4YMX

Crystal structure of the substrate binding protein of an amino acid ABC transporter

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

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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 U S A 112: 5243-5248

  • DOI: 10.1073/pnas.1415037112
  • Primary Citation of Related Structures:  
    4YMS, 4YMT, 4YMU, 4YMV, 4YMW, 4YMX

  • 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). 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 ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ABC-type amino acid transport system, periplasmic componentA, B260Caldanaerobacter subterraneus subsp. tengcongensis MB4Mutation(s): 0 
Gene Names: ArtI, TTE0512
Membrane Entity: Yes 
UniProt
Find proteins for Q8RCC4 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4))
Explore Q8RCC4 
Go to UniProtKB:  Q8RCC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RCC4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARG
Query on ARG
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ARG Binding MOAD:  4YMX Kd: 79 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.026α = 103.73
b = 41.409β = 102.74
c = 75.604γ = 90.12
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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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  (Full details and data files)

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