7TAK

Structure of a NAT transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.232 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Insight into the mechanism of H + -coupled nucleobase transport.

Weng, J.Zhou, X.Wiriyasermkul, P.Ren, Z.Chen, K.Gil-Iturbe, E.Zhou, M.Quick, M.

(2023) Proc Natl Acad Sci U S A 120: e2302799120-e2302799120

  • DOI: https://doi.org/10.1073/pnas.2302799120
  • Primary Citation of Related Structures:  
    7TAK

  • PubMed Abstract: 

    Members of the nucleobase/ascorbic acid transporter (NAT) gene family are found in all kingdoms of life. In mammals, the concentrative uptake of ascorbic acid (vitamin C) by members of the NAT family is driven by the Na + gradient, while the uptake of nucleobases in bacteria is powered by the H + gradient. Here, we report the structure and function of PurT Cp , a NAT family member from Colwellia psychrerythraea . The structure of PurT Cp was determined to 2.80 Å resolution by X-ray crystallography. PurT Cp forms a homodimer, and each protomer has 14 transmembrane segments folded into a transport domain (core domain) and a scaffold domain (gate domain). A purine base is present in the structure and defines the location of the substrate binding site. Functional studies reveal that PurT Cp transports purines but not pyrimidines and that purine binding and transport is dependent on the pH. Mutation of a conserved aspartate residue close to the substrate binding site reveals the critical role of this residue in H + -dependent transport of purines. Comparison of the PurT Cp structure with transporters of the same structural fold suggests that rigid-body motions of the substrate-binding domain are central for substrate translocation across the membrane.


  • Organizational Affiliation

    Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative membrane protein PurT
A, B
471Colwellia psychrerythraeaMutation(s): 0 
Gene Names: CPS_4258
Membrane Entity: Yes 
UniProt
Find proteins for Q47WB4 (Colwellia psychrerythraea (strain 34H / ATCC BAA-681))
Explore Q47WB4 
Go to UniProtKB:  Q47WB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47WB4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.713α = 90
b = 135.993β = 90
c = 79.169γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
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 StatesR01 GM119396

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Structure summary
  • Version 1.2: 2023-10-25
    Changes: Refinement description
  • Version 1.3: 2024-08-07
    Changes: Database references