4YMW

Crystal structure of an amino acid ABC transporter with histidines


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.804 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for substrate specificity of an amino acid ABC transporter

Yu, J.Ge, J.Heuveling, J.Schneider, E.Yang, M.

(2015) Proc.Natl.Acad.Sci.USA 112: 5243-5248

  • DOI: 10.1073/pnas.1415037112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ATP-binding cassette (ABC) transporters are ubiquitous integral membrane proteins that translocate a variety of substrates, ranging from ions to macromolecules, either out of or into the cytosol (hence defined as importers or exporters, respectively) ...

    ATP-binding cassette (ABC) transporters are ubiquitous integral membrane proteins that translocate a variety of substrates, ranging from ions to macromolecules, either out of or into the cytosol (hence defined as importers or exporters, respectively). It has been demonstrated that ABC exporters and importers function through a common mechanism involving conformational switches between inward-facing and outward-facing states; however, the mechanism underlying their functions, particularly substrate recognition, remains elusive. Here we report the structures of an amino acid ABC importer Art(QN)2 from Thermoanaerobacter tengcongensis composed of homodimers each of the transmembrane domain ArtQ and the nucleotide-binding domain ArtN, either in its apo form or in complex with substrates (Arg, His) and/or ATPs. The structures reveal that the straddling of the TMDs around the twofold axis forms a substrate translocation pathway across the membrane. Interestingly, each TMD has a negatively charged pocket that together create a negatively charged internal tunnel allowing amino acids carrying positively charged groups to pass through. Our structural and functional studies provide a better understanding of how ABC transporters select and translocate their substrates.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China and erwin.schneider@rz.hu-berlin.de maojunyang@tsinghua.edu.cn.,Division of Microbial Physiology, Department of Biology, Humboldt University of Berlin, D-10099 Berlin, Germany.,Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China and.,Division of Microbial Physiology, Department of Biology, Humboldt University of Berlin, D-10099 Berlin, Germany erwin.schneider@rz.hu-berlin.de maojunyang@tsinghua.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ABC-type polar amino acid transport system, ATPase component
J, A
240Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)Mutation(s): 0 
Gene Names: GlnQ
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Art(QN)2 amino acid importer
Find proteins for Q8RCC2 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4))
Go to UniProtKB:  Q8RCC2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ABC-type amino acid transport system, permease component
D, C
220Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)Mutation(s): 0 
Gene Names: ArtM
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Art(QN)2 amino acid importer
Find proteins for Q8RCC3 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4))
Go to UniProtKB:  Q8RCC3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HIS
Query on HIS

Download SDF File 
Download CCD File 
C, D
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.804 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 96.247α = 90.00
b = 115.264β = 90.00
c = 301.185γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-03-07 
  • Released Date: 2015-04-22 
  • Deposition Author(s): Ge, J., Yu, J., Yang, M.

Revision History 

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-05-06
    Type: Database references