Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains.
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.
Kelly
Libusha
L
Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, California, USA.
Fukushima
Hisayo
H
Karchin
Rachel
R
Gow
Jason M
JM
Chinn
Leslie W
LW
Pieper
Ursula
U
Segal
Mark R
MR
Kroetz
Deanna L
DL
Sali
Andrej
A
D018528:ATP-Binding Cassette Transporters / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000225:Adenine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D000595:Amino Acid Sequence; D001665:Binding Sites; D020022:Genetic Predisposition to Disease; D057809:HEK293 Cells; D006801:Humans; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D027425:ATP-Binding Cassette, Sub-Family C Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D063065:Organophosphonates / Q000737:chemistry / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D017434:Protein Structure, Tertiary; D015203:Reproducibility of Results; D016415:Sequence Alignment; D000068698:Tenofovir
D018528:ATP-Binding Cassette Transporters; D000225:Adenine; D027425:ATP-Binding Cassette, Sub-Family C Proteins; D063065:Organophosphonates; D000068698:Tenofovir; C073492:ABCC4 protein, human
PLoS Comput Biol. 2007 Feb 16;3(2):e26
17305420
PLoS Genet. 2007 Mar 9;3(3):e39
17352537
Bioinformatics. 2005 May 15;21(10):2185-90
15746281
J Lipid Res. 2001 Jul;42(7):1007-17
11441126
Hum Mutat. 2001 Apr;17(4):263-70
11295823
Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21
18045790
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D154-9
15608167
Acta Crystallogr D Biol Crystallogr. 2002 Jun;58(Pt 6  No 1):899-907
12037327
EMBO J. 2005 Jun 1;24(11):1901-10
15889153
Gastroenterology. 2008 Aug;135(2):336-7
18619457
Bioinformatics. 2005 Jun 15;21(12):2814-20
15827081
J Biol Chem. 2002 May 10;277(19):16860-7
11880368
EMBO J. 2001 Oct 15;20(20):5615-25
11598005
Hum Mutat. 2008 May;29(5):659-69
18300232
EMBO J. 2001 Sep 3;20(17):4964-72
11532960
J Pharmacol Exp Ther. 2008 Jun;325(3):859-68
18364470
J Mol Biol. 1995 Apr 7;247(4):536-40
7723011
Cancer Inform. 2008;6:203-16
19043619
Cancer Res. 2004 Jun 1;64(11):3790-7
15172985
Genome Res. 2001 Jul;11(7):1156-66
11435397
Nucleic Acids Res. 2003 Jul 1;31(13):3812-4
12824425
FEBS Lett. 2007 Mar 6;581(5):935-8
17303126
Protein Sci. 2006 Nov;15(11):2507-24
17075131
Nature. 2006 Sep 14;443(7108):180-5
16943773
J Pharmacol Exp Ther. 2008 May;325(2):435-42
18287207
Mol Cell. 2006 Oct 6;24(1):51-62
17018292
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D291-5
16381869
Proc Natl Acad Sci U S A. 2003 May 13;100(10):5896-901
12719533
J Mol Biol. 2006 Jun 16;359(4):940-9
16697012
J Biol Chem. 2005 Nov 4;280(44):36857-64
16107340
Pharmacol Rev. 2006 Mar;58(1):1-2
16507877
Bioinformatics. 2004 Feb 12;20(3):426-7
14960472
Nucleic Acids Res. 2002 Sep 1;30(17):3894-900
12202775
Bioinformatics. 1998;14(10):846-56
9927713
Bioinformatics. 2007 Mar 15;23(6):664-72
17234639
Annu Rev Genomics Hum Genet. 2005;6:123-42
16124856
Hum Mutat. 2001 Dec;18(6):499-515
11748843
J Pharmacol Exp Ther. 2004 Sep;310(3):1199-207
15100388
Proc Natl Acad Sci U S A. 2008 Apr 1;105(13):5069-74
18356296
Clin Pharmacol Ther. 2007 Feb;81(2):265-9
17259950
Nucleic Acids Res. 2009 Jan;37(Database issue):D347-54
18948282
Pflugers Arch. 2007 Feb;453(5):621-41
17187268
Structure. 2009 Sep 9;17(9):1213-22
19748342
BMC Bioinformatics. 2006 Mar 22;7:166
16551372
Proteins. 2008 Jun;71(4):1930-9
18186470
Science. 1974 Sep 6;185(4154):862-4
4843792
Biochem J. 2001 May 15;356(Pt 1):71-5
11336637
Biopolymers. 1983 Dec;22(12):2577-637
6667333
Pac Symp Biocomput. 2005;:397-408
15759645
Science. 2002 May 10;296(5570):1091-8
12004122
Protein Sci. 2007 Sep;16(9):2030-41
17766392
Nature. 2006 Mar 23;440(7083):477-83
16554808