7K5N

Ligand binding domain (tandem PAS/dCache) of Aeromonas caviae diguanylate cyclase with proline bound

  • Classification: SIGNALING PROTEIN
  • Organism(s): Aeromonas caviae
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2020-09-17 Released: 2021-08-18 
  • Deposition Author(s): Sweeney, E.G., Remington, S.J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Host-emitted amino acid cues regulate bacterial chemokinesis to enhance colonization.

Robinson, C.D.Sweeney, E.G.Ngo, J.Ma, E.Perkins, A.Smith, T.J.Fernandez, N.L.Waters, C.M.Remington, S.J.Bohannan, B.J.M.Guillemin, K.

(2021) Cell Host Microbe 29: 1221

  • DOI: https://doi.org/10.1016/j.chom.2021.06.003
  • Primary Citation of Related Structures:  
    7K5N

  • PubMed Abstract: 

    Animal microbiomes are assembled predominantly from environmental microbes, yet the mechanisms by which individual symbionts regulate their transmission into hosts remain underexplored. By tracking the experimental evolution of Aeromonas veronii in gnotobiotic zebrafish, we identify bacterial traits promoting host colonization. Multiple independently evolved isolates with increased immigration harbored mutations in a gene we named sensor of proline diguanylate cyclase enzyme (SpdE) based on structural, biochemical, and phenotypic evidence that SpdE encodes an amino-acid-sensing diguanylate cyclase. SpdE detects free proline and to a lesser extent valine and isoleucine, resulting in reduced production of intracellular c-di-GMP, a second messenger controlling bacterial motility. Indeed, SpdE binding to amino acids increased bacterial motility and host colonization. Hosts serve as sources of SpdE-detected amino acids, with levels varying based on microbial colonization status. Our work demonstrates that bacteria use chemically regulated motility, or chemokinesis, to sense host-emitted cues that trigger active immigration into hosts.


  • Organizational Affiliation

    Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sensor domain-containing diguanylate cyclase271Aeromonas caviaeMutation(s): 0 
Gene Names: C0708_15830C1C92_04435
UniProt
Find proteins for A0A3S5WQC2 (Aeromonas caviae)
Explore A0A3S5WQC2 
Go to UniProtKB:  A0A3S5WQC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3S5WQC2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.188α = 90
b = 86.188β = 90
c = 75.078γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01GM125576
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01HD22486
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States5F32DK108591-03

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description