ABCMdb

PMID: 17726488

Degiorgio D, Colombo C, Seia M, Porcaro L, Costantino L, Zazzeron L, Bordo D, Coviello DA
Molecular characterization and structural implications of 25 new ABCB4 mutations in progressive familial intrahepatic cholestasis type 3 (PFIC3).
Eur J Hum Genet. 2007 Dec;15(12):1230-8. Epub 2007 Aug 29., [PubMed]

Sentences

No. Mutations Sentence Comment

18 ABCB1 p.Pro726Thr ABCB1 p.Ala250Pro ABCB1 p.Gly723Glu ABCB4 p.Arg590Gln ABCB4 p.Thr175Ala ABCB4 p.Thr775Met ABCB4 p.Ser320Phe ABCB4 p.Leu701Pro ABCB4 p.Ala511Thr ABCB4 p.Ala364Val ABCB4 p.Glu558Lys ABCB4 p.Ala737Val ABCB4 p.Ala286Val ABCB4 p.Ala1193Thr ABCB4 p.Glu888* ABCB4 p.Tyr403His ABCB4 p.Phe357Leu ABCB4 p.Gly954Ser ABCB4 p.Tyr279* ABCB4 p.Thr715Ile ABCB4 p.Val475Ala ABCB4 p.Gly762* ABCB4 p.Met630Val ABCB4 p.Ala840Asp ABCB4 p.Arg159* ABCB4 p.Gly126Glu ABCB4 p.Thr593Ala The two TMDs contain specific sites for substrate binding and translocation, whereas the two NBDs, which display a high degree of sequence similarity with the equivalent domain of ABC transporters, couple the energy obtained from ATP hydrolysis to substrate transport.8 The ICDs are deemed to be involved in mediating the coupling between NBD conformational changes and the reorientation of TM helices concomitant with substrate extrusion.9 The ABCB1 gene, one of the most extensively studied ABC transporters, is responsible for the human multidrug resistance phenotype that is a rapidly growing obstacle to the treatment of numerous infectious diseases, including human immunodeficiency10 and malaria.11 The properties of this transporter are also exploited in cancer pharmacological therapy where ABCB1 translocates the chemotherapeutic drugs and other molecules with a broad but defined specificity.12 A gene duplication of ABCB1 and additional mutations selected as advantageous have created in mammals the T715I G723E L724AfsX744 A737V G954S G762X T775M G126E S320F A840D OUT IN Linker region F357L L701P A364V NBD-NH2 terminal NBD-COOH terminal A1193T NH2 COOH 1 2 54 6 7 8 129 11 10 EC2EC1 ICD2 A250P Y279X A286V ICD1 R159X T175A ICD3 EC3 EC4 EC6EC5 ICD4 ICD6 ICD5 E888X Y403H V475A A511T E558K R590Q T593A M630V 3 S379KfsX413 P726T Figure 1 (a) Localization of the 29 mutations identified in this study in the ABCB4 protein, schematically represented in its domains. Login to comment 74 ABCB4 p.Leu701Pro This mutation leads to the formation of a stop codon at position 413 (p.S379KfsX413) resulting into a truncated protein comprised of the first TMD, with likely impairment of floppase activity; the patient was compound heterozygous with the missense mutation c.2102T4C (p.L701P) (Table 3). Login to comment 76 ABCB4 p.Tyr403His ABCB4 p.Gly954Ser Two patients were homozygous, one for the mutation p.G954S and the second for p.Y403H (Table 3). Login to comment 77 ABCB4 p.Thr175Ala ABCB4 p.Ser320Phe Notably, two mutations already described were found in members of different families that are not part of a genetic isolate: p.T175A and p.S320F were identified in unrelated Caucasian patients (three and two cases, respectively). Login to comment 80 ABCB4 p.Glu888* ABCB4 p.Tyr279* ABCB4 p.Gly762* ABCB4 p.Arg159* Nonsense mutations The four novel nonsense mutations identified in this study are p.R159X, p.Y279X, p.G762X and p.E888X (Table 2). Login to comment 82 ABCB4 p.Arg159* The patient carrying the p.R159X mutation is heterozygous and the second mutated allele is still unknown; the other three cases show one nonsense mutation associated with three distinct missense mutations (Table 3). Login to comment 84 ABCB4 p.Arg590Gln ABCB4 p.Thr175Ala ABCB4 p.Thr775Met ABCB4 p.Ser320Phe ABCB4 p.Pro726Thr ABCB4 p.Leu701Pro ABCB4 p.Ala511Thr ABCB4 p.Ala364Val ABCB4 p.Ala250Pro ABCB4 p.Glu558Lys ABCB4 p.Ala737Val ABCB4 p.Ala286Val ABCB4 p.Ala1193Thr ABCB4 p.Glu888* ABCB4 p.Tyr403His ABCB4 p.Phe357Leu ABCB4 p.Gly954Ser ABCB4 p.Gly723Glu ABCB4 p.Tyr279* ABCB4 p.Thr715Ile ABCB4 p.Val475Ala ABCB4 p.Gly762* ABCB4 p.Met630Val ABCB4 p.Ala840Asp ABCB4 p.Arg159* ABCB4 p.Gly126Glu ABCB4 p.Thr593Ala There are no PFIC3 epidemiologic data available to date; however, knowing that the number of newborns in Italy has been on average 500 000/year in the last 14 years (http://demo.istat.it/), since we observed 18 patients with ABCB4-mutated alleles born within a 14-year period (with Table 2 Mutations identified in ABCB4 Type of mutationb Exons cDNA locusa Missense Frameshift or nonsense ABCB4-predicted domain GenBank accession numberc Exon 6 c.377G4A G126E TM2 DQ861346 Exon 6 c.523A4G T175A ICD1 Exon 6 c.475C4T R159X ICD1 DQ861347 Exon 8 c.748G4C A250P ICD2 DQ861349 Exon 9 c.837T4A Y279X ICD2 DQ861348 Exon 9 c.857C4T A286V ICD2 DQ861350 Exon 9 c.959C4T S320F TM5 Exon 10 c.1069T4C F357L ICD3 DQ861351 Exon 10 c.1091C4T A364V ICD3 DQ861352 Exon 11 c.1135_1136insAA S379KfsX413 ICD3 DQ861353 Exon 11 c.1207T4C Y403H NBD-NH2 A-loop EF035007 Exon 13 c.1424T4C V475A NBD-NH2 ter DQ861354 Exon 13 c.1531G4A A511T NBD-NH2 ter DQ861355 Exon 14 c.1672G4A E558K NBD-NH2 ter DQ861356 Exon 15 c.1769G4A R590Q NBD-NH2 ter Exon 15 c.1777A4G T593A NBD-NH2 ter DQ861357 Exon 15 c.1888A4G M630V NBD-NH2 ter DQ861358 Exon 17 c.2102T4C L701P Linker region DQ861359 Exon 17 c.2144C4T T715I TM7 DQ861360 Exon 17 c.2168G4A G723E TM7 DQ861361 Exon 17 c.2169_2170insG L724AfsX744 TM7 DQ861362 Exon 17 c.2176C4A P726T TM7 DQ861363 Exon 17 c.2210C4T A737V EC4 DQ861364 Exon 18 c.2284G4T G762X TM8 DQ861365 Exon 19 c.2324C4T T775M TM8 Exon 21 c.2519C4A A840D TM9 DQ861366 Exon 21 c.2662G4T E888X ICD5 DQ861367 Exon 23 c.2860G4A G954S TM11 DQ861368 Exon 27 c.3577G4A A1193T NBD-COOH ter DQ861369 a cDNA sequence is based on reference sequence GenBank NM_018849. Login to comment 102 ABCB4 p.Arg590Gln ABCB4 p.Ala511Thr ABCB4 p.Glu558Lys ABCB4 p.Ala1193Thr ABCB4 p.Tyr403His ABCB4 p.Val475Ala ABCB4 p.Thr593Ala Table 3) includes seven cases: p.Y403H, p.V475A, p.A511T, p.E558K, p.R590Q, p.T593A and p.A1193T. Login to comment 107 ABCB4 p.Glu558Lys ABCB4 p.Tyr403His In particular, the two missense mutations p.Y403H and p.E558K are located in protein sites already extensively investigated in other ABC transporters. Login to comment 110 ABCB1 p.Ala250Pro ABCB4 p.Ala511Thr ABCB4 p.Ala364Val ABCB4 p.Glu558Lys ABCB4 p.Ala286Val ABCB4 p.Phe357Leu ABCB4 p.Val475Ala ABCB4 p.Gly126Glu Apart M630, located in the NBD, the remaining mutations involve either the helical loops (A250, A286, F357, A364) or TM segments (G126, P726, A840, G954; Figure 1b); the ...122_GLGAGVLVA_130... ...434_GLGAGVLVA_442... ...119_GLGGGVLVA_127... ...119_GLGGGVLLA_127... ...276_GLGAGVLVA_284... ...10_GLGGGVLIA_18.... ...120_GIGAGVLVA_128... ....73_GLMILRGIT_81.... ....73_GLMILRGIT_81.... ....73_GLMFVRGLS_81.... ...69_IFVIVRPPI_77.... Hs_ABCB4 Pt_ABCB4 Mm_ABCB4 Rn_ABCB4 Bt_ABCB4 Md_ABCB4 Hs_ABCB1 Esch-coli_Msba Salm-typh_Msba Vibrio-ch_Msba Staph-au_Sav1866 246_LAAYAKAGA_254... 558_LAAYAKAGA_566... 243_LAAYAKAGA_251... 243_LAAYAKAGA_251... 400_LAAYAKAGA_408... 134_LAAYAKAGA_142... 244_LLAYAKAGA_252... 197_QNTMGQVTT_205... 197_QNTMGQVTT_205... 197_QTAMGHVTS_205... 193_SQALAEVQG_201... 282_HLENAKEIG_290... 594_HLENAKEIG_602... 279_HLENAKKIG_287... 279_HLENAKKIG_287... 436_HLENAKRIG_444... 170_HLENAKKIG_178... 280_NLEEAKRIG_288... 233_VSNRMRLQG_241... 233_VSNKMRLQG_241... 233_VSNSMRQQT_241... 229_KNTNFLTRA_237... 353_CIDAFANARGAAYVIF_368.... 665_CIDAFANARGAAYVIF_680.... 350_CIDAFANARGAAYVIF_365.... 350_CIDAFPNARGAAYVIF_365.... 507_CIDAFANARGAAYAIF_522.... 241_CIDSFANARGAAYAIF_256.... 351_SIEAFANARGAAYEIF_366.... 304_VNAQFQRGMAACQTLF_319.... 304_VNAQFQRGMAACQTLF_319.... 304_VTSEFQRGMAACQTLF_319.... 300_SFTTLTQSFASMDRVF_315.... G126E A250P A286V F357L A364V 399_VHFSYPSRA_407.... 711_VHFSYPSRA_719.... 396_VHFSYPSRA_404.... 396_VHFSYPSRA_404.... 553_VHFSYPARP_561.... 287_VHFSYPSRA_295.... 397_VHFSYPSRK_405.... 347_VTFTYPGR-_354.... 347_VTFTYPGR-_354.... 347_VTFTYQGK-_354.... 345_VSFQYNDN-_352.... 471_IIGVVSQEP_479.... 783_IIGVVSQEP_791.... 468_IIGVVSQEP_476.... 468_FIGVVSQEP_476.... 625_IIGVVSQEP_633.... 359_IIGVVSQEP_367.... 469_IIGVVSQEP_477.... 418_QVALVSQNV_426.... 418_QVALVSQNV_426.... 418_HFALVSQNV_426.... 416_QIGLVQQDN_424.... V475A Hs_ABCB4 Pt_ABCB4 Mm_ABCB4 Rn_ABCB4 Bt_ABCB4 Md_ABCB4 Hs_ABCB1 Esch-coli_Msba Salm-typh_Msba Vibrio-ch_Msba Staph-au_Sav1866 ...507_KEANAYEFI_515... ...819_KEANAYEFI_827... ...504_KEANAYDFI_512... ...504_KEANAYDFI_512... ...661_KEANAYEFI_669... ...395_KDANAYEFI_403... ...505_KEANAYDFI_513... ...455_RMAYAMDFI_463... ...455_RMAYAMDFI_463... ...455_RQAHAMEFI_463... ..452_KMANAHDFI_460... A511T 554_LLLDEATSA_562... 866_LLLDEATSA_874... 551_LLLDEATSA_559... 551_LLLDEATSA_559... 708_LLLDEATSA_716... 442_LLLDEATSA_450... 552_LLLDEATSA_560... 502_LILDEATSA_510... 502_LILDEATSA_510... 502_LILDEATSA_510... 499_LILDEATSA_507... E558K 586_VIAHRLSTVRNA_597... 898_VIAHRLSTVRNA_909... 583_VIAHRLSTIRNA_594... 583_VIAHRLSTVRNA_594... 740_VIAHRLSTIRNA_751... 474_VIAHRLSTIRNA_485... 584_VIAHRLSTVRNA_595... 534_VIAHRLSTIEKA_545... 534_VIAHRLSTIEQA_545... 534_VIAHRLSTIEQA_545... 531_IVAHRLSTITHA_542... 626_KLVNMQTSG_634.. 938_KLVNMQTSG_946.. 623_RLVNMQTAG_631.. 623_RLVNMQTSG_631.. 780_RLVNTQISG_788.. 514_KLVNMQYIF_522... 624_KLVTMQTAG_632.. 574_QLHKMQFGQ_582.. 574_QLHKMQFGQ_582.. 574_QLHRIQFGE_582.. 570_HLYSIQN--_576.. 697_FLKVLKLNKTEWPYFVVGTVCAIANGGLQPAFSVIFSEIIAIF_739. Login to comment 116 ABCB4 p.Leu701Pro ABCB4 p.Ala737Val ABCB4 p.Tyr403His ABCB4 p.Gly954Ser ABCB4 p.Thr715Ile ABCB4 p.Met630Val 13_FRRLWPTIAPFKAGLIVAGVALILNAASDTFMLSLLKPLLDDG_55.. 13_FRRLWPTIAPFKAGLIVAGIALILNAASDTFMLSLLKPLLDDG_55.. 13_FKRLWTYIRLYKAGLVVSTIALVINAAADTYMISLLKPLLDEG_55.. 2_IKRYLQFVKPYKYRIFATIIVGIIKFGIPMLIPLLIKYAIDGV_44.. ...836_AQNIANLGT_844... ..1148_AQNIANLGT_1156.. ...833_AQNTANLGT_841... ...835_AQNTANLGT_843... ...987_AQNTANLGT_995... ...748_AQNTANLGT_756... ...837_TQNIANLGT_845... ...147_VREGASIIG_155... ...147_VREGASIIG_155... ...147_VREGASIIG_155... ..143_WLDCITIII_151... Hs_ABCB4 Pt_ABCB4 Mm_ABCB4 Rn_ABCB4 Bt_ABCB4 Md_ABCB4 Hs_ABCB1 Esch-coli_Msba Salm-typh_Msba Vibrio-ch_Msba Staph-au_Sav1866 950_FSYAGCFRF_958.... 1262_FSYAGCFRF_1270.... 947_FSYAGCFRF_955.... 949_FSYAGCFRF_957.... 1101_FSYAGCFRF_1109 862_FSYAGCFRF_870.... 951_FSYAGCFRF_959.... 261_LALAFVLYA_269.... 261_LALAFVLYA_269.... 261_LALFAVLFL_269.... 257_IGPIIVIGV_265.... 1189_RIAIARALI_1197.... 1494_RIAIARALI_1502.... 1179_RIAIARALI_1187.... 1181_RIAIARALI_1189.... --------- 1093_RIAIARALI_1101.... 1183_RIAIARALV_1191.... .488_RIAIARALL_496.... .488_RIAIARALL_496.... .488_RVAIARALL_496.... .485_RLSIARIFL_493.... Y403H T593AR590Q M630V L701P T715I P726TG723E A737V G954S A1193TA840D Figure 2 Multiple sequence alignment of ABCB4 protein sequences. Login to comment 122 ABCB1 p.Pro726Thr ABCB4 p.Gly954Ser ABCB4 p.Ala840Asp ABCB4 p.Gly126Glu changes p.G126E, p.P726T, p.A840D and p.G954S that involve substitution of neutral residue with a polar residue, could cause structural perturbations affecting the correct interaction of the respective TM segment with the cell membrane phospholipid bilayer. Login to comment 123 ABCB1 p.Gly955Val Previous mutagenesis and biochemical studies carried out on human ABCB1 have assessed that Ala841, part of TM9, structurally equivalent to Ala840 in ABCB4, is involved in drug binding24,25 and interferes with the ability of the two structural modules (TMDs and NBDs) to form correct interactions.25 Furthermore, the position Gly954 was already described as ABCB1 mutant G955V that shows altered drug-stimulated ATPase activities.26 (c) The remaining four novel missense mutations described here (green bars, Figure 2) are affected residues conserved only in mammals ABCB4 (category named C in Table 3). Login to comment 124 ABCB4 p.Leu701Pro Among them, p.L701P involves the linker region (Figure 1a). Login to comment 126 ABCB1 p.Gly723Glu In this regard, transfected mammalian cell lines with ABCB1 mutants showed that insertion of a rigid structure (a-helical peptide) in this flexible connecting segment affects the cell surface localization of ABCB1.27 The mutation p.G723E brings a charged residue within the hydrophobic environment of the membrane, with very unfavorable energetic effects. Login to comment 132 ABCB4 p.Ala364Val ABCB4 p.Ala250Pro ABCB4 p.Ala737Val ABCB4 p.Ala286Val ABCB4 p.Phe357Leu ABCB4 p.Thr715Ile ABCB4 p.Met630Val The structural or functional relevance of the remaining seven amino-acid substitutions (p.A250P, p.A286V, p.F357L, p.A364V, p.M630V, p.T715I and p.A737V) is less clear and the induced effect on ABCB4 is less evident. Login to comment