6U1P | pdb_00006u1p

Crystal structure of VpsU (VC0916) from Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb6U1P/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-16 Released: 2020-08-19 
• Deposition Author(s): Tripathi, S.M., Schwechheimer, C., Herbert, K., Osorio, J., Yildiz, F.H., Rubin, S.M.
• 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: 2.20 Å
• R-Value Free: 
  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

A tyrosine phosphoregulatory system controls exopolysaccharide biosynthesis and biofilm formation in Vibrio cholerae.

Schwechheimer, C., Hebert, K., Tripathi, S., Singh, P.K., Floyd, K.A., Brown, E.R., Porcella, M.E., Osorio, J., Kiblen, J.T.M., Pagliai, F.A., Drescher, K., Rubin, S.M., Yildiz, F.H.

(2020) PLoS Pathog 16: e1008745-e1008745

• PubMed: 32841296 
• DOI: https://doi.org/10.1371/journal.ppat.1008745
• Primary Citation Related Structures: 
  6U1P, 6U1Q


• PubMed Abstract: 
  

  Production of an extracellular matrix is essential for biofilm formation, as this matrix both secures and protects the cells it encases. Mechanisms underlying production and assembly of matrices are poorly understood. Vibrio cholerae, relies heavily on biofilm formation for survival, infectivity, and transmission. Biofilm formation requires Vibrio polysaccharide (VPS), which is produced by vps gene-products, yet the function of these products remains unknown. Here, we demonstrate that the vps gene-products vpsO and vpsU encode respectively for a tyrosine kinase and a cognate tyrosine phosphatase. Collectively, VpsO and VpsU act as a tyrosine phosphoregulatory system to modulate VPS production. We present structures of VpsU and the kinase domain of VpsO, and we report observed autocatalytic tyrosine phosphorylation of the VpsO C-terminal tail. The position and amount of tyrosine phosphorylation in the VpsO C-terminal tail represses VPS production and biofilm formation through a mechanism involving the modulation of VpsO oligomerization. We found that tyrosine phosphorylation enhances stability of VpsO. Regulation of VpsO phosphorylation by the phosphatase VpsU is vital for maintaining native VPS levels. This study provides new insights into the mechanism and regulation of VPS production and establishes general principles of biofilm matrix production and its inhibition.

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Organizational Affiliation: 
• Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, United States of America.
Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, California, United States of America.
Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Department of Physics, Philipps-Universität Marburg, Marburg, Germany.

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

Macromolecule Content 

• Total Structure Weight: 37.84 kDa 
• Atom Count: 2,420 
• Modeled Residue Count: 299 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low molecular weight phosphotyrosine protein phosphatase	A, B	166	Vibrio cholerae	Mutation(s): 0  Gene Names: etp EC: 3.1.3.48
UniProt
Find proteins for Q9KTI6 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KTI6  Go to UniProtKB:  Q9KTI6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.323	α = 90
b = 80.323	β = 90
c = 105.053	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Tripathi, S.M., Schwechheimer, C., Herbert, K., Osorio, J., Yildiz, F.H., Rubin, S.M.

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

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 1.1: 2020-10-07
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description