ABCMdb

PMID: 20799350

Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A
Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains.
Protein Sci. 2010 Nov;19(11):2110-21., [PubMed]

Sentences

No. Mutations Sentence Comment

30 ABCC6 p.Gly1302Arg ABCC2 p.Gln1382Arg Mutations in the ATP-binding site also disrupt function, such as G1302R in the Pseudoxanthoma elasticum- associated ABCC6 gene.15 Finally, mutations such as the Dubin-Johnson syndrome-associated Q1382R in ABCC2 are in a mobile region of the NBD (the ''Q-loop``) that is hypothesized to transmit a conformational change between the NBDs and TMDs of an ABC transporter.16 While it is preferable to experimentally characterize the effects of each of the thousands of reported variants in ABC transporters, this approach is not feasible given the large number of variants. Login to comment 48 ABCC4 p.Gly487Glu ABCC4 p.Lys498Glu ABCC4 p.Val1071Ile Experimentally characterized nsSNPs, G487E and K498E (NBD1), and V1071I (NBD2) are indicated in red. Login to comment 50 ABCC6 p.Arg765Gln ABCC7 p.Arg560Thr ABCC7 p.Arg560Ser ABCC7 p.Ala613Thr ABCC7 p.Arg560Lys ABCC7 p.Ala559Thr ABCC7 p.Asp614Gly ABCC7 p.Gly544Val ABCC7 p.Leu610Ser ABCB11 p.Ala570Thr ABCC8 p.Asp1471Asn ABCC9 p.Ala1513Thr ABCC8 p.Arg1493Trp ABCC8 p.Gly1478Arg ABCD1 p.Arg660Trp ABCD1 p.Thr668Ile ABCD1 p.Arg617Cys ABCD1 p.His667Asp ABCD1 p.Arg617His ABCD1 p.Arg660Pro ABCD1 p.Arg617Gly ABCA1 p.Ala2109Thr ABCA1 p.Met1091Thr ABCA1 p.Asp1099Tyr ABCA1 p.Ala1046Asp ABCA4 p.Arg2139Trp ABCA4 p.Glu2131Lys ABCA12 p.Glu1539Lys ABCA4 p.Arg1129Leu ABCA4 p.Glu1122Lys ABCA4 p.Arg1129Cys ABCA4 p.His2128Arg ABCB4 p.Ala546Asp ABCD1 p.Ala616Val ABCC8 p.Asp1471His ABCC8 p.Leu1543Pro ABCC8 p.Lys889Thr ABCC8 p.Arg1493Gln ABCC8 p.Arg841Gly Disease-associated nsSNPs at Three Structural Hotspots in Human ABC Transporter NBDs Gene Disease Position ARA motif ABCB11 BRIC2 A570T ABCD1 X-ALD A616V CFTR CF A559T ABCC6 PXE R765Q ABCC8 HHF1 R841G ABCC8 HHF1 R1493Q ABCC8 HHF1 R1493W ABCD1 X-ALD R617C ABCD1 X-ALD R617G ABCD1 X-ALD R617H CFTR CF R560K CFTR CF R560S CFTR CF R560T ABCA1 HDLD1 A1046D ABCB4 ICP A546D C-loop 1 motif ABCC8 HHF1 D1471H ABCC8 HHF1 D1471N CFTR CBAVD G544V ABCC8 HHF1 G1478R C-loop2 motif ABCA4 STGD1 H2128R ABCC8 HHF1 K889T ABCD1 X-ALD R660P ABCD1 X-ALD R660W ABCA1 HDLD2 M1091T ABCA4 STGD1 E2131K ABCA12 LI2 E1539K ABCA4 STGD1 and CORD3 E1122K CFTR CF L610S ABCC8 HHF1 L1543P ABCA1 Colorectal cancer sample; somatic mutation A2109T ABCC9 CMD1O A1513T ABCD1 X-ALD H667D CFTR CF A613T ABCA1 HDLD2 D1099Y ABCD1 X-ALD T668I CFTR CF D614G ABCA4 STGD1 R2139W ABCA4 STGD1 R1129C ABCA4 ARMD2, STGD1, and FFM R1129L Disease abbreviations are as follows: BRIC2, benign recurrent intrahepatic cholestasis type 2; X-ALD, X-linked adrenoleukodystrophy; CF, cystic fibrosis; PXE, Pseudoxanthoma elasticum; HHF1, familial hyperinsulinemic hypoglycemia-1; HDLD1, high density lipoprotein deficiency type 1; ICP, intrahepatic cholestasis of pregnancy; CBAVD, congenital bilateral absence of the vas deferens; STGD1, Stargardt disease type 1; HDLD2, high density lipoprotein deficiency type 2; LI2, ichthyosis lamellar type 2; CORD3, cone-rod dystrophy type 3; CMD1O, cardiomyopathy dilated type 1O; ARMD2, age-related macular degeneration type 2; FFM, fundus flavimaculatus. Login to comment 62 ABCA4 p.His2128Arg Only one mutation affects the conserved histidine, H2128R in ABCA4. Login to comment 72 ABCG2 p.Gln141Lys ABCG2 p.Ile206Leu ABCG2 p.Pro269Ser ABCC6 p.Arg1268Gln ABCC6 p.Ile742Val ABCC6 p.Arg724Lys ABCB1 p.Ser1141Thr ABCB1 p.Pro1051Ala ABCB1 p.Thr1256Lys ABCB1 p.Val1251Ile ABCB1 p.Trp1108Arg ABCB11 p.Val444Ala ABCB11 p.Asn591Ser ABCB11 p.Glu592Gln ABCB11 p.Gln558His ABCB11 p.Glu1186Lys ABCC6 p.Pro664Ser ABCC6 p.Ala1291Thr ABCC4 p.Gly487Glu ABCC4 p.Thr1142Met ABCC4 p.Lys498Glu ABCC3 p.Arg1381Ser ABCC2 p.Cys1515Tyr ABCC3 p.Gln1365Arg ABCC3 p.Arg1348Cys ABCC3 p.Arg1297His ABCC4 p.Val1071Ile ABCC4 p.Arg1220Gln ABCC3 p.Val765Leu ABCC2 p.Leu849Arg ABCC2 p.Ile670Thr ABCC3 p.Lys718Met ABCC6 p.Gly1327Glu ABCC6 p.Arg769Lys ABCC3 p.Thr809Met ABCC3 p.Asp770Asn ABCC6 p.Glu1369Lys ABCC6 p.Leu1416Arg ABCC6 p.Ile1330Leu ABCC6 p.Arg1461His Predictions of the Functional Effects of 40 nsSNPs in ABC Transporters Comon name HUGO name Mutation NBD Prediction BSEP ABCB11 E592Q NBD1 Neutral BSEP ABCB11 N591S NBD1 Neutral BSEP ABCB11 Q558H NBD1 Neutral BSEP ABCB11 V444A NBD1 Neutral BSEP ABCB11 E1186K NBD2 Disease MDR1 ABCB1 P1051A NBD2 Neutral MDR1 ABCB1 S1141T NBD2 Neutral MDR1 ABCB1 T1256K NBD2 Disease MDR1 ABCB1 V1251I NBD2 Neutral MDR1 ABCB1 W1108R NBD2 Disease MRP2 ABCC2 I670T NBD1 Disease MRP2 ABCC2 L849R NBD1 Disease MRP2 ABCC2 C1515Y NBD2 Disease MRP3 ABCC3 D770N NBD1 Neutral MRP3 ABCC3 K718M NBD1 Neutral MRP3 ABCC3 T809M NBD1 Disease MRP3 ABCC3 V765L NBD1 Disease MRP3 ABCC3 Q1365R NBD2 Disease MRP3 ABCC3 R1297H NBD2 Disease MRP3 ABCC3 R1348C NBD2 Disease MRP3 ABCC3 R1381S NBD2 Disease MRP4 ABCC4 G487E NBD1 Disease MRP4 ABCC4 K498E NBD1 Neutral MRP4 ABCC4 R1220Q NBD2 Neutral MRP4 ABCC4 T1142M NBD2 Neutral MRP4 ABCC4 V1071I NBD2 Neutral MRP6 ABCC6 I1330L NBD1 Neutral MRP6 ABCC6 I742V NBD1 Neutral MRP6 ABCC6 P664S NBD1 Neutral MRP6 ABCC6 R724K NBD1 Neutral MRP6 ABCC6 R769K NBD1 Neutral MRP6 ABCC6 A1291T NBD2 Neutral MRP6 ABCC6 E1369K NBD2 Neutral MRP6 ABCC6 G1327E NBD2 Disease MRP6 ABCC6 L1416R NBD2 Disease MRP6 ABCC6 R1268Q NBD2 Disease MRP6 ABCC6 R1461H NBD2 Disease MXR ABCG2 I206L NBD1 Neutral MXR ABCG2 P269S NBD1 Disease MXR ABCG2 Q141K NBD1 Neutral nsSNPs. Login to comment 78 ABCC4 p.Lys498Glu The K498E nsSNP was found with a frequency of 0.025 in the African-American population. Login to comment 84 ABCC4 p.Gly487Glu The G487E nsSNP was found in only one Asian individual. Login to comment 89 ABCC4 p.Val1071Ile The V1071I nsSNP was found in one African-American. Login to comment 105 ABCC4 p.Gly487Glu ABCC4 p.Lys498Glu The K498E variant had no effect on MRP4 transport, while the G487E variant showed moderate reduction in function (P < 0.05, Fig. 7). Login to comment 106 ABCC4 p.Val1071Ile The V1071I variant dramatically decreased TFV transport to $40% of the reference (P < 0.001; Fig. 7). Login to comment 107 ABCC4 p.Val1071Ile Thus, two of the three predictions were validated, while the V1071I nsSNP prediction was invalidated. Login to comment 110 ABCC4 p.Val1071Ile In contrast, the V1071I variant, which was predicted incorrectly, had significantly less expression on the plasma membrane compared with the reference (Supporting Information Fig. 2). Login to comment 112 ABCC4 p.Gly487Glu ABCC4 p.Lys498Glu ABCC4 p.Val1071Ile Structural models of MRP4 nsSNPs G487E, K498E, and V1071I. Login to comment 113 ABCC4 p.Gly487Glu ABCC1 p.Lys498Glu The models for G487E and K498E were based on the crystallographic structure of the human multidrug resistance protein MRP1 (PDB ID: 2CBZ). Login to comment 114 ABCC4 p.Val1071Ile The model for V1071I was based on the structure of a multidrug resistance protein from Plasmodium yoelii (PDB ID: 2GHI). Login to comment 146 ABCC4 p.Gly487Glu ABCC4 p.Lys498Glu ABCC4 p.Val1071Ile The distribution of disease-associated mutations is nonsymmetric in NBD1 and NBD2, rationalizing experimental work indicating that the two NBDs in an individual transporter are not functionally equivalent.34 Experimental characterization of ABCC4 nsSNPs and validation of a prediction model using a cell-based assay Predictions of functional impact of three ABCC4 nsSNPs (G487E, K498E, and V1071I) were chosen for experimental validation using HEK293 cells stably transfected with the reference transporter and its variants. Login to comment 147 ABCC4 p.Gly487Glu Previously, we reported that the G487E nsSNP showed significantly reduced transport of two antiviral agents, azidothymidine and adefovir, compared with the reference following transient Figure 7. Login to comment 153 ABCC4 p.Gly487Glu ABCC4 p.Gly487Glu ABCC4 p.Gly487Glu The decreased transport of TFV by the G487E variant is in accordance with previous reports using alternate substrates.29,35 Using Xenopus laevis oocytes, it was shown that G487E influenced the transport of 6-mercaptopurine and adefovir.35 As predicted, this effect could be due to the impact of the G487E nsSNP on the conformation of the loop near the membrane, which affects transporter function. Login to comment 154 ABCC4 p.Gly487Glu ABCC4 p.Val1071Ile It is also consistent with the radical chemical change at this position, as quantified by the relatively higher Grantham value for G487E (D ¼ 98).36 The V1071I variant is buried and lies outside the range of known functional sites. Login to comment 156 ABCC4 p.Val1071Ile The V1071I MRP4 variant shows a significant reduction in transport function (Fig. 7). Login to comment 158 ABCC4 p.Val1071Ile The mechanism for the reduced plasma membrane expression of the V1071I variant remains unclear but may be related to changes in stability. Login to comment 159 ABCC4 p.Lys498Glu Finally, the lack of an effect of the K498E variant on TFV transport is consistent with our prediction that this surface-exposed site is not affected by a change in charge. Login to comment 162 ABCB1 p.Trp1108Arg The W1108R variant, predicted correctly by our algorithm to be deleterious (Table II), showed decreased resistance to the anticancer drugs daunorubicin and doxorubicin as well as to valinomycin, when compared with the reference P-glycoprotein in a yeast-based assay, suggesting a functional defect in the transporter. Login to comment 163 ABCB1 p.Ser1141Thr In contrast, the S1141T variant showed either normal or increased transport in the yeast assay, suggesting that the transporter was functioning properly.37 This variant was correctly predicted to be neutral. Login to comment 164 ABCB1 p.Ser1141Thr ABCB1 p.Val1251Ile Finally, in transfected HEK293T cells, the S1141T variant showed increased function, suggesting that the transporter is functioning normally, but also with substrate dependence as for the V1251I nsSNP.38 This variant was predicted correctly to be neutral. Login to comment 165 ABCB1 p.Val1251Ile The V1251I variant of P-glycoprotein showed decreased transport of BODIPY-FL-paclitaxel, but increased transport of calcein-AM in an assay using transfected HEK293T cells. Login to comment