7KB3 | pdb_00007kb3

The structure of a sensor domain of a histidine kinase (VxrA) from Vibrio cholerae O1 biovar eltor str. N16961, 2nd form

• PDB DOI: https://doi.org/10.2210/pdb7KB3/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-10-01 Released: 2020-10-14 
• Deposition Author(s): Tan, K., Wu, R., Jedrzejczak, R., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.227 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae - A Hairpin-swapped Dimer and its Conformational Change.

Tan, K., Teschler, J.K., Wu, R., Jedrzejczak, R.P., Zhou, M., Shuvalova, L.A., Endres, M.J., Welk, L.F., Kwon, K., Anderson, W.F., Satchell, K.J.F., Yildiz, F.H., Joachimiak, A.

(2021) J Bacteriol 

• PubMed: 33753465 
• DOI: https://doi.org/10.1128/JB.00643-20
• Primary Citation Related Structures: 
  4R7Q, 7KB3, 7KB7, 7KB9, 7LA6


• PubMed Abstract: 
  

  VxrA and VxrB are cognate histidine kinase (HK) - response regulator (RR) pairs of a two-component signaling system (TCS) found in Vibrio cholerae , a bacterial pathogen that causes cholera. The VxrAB TCS positively regulates virulence, the Type VI Secretion System, biofilm formation, and cell wall homeostasis in V. cholerae , providing protection from environmental stresses and contributing to the transmission and virulence of the pathogen. The VxrA HK has a unique periplasmic sensor domain (SD) and, remarkably, lacks a cytoplasmic linker domain between the second transmembrane helix and the dimerization and histidine phosphotransfer (DHp) domain, indicating that this system may utilize a potentially unique signal sensing and transmission TCS mechanism. In this study, we have determined several crystal structures of VxrA-SD and its mutants. These structures reveal a novel structural fold forming an unusual β hairpin-swapped dimer. A conformational change caused by relative rotation of the two monomers in a VxrA-SD dimer could potentially change the association of transmembrane helices and, subsequently, the pairing of cytoplasmic DHp domains. Based on the structural observation, we propose a putative scissor-like closing regulation mechanism for the VxrA HK. IMPORTANCE V. cholerae has a dynamic life cycle, which requires rapid adaptation to changing external conditions. Two-component signal transduction (TCS) systems allow V. cholerae to sense and respond to these environmental changes. The VxrAB TCS positively regulates a number of important V. cholerae phenotypes, including virulence, the Type Six Secretion System, biofilm formation, and cell wall homeostasis. Here, we provide the crystal structure of the VxrA sensor histidine kinase sensing domain and propose a mechanism for signal transduction. The cognate signal for VxrAB remains unknown, however, in this work we couple our structural analysis with functional assessments of key residues to further our understanding of this important TCS.

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Organizational Affiliation: 
• Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA.
Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, USA.
Bioscience Division, Argonne National Laboratory, Lemont, IL 60439, USA.
Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
Infectious Disease Group, J. Craig Venter Institute, Rockville, MD 20850, USA.
GSK, Collegeville, PA 19426, USA.
Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, USA [e-mail] [e-mail].
Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA [e-mail] [e-mail].
Department of Biochemistry and Molecular Biology, the University of Chicago, Chicago, IL 60367, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 101.52 kDa 
• Atom Count: 7,135 
• Modeled Residue Count: 872 
• Deposited Residue Count: 888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor histidine kinase	A, B, C, D	222	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC_A0565 EC: 2.7.13.3
UniProt
Find proteins for Q9KM24 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KM24  Go to UniProtKB:  Q9KM24

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRT	Y [auth C]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N
PEG	HA [auth D], Q [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	CA [auth D], DA [auth D], E [auth A], EA [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	F [auth A], FA [auth D], G [auth A], GA [auth D], O [auth B], P [auth B], V [auth C], W [auth C], X [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	AA [auth C], BA [auth C], H [auth A], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], OA [auth D], R [auth B], S [auth B], T [auth B], U [auth B], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.227 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.085	α = 90
b = 116.677	β = 90
c = 120.747	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SBC-Collect	data collection

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Tan, K., Wu, R., Jedrzejczak, R., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2022-11-16
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary