8G52 | pdb_00008g52

Crystal structure of a bacterial TPAT family transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 
    0.222 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structures and Mechanisms of a Novel Bacterial Transport System for Fatty Acids.

Zhai, L.Chou, J.C.Oo, H.Dassama, L.M.K.

(2023) Chembiochem 24: e202300156-e202300156

  • DOI: https://doi.org/10.1002/cbic.202300156
  • Primary Citation Related Structures: 
    8G52, 8G53

  • PubMed Abstract: 

    Bacterial acquisition of metabolites is largely facilitated by transporters with unique substrate scopes. The tripartite ATP-independent periplasmic (TRAP) transporters comprise a large family of bacterial proteins that facilitate the uptake of a variety of small molecules. It has been reported that some TRAP systems encode a fourth protein, the T component. The T-component, or TatT, is predicted to be a periplasmic-facing lipoprotein that enables the uptake of metabolites from the outer membrane. However, no substrates were revealed for any TatT and their functional role(s) remained enigmatic. We recently identified a homolog in Methylococcus capsulatus that binds to sterols, and herein, we report two additional homologs that demonstrate a preference for long-chain fatty acids. Our bioinformatics, quantitative analyses of protein-ligand interactions, and high-resolution crystal structures suggest that TatTs might facilitate the trafficking of hydrophobic or lipophilic substrates and represent a new class of bacterial lipid and fatty acid transporters.


  • Organizational Affiliation
    • Department of Chemistry and Sarafan ChEM-H Institute, Stanford University, Stanford, CA, 94305, USA.

Macromolecule Content 

  • Total Structure Weight: 72.54 kDa 
  • Atom Count: 4,548 
  • Modeled Residue Count: 558 
  • Deposited Residue Count: 658 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TPR_REGION domain-containing protein
A, B
329Enhygromyxa salinaMutation(s): 0 
Gene Names: DB30_07757
UniProt
Find proteins for A0A0C2DGE5 (Enhygromyxa salina)
Explore A0A0C2DGE5 
Go to UniProtKB:  A0A0C2DGE5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0C2DGE5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free:  0.222 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.695α = 90
b = 85.409β = 90.14
c = 73.686γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-08-09
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary