93022C00035

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Database references