5V6C

Crystal Structure of the Second beta-Prism Domain of RbmC from V. cholerae

DOI: 10.2210/pdb5V6C/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-03-16 Released: 2018-01-24
Deposition Author(s): De, S., Kaus, K., Sinclair, S., Case, B.C., Olson, R.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.217
R-Value Work: 0.173
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural basis of mammalian glycan targeting by Vibrio cholerae cytolysin and biofilm proteins.

De, S., Kaus, K., Sinclair, S., Case, B.C., Olson, R.

(2018) PLoS Pathog 14: e1006841-e1006841

PubMed: 29432487 Search on PubMedSearch on PubMed Central
DOI: 10.1371/journal.ppat.1006841
Primary Citation of Related Structures:
5V6F, 5V6K, 5V6C

PubMed Abstract:

Vibrio cholerae is an aquatic gram-negative microbe responsible for cholera, a pandemic disease causing life-threatening diarrheal outbreaks in populations with limited access to health care. Like most pathogenic bacteria, V. cholerae secretes virulence factors to assist colonization of human hosts, several of which bind carbohydrate receptors found on cell-surfaces. Understanding how pathogenic virulence proteins specifically target host cells is important for the development of treatment strategies to fight bacterial infections. Vibrio cholerae cytolysin (VCC) is a secreted pore-forming toxin with a carboxy-terminal β-prism domain that targets complex N-glycans found on mammalian cell-surface proteins. To investigate glycan selectivity, we studied the VCC β-prism domain and two additional β-prism domains found within the V. cholerae biofilm matrix protein RbmC. We show that the two RbmC β-prism domains target a similar repertoire of complex N-glycan receptors as VCC and find through binding and modeling studies that a branched pentasaccharide core (GlcNAc2-Man3) represents the likely footprint interacting with these domains. To understand the structural basis of V. cholerae β-prism selectivity, we solved high-resolution crystal structures of fragments of the pentasaccharide core bound to one RbmC β-prism domain and conducted mutagenesis experiments on the VCC toxin. Our results highlight a common strategy for cell-targeting utilized by both toxin and biofilm matrix proteins in Vibrio cholerae and provide a structural framework for understanding the specificity for individual receptors. Our results suggest that a common strategy for disrupting carbohydrate interactions could affect multiple virulence factors produced by V. cholerae, as well as similar β-prism domains found in other vibrio pathogens.

Organizational Affiliation:

Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut, United States of America.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolysin-related protein	A, B, C	138	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_0930
Find proteins for Q9KTH2 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KTH2 Go to UniProtKB: Q9KTH2
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain E [A] SDF format, chain F [B] SDF format, chain G [B] SDF format, chain H [C] SDF format, chain I [C] MOL2 format, chain D [A] MOL2 format, chain E [A] MOL2 format, chain F [B] MOL2 format, chain G [B] MOL2 format, chain H [C] MOL2 format, chain I [C]	A, B, C	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction