9IBO | pdb_00009ibo

VC0430/VcGluP bound to glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.190 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Vibrio cholerae biofilm matrix assembly and growth are shaped by a glutamate-specific TAXI/TRAP protein.

Potapova, A.Oguchi, R.Jimmy, S.Evans, C.R.Yarrington, K.D.Winans, J.B.Piepoli, S.Older, E.A.Schakel, O.F.Wetherington, M.T.Garvey, W.Floyd, K.A.Vinogradov, E.Yunker, P.J.Sanchez, L.M.Nadell, C.D.Limoli, D.H.Dietrich, L.E.P.Sondermann, H.Yildiz, F.H.

(2025) Proc Natl Acad Sci U S A 122: e2504869122-e2504869122

  • DOI: https://doi.org/10.1073/pnas.2504869122
  • Primary Citation of Related Structures:  
    9IBO, 9IBP

  • PubMed Abstract: 

    Biofilms are critical for the environmental persistence, survival, and infectivity of Vibrio cholerae , the causative agent of cholera. Here, we find that GluP, a glutamate-specific TRAP-TAXI protein, is an uncharacterized matrix component that plays a critical role in biofilm architecture. Loss of GluP reduces biofilm corrugation, expands colony size, and disperses cells from microcolonies, arguing that this factor maintains biofilm structure and organization. While GluP does not affect the abundance or localization of known matrix proteins, its absence reduces Vibrio exopolysaccharide (VPS) production. We determined the crystal structure of GluP, which revealed that GluP binds glutamate, and its biofilm-related phenotypes depend on this binding capability. We further examined the role of GluP in V. cholerae growth under defined conditions where L-glutamate serves as a carbon source, nitrogen source, or both. GluP-deficient strains specifically showed reduced growth when glucose was the carbon source and glutamate the nitrogen source. This defect is dependent on glutamate binding by GluP and highlights its role in coordinating nutrient acquisition and biofilm formation. Importantly, both biofilm assembly and growth defects occurred independently of the predicted membrane component of the Glu TRAP-TAXI system, GluQM. These findings indicate that GluP plays a dual role in biofilm assembly and growth, providing insight into its functional importance in V. cholerae physiology.


  • Organizational Affiliation
    • Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, CA 95064.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TAXI family TRAP transporter solute-binding subunit299Vibrio choleraeMutation(s): 0 
Gene Names: EYB64_18220
UniProt
Find proteins for A0A7Z7VJH2 (Vibrio cholerae)
Explore A0A7Z7VJH2 
Go to UniProtKB:  A0A7Z7VJH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7Z7VJH2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.190 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.827α = 90
b = 128.827β = 90
c = 178.484γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI114261

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release