Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains

Libusha Kelly, Hisayo Fukushima, Rachel Karchin, Jason M. Gow, Leslie W. Chinn, Ursula Pieper, Mark R. Segal, Deanna L. Kroetz, Andrej Sali

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


The human ATP-binding cassette (ABC) transporter superfamily consists of 48 integral membrane proteins that couple the action of ATP binding and hydrolysis to the transport of diverse substrates across cellular membranes. Defects in 18 transporters have been implicated in human disease. In hundreds of cases, disease phenotypes and defects in function can be traced to nonsynonymous single nucleotide polymorphisms (nsSNPs). The functional impact of the majority of ABC transporter nsSNPs has yet to be experimentally characterized. Here, we combine experimental mutational studies with sequence and structural analysis to describe the impact of nsSNPs in human ABC transporters. First, the disease associations of 39 nsSNPs in 10 transporters were rationalized by identifying two conserved loops and a small α-helical region that may be involved in interdomain communication necessary for transport of substrates. Second, an approach to discriminate between disease-associated and neutral nsSNPs was developed and tailored to this superfamily. Finally, the functional impact of 40 unannotated nsSNPs in seven ABC transporters identified in 247 ethnically diverse individuals studied by the Pharmacogenetics of Membrane Transporters consortium was predicted. Three predictions were experimentally tested using human embryonic kidney epithelial (HEK) 293 cells stably transfected with the reference multidrug resistance transporter 4 and its variants to examine functional differences in transport of the antiviral drug, tenofovir. The experimental results confirmed two predictions. Our analysis provides a structural and evolutionary framework for rationalizing and predicting the functional effects of nsSNPs in this clinically important membrane transporter superfamily. Published by Wiley-Blackwell.

Original languageEnglish (US)
Pages (from-to)2110-2121
Number of pages12
JournalProtein Science
Issue number11
StatePublished - Nov 2010
Externally publishedYes


  • ABC transporters
  • Genetic variation
  • Multidrug resistance
  • Structural modeling

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology


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