9IBP | pdb_00009ibp

VCA0144 from Vibrio cholerae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.182 (Depositor), 0.182 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 
    0.152 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


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
Immunogenic protein
A, B
327Vibrio choleraeMutation(s): 0 
Gene Names: D6U24_11590ERS013165_01132KIN13_00845
UniProt
Find proteins for A0A0H4JT42 (Vibrio cholerae)
Explore A0A0H4JT42 
Go to UniProtKB:  A0A0H4JT42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H4JT42
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
I [auth B]
J [auth B]
C [auth A],
D [auth A],
E [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.182 (Depositor), 0.182 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 0.152 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.4α = 90
b = 123.4β = 90
c = 226.085γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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