5I6C | pdb_00005i6c

The structure of the eukaryotic purine/H+ symporter, UapA, in complex with Xanthine

• PDB DOI: https://doi.org/10.2210/pdb5I6C/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Aspergillus nidulans FGSC A4
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2016-02-16 Released: 2016-04-27 
• Deposition Author(s): Alguel, Y., Amillis, S., Leung, J., Lambrinidis, G., Capaldi, S., Scull, N.J., Craven, G., Iwata, S., Armstrong, A., Mikros, E., Diallinas, G., Cameron, A.D., Byrne, B.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 
  0.327 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.296 (Depositor), 0.303 (DCC) 
• R-Value Observed: 
  0.298 (Depositor) 

Literature

Structure of eukaryotic purine/H(+) symporter UapA suggests a role for homodimerization in transport activity.

Alguel, Y., Amillis, S., Leung, J., Lambrinidis, G., Capaldi, S., Scull, N.J., Craven, G., Iwata, S., Armstrong, A., Mikros, E., Diallinas, G., Cameron, A.D., Byrne, B.

(2016) Nat Commun 7: 11336-11336

• PubMed: 27088252 
• DOI: https://doi.org/10.1038/ncomms11336
• Primary Citation Related Structures: 
  5I6C


• PubMed Abstract: 
  

  The uric acid/xanthine H(+) symporter, UapA, is a high-affinity purine transporter from the filamentous fungus Aspergillus nidulans. Here we present the crystal structure of a genetically stabilized version of UapA (UapA-G411VΔ1-11) in complex with xanthine. UapA is formed from two domains, a core domain and a gate domain, similar to the previously solved uracil transporter UraA, which belongs to the same family. The structure shows UapA in an inward-facing conformation with xanthine bound to residues in the core domain. Unlike UraA, which was observed to be a monomer, UapA forms a dimer in the crystals with dimer interactions formed exclusively through the gate domain. Analysis of dominant negative mutants is consistent with dimerization playing a key role in transport. We postulate that UapA uses an elevator transport mechanism likely to be shared with other structurally homologous transporters including anion exchangers and prestin.

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Organizational Affiliation: 
• Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
Faculty of Biology, University of Athens, Panepistimioupolis, 15781, Athens, Greece.
Faculty of Pharmacy, University of Athens, Panepistimioupolis, 15771 Athens, Greece.
Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
Department of Chemistry, Imperial College London, London SW7 2AZ, UK.
JST, Research Acceleration Program, Membrane Protein Crystallography Project, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.
School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 124.76 kDa 
• Atom Count: 7,127 
• Modeled Residue Count: 948 
• Deposited Residue Count: 1,148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uric acid-xanthine permease	A, B	574	Aspergillus nidulans FGSC A4	Mutation(s): 1  Gene Names: uapA, AN6932 Membrane Entity: Yes
UniProt
Find proteins for Q07307 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)) Explore Q07307  Go to UniProtKB:  Q07307

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMT	D [auth A], E [auth A], G [auth B], H [auth B]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
XAN	C [auth A], F [auth B]	XANTHINE C5 H4 N4 O2 LRFVTYWOQMYALW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free:  0.327 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.296 (Depositor), 0.303 (DCC) 
• R-Value Observed: 0.298 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.09	α = 90
b = 173.83	β = 111.11
c = 82.39	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
SHARP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-04-27 
Deposition Author(s): Alguel, Y., Amillis, S., Leung, J., Lambrinidis, G., Capaldi, S., Scull, N.J., Craven, G., Iwata, S., Armstrong, A., Mikros, E., Diallinas, G., Cameron, A.D., Byrne, B.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	--

Revision History  

• Version 1.0: 2016-04-27
  Type: Initial release
  
• Version 1.1: 2016-05-04
  Changes: Database references
• Version 1.2: 2017-08-30
  Changes: Author supporting evidence
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary