6PWJ

Vibrio cholerae LapD S helix-GGDEF-EAL (apo)

PDB DOI: 10.2210/pdb6PWJ/pdb

Classification: SIGNALING PROTEIN
Organism(s): Vibrio cholerae O1 str. 2010EL-1786
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-23 Released: 2019-10-09
Deposition Author(s): Giglio, K.M., Cooley, R.B., Sondermann, H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.243
R-Value Work: 0.199
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

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

Literature

A Conserved Regulatory Circuit Controls Large Adhesins in Vibrio cholerae.

Kitts, G., Giglio, K.M., Zamorano-Sanchez, D., Park, J.H., Townsley, L., Cooley, R.B., Wucher, B.R., Klose, K.E., Nadell, C.D., Yildiz, F.H., Sondermann, H.

(2019) mBio 10

PubMed: 31796544 Search on PubMedSearch on PubMed Central
DOI: 10.1128/mBio.02822-19
Primary Citation of Related Structures:
6PWJ, 6PWK

PubMed Abstract:

The dinucleotide second messenger c-di-GMP has emerged as a central regulator of reversible cell attachment during bacterial biofilm formation. A prominent cell adhesion mechanism first identified in pseudomonads combines two c-di-GMP-mediated processes: transcription of a large adhesin and its cell surface display via posttranslational proteolytic control. Here, we characterize an orthologous c-di-GMP effector system and show that it is operational in Vibrio cholerae , where it regulates two distinct classes of adhesins. Through structural analyses, we reveal a conserved autoinhibition mechanism of the c-di-GMP receptor that controls adhesin proteolysis and present a structure of a c-di-GMP-bound receptor module. We further establish functionality of the periplasmic protease controlled by the receptor against the two adhesins. Finally, transcription and functional assays identify physiological roles of both c-di-GMP-regulated adhesins in surface attachment and biofilm formation. Together, our studies highlight the conservation of a highly efficient signaling effector circuit for the control of cell surface adhesin expression and its versatility by revealing strain-specific variations. IMPORTANCE Vibrio cholerae , the causative agent of the diarrheal disease cholera, benefits from a sessile biofilm lifestyle that enhances survival outside the host but also contributes to host colonization and infectivity. The bacterial second messenger c-di-GMP has been identified as a central regulator of biofilm formation, including in V. cholerae ; however, our understanding of the pathways that contribute to this process is incomplete. Here, we define a conserved signaling system that controls the stability of large adhesion proteins at the cell surface of V. cholerae , which are important for cell attachment and biofilm formation. Insight into the regulatory circuit underlying biofilm formation may inform targeted strategies to interfere with a process that renders this bacterium remarkably adaptable to changing environments.

Organizational Affiliation:

Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA fyildiz@ucsc.edu hs293@cornell.edu.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GGDEF and EAL domain-containing protein	A, B	418	Vibrio cholerae O1 str. 2010EL-1786	Mutation(s): 0
UniProt
Find proteins for A0A0H3AFX3 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H3AFX3 Go to UniProtKB: A0A0H3AFX3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3AFX3
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.243
R-Value Work: 0.199
R-Value Observed: 0.202
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.83	α = 90
b = 129.83	β = 90
c = 114.441	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2019-07-23
Released Date: 2019-10-09

Deposition Author(s):

Giglio, K.M.

Cooley, R.B.

Sondermann, H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM123609
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103485
National Science Foundation (NSF, United States)	United States	DMR-1332208