ABCMdb

ABCC7 p.Phe508Ser

ClinVar:	c.1523T>C , p.Phe508Ser ? , not provided c.1523T>G , p.Phe508Cys N , Benign
CF databases:	c.1521_1523delCTT , p.Phe508del D , CF-causing c.1523T>C , p.Phe508Ser (CFTR1) D , This mutation was found in a patient with CBAVD. c.1523T>G , p.Phe508Cys (CFTR1) ? ,
Predicted by SNAP2:	A: D (95%), C: D (75%), D: D (95%), E: D (95%), G: D (95%), H: D (95%), I: D (95%), K: D (95%), L: D (95%), M: D (95%), N: D (95%), P: D (95%), Q: D (95%), R: D (95%), S: D (95%), T: D (95%), V: D (95%), W: D (95%), Y: D (95%),
Predicted by PROVEAN:	A: D, C: D, D: D, E: D, G: D, H: D, I: D, K: D, L: D, M: D, N: D, P: D, Q: D, R: D, S: D, T: D, V: D, W: D, Y: D,

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[hide] Side chain and backbone contributions of Phe508 to... Nat Struct Mol Biol. 2005 Jan;12(1):10-6. Epub 2004 Dec 26. Thibodeau PH, Brautigam CA, Machius M, Thomas PJ
Side chain and backbone contributions of Phe508 to CFTR folding.
Nat Struct Mol Biol. 2005 Jan;12(1):10-6. Epub 2004 Dec 26., [PMID:15619636]

Abstract [show]
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

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17 Finally, to assess the specific structural consequences of these mutations, the crystal structures of two mutant NBD1 proteins, F508S, a previously identified non-CF-causing mutation (http://www. Login to comment
33 The F508A,F508M,F508P,F508D,F508Q,F508R and F508S mutant proteins were more similar to the wild type than the ∆F508 protein in their temperature-dependence of refolding (Fig. 1b,c). Login to comment
43 The missense mutant proteins F508A, F508M,F508P,F508D,F508Q,F508R and F508S had similar ∆Gunfolding and m-values, 3.4-3.8 kcal mol-1 and 1.5-1.7 kcal mol-1 M-1 denaturant, respectively, highlighting the fact that changes in the bulk or chemical properties of the substituted side chain had little effect on the native-state stabilities of these domains as measured by denaturation with GuHCl (Table 1). Login to comment
46 How does the isolated NBD accommodate such Temperature (ºC) 4 10 16 22 Fractionalyield 0.0 0.5 1.0 Temperature (ºC) 4 10 16 22 Temperature (ºC) 4 10 16 22 Wild type ∆F508 Wild type ∆F508 ̄ F508A ̄ F508M F508P F508W ͷ F508W W496F Wild type ∆F508 F508Q F508R F508D F508S a b c Figure 1 NBD1 folding efficiency as a function of folding temperature. Login to comment
53 Table 1 Stability of wild-type and mutant NBD proteins Protein ∆Gunfolding ∆∆Gunfolding m-value (kcal mol-1) (kcal mol-1) (kcal mol-1 M-1) Wild type 3.7 ± 0.1 0 1.7 ∆F508 3.6 ± 0.1 0.1 1.7 F508A 3.6 ± 0.2 0.1 1.6 F508M 3.5 ± 0.1 0.1 1.6 F508P 3.5 ± 0.3 0.2 1.6 F508D 3.6 ± 0.1 0.1 1.6 F508Q 3.5 ± 0.2 0.2 1.6 F508R 3.4 ± 0.3 0.3 1.6 F508S 3.8 ± 0.2 -0.1 1.6 considerable changes in amino acid character at position 508 when this position is critical to the proper biogenesis of the full-length protein, and what are the underlying structural changes associated with these substitutions? Login to comment
54 NBD1 structure To directly assess the structural changes associated with the substitution of residues at position 508, crystal structures of two missense-mutant proteins were determined for the highly similar murine NBD1: F508S, a previously identified non-CF-causing variant, and F508R,a previously described maturation- deficientmutation.Theproteinswereexpressed and purified essentially as described for the wild-type protein and crystallized under conditions similar to the wild-type protein in the presence of Mg2+ andATP with sodium acetate as the precipitant26. Login to comment
55 Tetragonal bipyramidal crystals grew for the F508R proteins, whereas the F508S protein spontaneously crystallized as large tetragonal plates. Login to comment
56 The F508S and F508R crystals diffracted to 2.7 and 3.1 Å,respectively and structures were determined with final R/Rfree valuesof 0.207/0.262and0.254/0.266, respectively (Table 2). Login to comment
59 All of the major structural elements are conserved and the r.m.s. deviations between the Cα atoms of the wild type and F508S or F508R structures were <0.33 Å (Fig.2a)26. Login to comment
67 The conformation of ATP in the wild-type26 and F508S structures is very similar, with a noncanonical interaction between the NBD and ATP and unusual torsional angles in the ATP molecule (SupplementaryFig.1online).In the F508R structure,the two monomers that occur in the asymmetric unit contain ATP in different conformations. Login to comment
68 In one monomer, the ATP is bound in an orientation similar to that observed in the wild-type and F508S structures.The ATP bound to the other monomer,however,adopts a more conventional orientation (Supplementary Fig. 1 online). Login to comment
71 Examination of the calculated molecular surface of the wild-type, F508S and F508R proteins is revealing. Login to comment
73 Quantification of the surface-accessibility of position 508 reveals that the wild-type and F508S side chains are very similar at 8.5 and 9.6 Å2 respectively.The F508R protein has greater average accessible surface area at position 508, with a value of 16.8 Å2. Login to comment
78 Wild type, green; F508S variant, orange; F508R variant, blue. Login to comment
79 The r.m.s. deviations between the wild-type and F508S or F508R structures are ~0.3 Å. Login to comment
84 The 2Fo - Fc electron density map (contoured at 1 σ) calculated with the F508S data at a resolution of 2.7 Å superposed on the final F508S model. Login to comment
91 Band C levels in F508A, F508G, F508L and F508V as well as the polar amino acid substitutions F508S, F508T, F508N and F508Q were evident, but substantially reduced relative to wild-type band C levels. Login to comment
92 The known polymorphism F508C and the non-CF-causing variant F508S both showed measurable quantities of band C at steady-state levels, as would be expected for non-CF-causingsubstitutions.Thehydrophobicaminoacidsubstitutions F508I,F508W and F508Y did not produce substantial steady-state levels of band C as measured by western blotting, nor did the ionizable amino acid substitutions F508D, F508E, F508K, F508H or F508R. Login to comment
103 Most notably, the crystal structures of F508S and F508R both indicate that substitutions for Phe508 do not substantially impact the structure of NBD1,providing further evidence for the high tolerance for substitution at this position in the isolated domain. Login to comment
113 W ild type ∆∆F508 F508 F508D F508K F508E F508R F508H F508S F508T F508N F508Q C B Charged Polar F508A F508C F508I F508L ∆F508 F508 W ild type C B F508W F508Y F508G F508P Hydrophobic F508M F508V ̅̆ ̆ ̅ Figure 3 Maturation of full-length CFTR mutants. Login to comment
117 (F508S has been associated with congenital bilateral absence of (the vas deferens, but not CF.) Login to comment
180 The structure of F508S was determined using the mNBD1 structure (PDB entry 1R0W)26 stripped of water molecules, ions and ATP as the starting model. Login to comment
186 The atomic coordinates and structure factors for the F508S and F508R NBD1 structures have been deposited in the Protein Data Bank (accession codes 1XF9 and 1XFA, respectively). Login to comment
188 Table 2 Data collection and refinement statistics F508S F508R Data collection Space group P4212 I4122 Cell dimensions (Å) a 170.45 139.99 b 170.45 139.99 c 109.07 278.72 Resolution (Å) 40.4-2.7 (2.75-2.7) 44.3-3.1 (3.15-3.1) Rsym 0.078 (0.431) 0.071 (0.987) I / σI 22.9 (2.3) 34.8 (2.5) Completeness (%) 98.8 (95.6) 99.9 (100) Redundancy 7.7 (3.3) 11.9 (10.7) Refinement Resolution (Å) 40.4-2.7 44.3-3.1 No. Login to comment

[hide] Building an understanding of cystic fibrosis on th... J Bioenerg Biomembr. 2007 Dec;39(5-6):499-505. Mendoza JL, Thomas PJ
Building an understanding of cystic fibrosis on the foundation of ABC transporter structures.
J Bioenerg Biomembr. 2007 Dec;39(5-6):499-505., [PMID:18080175]

Abstract [show]
Cystic fibrosis (CF) is a fatal disease affecting the lungs and digestive system by impairment of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). While over 1000 mutations in CFTR have been associated with CF, the majority of cases are linked to the deletion of phenylalanine 508 (delta F508). F508 is located in the first nucleotide binding domain (NBD1) of CFTR. This mutation is sufficient to impair the trafficking of CFTR to the plasma membrane and, thus, its function. As an ABC transporter, recent structural data from the family provide a framework on which to consider the effect of the delta F508 mutation on CFTR. There are fifty-seven known structures of ABC transporters and domains thereof. Only six of these structures are of the intact transporters. In addition, modern bioinformatic tools provide a wealth of sequence and structural information on the family. We will review the structural information from the RCSB structure repository and sequence databases of the ABC transporters. The available structural information was used to construct a model for CFTR based on the ABC transporter homologue, Sav1866, and provide a context for understanding the molecular pathology of Cystic Fibrosis.

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67 In contrast to the large number of sequences available for the NBD align- Table 1 ABC transporter structures in the research collaboratory for structural bioinformatics (RCSB) database Release Date PDB Protein Resolution Species NBD Structures Jun-05 1Z47 CysA 1.9 Alicyclobacillus acidocaldarius Sep-03 1OXX GlcV G144A 1.45 Sulfolobus solfataricus Jun-03 1OXT GlcV nucleotide free 2.1 Sulfolobus solfataricus Jun-03 1OXU GlcV w/ ADP 2.1 Sulfolobus solfataricus Jun-03 1OXV GlcV w/ AMP.PNP 2.1 Sulfolobus solfataricus Jun-03 1OXS GlcV w/ iodide ions 1.65 Sulfolobus solfataricus Nov-99 1B0U HisP w/ ATP 1.5 Salmonella typimurium Jun-03 1MT0 HlyB (467-707) 2.6 Escherichia coli Aug-06 2FFB HlyB E631Q w/ ADP 1.9 Escherichia coli Aug-06 2FGK HlyB E631Q w/ ATP 2.7 Escherichia coli Aug-06 2FFA HlyB H662A w/ ADP 1.7 Escherichia coli Aug-06 2FGJ HlyB H662A w/ ATP 2.6 Escherichia coli Jun-05 1XEF HlyB w/ ATP 2.5 Escherichia coli Aug-06 2FF7 HlyB w/ADP 1.6 Escherichia coli Dec-03 1MV5 LmrA w/ ADP, ATP 3.1 Lactococcus lactis Dec-00 1G29 MalK 1.9 Thermococcus litoralis Sep-03 1Q1E MalK 2.9 Escherichia coli Dec-04 1VCI MalK w/ ATP 2.9 Pyrococcus horikoshii Aug-07 2QRR metN 1.71 Vibrio parahaemolyticus Aug-07 2QSW metN C-terminal domain 1.5 Enterococcus faecalis Jul-02 1L2T MJ0796 E171Q Dimeric Structure 1.9 Methanococcus jannaschii Jul-01 1F3O MJ0796 w/ ADP 2.7 Methanococcus jannaschii Nov-01 1GAJ MJ1267 2.5 Methanococcus jannaschii Jul-01 1G6H MJ1267 w/ ADP 1.6 Methanococcus jannaschii Feb-03 1G9X MJ1267 w/ ADP 2.6 Methanococcus jannaschii May-06 2CBZ MRP1-NBD1 1.5 Homo sapiens Nov-04 1V43 Multi-sugar transporter 2.2 Pyrococcus horikoshii Aug-04 1SGW Putative 1.7 Pyrococcus furiosus Apr-07 2P0S Putative 1.6 Porphyromonas gingivalis Sep-07 2IHY Putative 1.9 Staphylococcus aureus Jan-06 2D3W SufC 2.5 Escherichia coli Oct-06 2IXE Tap1 D645N w/ ATP 2 Rattus norvegicus Oct-06 2IXF Tap1 D645Q, Q678H w/ ATP 2 Rattus norvegicus Oct-06 2IXG Tap1 S621A, G622V, D645N w/ ATP 2.7 Homo sapiens Sep-01 1JJ7 Tap1 w/ ADP 2.4 Homo sapiens Aug-02 1JI0 Thermatoga w/ ATP 2 Sulfolobus solfataricus Nov-04 1VPL TM0544 2.1 Thermotoga maritima CFTR NBD Structures Nov-04 1XMJ Human CFTR dF508 NBD1 2.3 Homo sapiens Nov-05 2BBT Human CFTR dF508 NBD1 w/ two solublizing mutations 2.3 Homo sapiens Nov-05 2BBS Human CFTR dF508 NBD1 w/ 3M 2.05 Homo sapiens Nov-05 2BBO Human CFTR NBD1 2.55 Homo sapiens Nov-04 1XMI Human CFTR NBD1-F508A w/ ATP 2.25 Homo sapiens Dec-04 1XFA Murine CFTR-F508R 3.1 Mus musculus Dec-04 1XF9 Murine CFTR-F508S 2.7 Mus musculus Dec-03 1R0W Murine CFTR NBD1 2.2 Mus musculus Dec-03 1R0Z Murine CFTR NBD1 - phosphorylated w/ ATP 2.35 Mus musculus J Bioenerg Biomembr (2007) 39:499-505 501501 ments in Pfam, only 6,419 transmembrane sequences are in the MSA of ABC transporter TMDs, PF00664 (Sonnhammer et al. 1997). Login to comment

[hide] CFTR function and prospects for therapy. Annu Rev Biochem. 2008;77:701-26. Riordan JR
CFTR function and prospects for therapy.
Annu Rev Biochem. 2008;77:701-26., [PMID:18304008]

Abstract [show]
Mutations in the gene coding for the cystic fibrosis transmembrane conductance regulator (CFTR) epithelial anion channel cause cystic fibrosis (CF). The multidomain integral membrane glycoprotein, a member of the adenine nucleotide-binding cassette (ABC) transporter family, conserved in metazoan salt-transporting tissues, is required to control ion and fluid homeostasis on epithelial surfaces. This review considers different therapeutic strategies that have arisen from knowledge of CFTR structure and function as well as its biosynthetic processing, intracellular trafficking, and turnover.

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418 However, this 710 Riordan was also found to be the case with the isolated domains containing either F508S or F508R substitutions (110). Login to comment

[hide] Structure and dynamics of NBD1 from CFTR character... J Mol Biol. 2010 Feb 19;396(2):406-30. Epub 2009 Nov 26. Lewis HA, Wang C, Zhao X, Hamuro Y, Conners K, Kearins MC, Lu F, Sauder JM, Molnar KS, Coales SJ, Maloney PC, Guggino WB, Wetmore DR, Weber PC, Hunt JF
Structure and dynamics of NBD1 from CFTR characterized using crystallography and hydrogen/deuterium exchange mass spectrometry.
J Mol Biol. 2010 Feb 19;396(2):406-30. Epub 2009 Nov 26., 2010-02-19 [PMID:19944699]

Abstract [show]
The DeltaF508 mutation in nucleotide-binding domain 1 (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) is the predominant cause of cystic fibrosis. Previous biophysical studies on human F508 and DeltaF508 domains showed only local structural changes restricted to residues 509-511 and only minor differences in folding rate and stability. These results were remarkable because DeltaF508 was widely assumed to perturb domain folding based on the fact that it prevents trafficking of CFTR out of the endoplasmic reticulum. However, the previously reported crystal structures did not come from matched F508 and DeltaF508 constructs, and the DeltaF508 structure contained additional mutations that were required to obtain sufficient protein solubility. In this article, we present additional biophysical studies of NBD1 designed to address these ambiguities. Mass spectral measurements of backbone amide (1)H/(2)H exchange rates in matched F508 and DeltaF508 constructs reveal that DeltaF508 increases backbone dynamics at residues 509-511 and the adjacent protein segments but not elsewhere in NBD1. These measurements also confirm a high level of flexibility in the protein segments exhibiting variable conformations in the crystal structures. We additionally present crystal structures of a broader set of human NBD1 constructs, including one harboring the native F508 residue and others harboring the DeltaF508 mutation in the presence of fewer and different solubilizing mutations. The only consistent conformational difference is observed at residues 509-511. The side chain of residue V510 in this loop is mostly buried in all non-DeltaF508 structures but completely solvent exposed in all DeltaF508 structures. These results reinforce the importance of the perturbation DeltaF508 causes in the surface topography of NBD1 in a region likely to mediate contact with the transmembrane domains of CFTR. However, they also suggest that increased exposure of the 509-511 loop and increased dynamics in its vicinity could promote aggregation in vitro and aberrant intermolecular interactions that impede trafficking in vivo.

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132 Bright green and magenta represent human F508 and F508A structures, respectively, shades of red/orange represent human ΔF508 human structures, and shades of blue/cyan represent murine structures (F508, F508S, or F508R). Login to comment

[hide] The cystic fibrosis-causing mutation deltaF508 aff... J Biol Chem. 2010 Nov 12;285(46):35825-35. Epub 2010 Jul 28. Thibodeau PH, Richardson JM 3rd, Wang W, Millen L, Watson J, Mendoza JL, Du K, Fischman S, Senderowitz H, Lukacs GL, Kirk K, Thomas PJ
The cystic fibrosis-causing mutation deltaF508 affects multiple steps in cystic fibrosis transmembrane conductance regulator biogenesis.
J Biol Chem. 2010 Nov 12;285(46):35825-35. Epub 2010 Jul 28., 2010-11-12 [PMID:20667826]

Abstract [show]
The deletion of phenylalanine 508 in the first nucleotide binding domain of the cystic fibrosis transmembrane conductance regulator is directly associated with >90% of cystic fibrosis cases. This mutant protein fails to traffic out of the endoplasmic reticulum and is subsequently degraded by the proteasome. The effects of this mutation may be partially reversed by the application of exogenous osmolytes, expression at low temperature, and the introduction of second site suppressor mutations. However, the specific steps of folding and assembly of full-length cystic fibrosis transmembrane conductance regulator (CFTR) directly altered by the disease-causing mutation are unclear. To elucidate the effects of the DeltaF508 mutation, on various steps in CFTR folding, a series of misfolding and suppressor mutations in the nucleotide binding and transmembrane domains were evaluated for effects on the folding and maturation of the protein. The results indicate that the isolated NBD1 responds to both the DeltaF508 mutation and intradomain suppressors of this mutation. In addition, identification of a novel second site suppressor of the defect within the second transmembrane domain suggests that DeltaF508 also effects interdomain interactions critical for later steps in the biosynthesis of CFTR.

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254 Consistent with this, structures of NBD1 F508S and F508R and trafficking of F508S and F508R full-length CFTR demonstrate that the severity of physicochemical alterations at the 508 position correlate with protein trafficking (12, 26). Login to comment

[hide] Correction of both NBD1 energetics and domain inte... Cell. 2012 Jan 20;148(1-2):150-63. Rabeh WM, Bossard F, Xu H, Okiyoneda T, Bagdany M, Mulvihill CM, Du K, di Bernardo S, Liu Y, Konermann L, Roldan A, Lukacs GL
Correction of both NBD1 energetics and domain interface is required to restore DeltaF508 CFTR folding and function.
Cell. 2012 Jan 20;148(1-2):150-63., [PMID:22265408]

Abstract [show]
The folding and misfolding mechanism of multidomain proteins remains poorly understood. Although thermodynamic instability of the first nucleotide-binding domain (NBD1) of DeltaF508 CFTR (cystic fibrosis transmembrane conductance regulator) partly accounts for the mutant channel degradation in the endoplasmic reticulum and is considered as a drug target in cystic fibrosis, the link between NBD1 and CFTR misfolding remains unclear. Here, we show that DeltaF508 destabilizes NBD1 both thermodynamically and kinetically, but correction of either defect alone is insufficient to restore DeltaF508 CFTR biogenesis. Instead, both DeltaF508-NBD1 energetic and the NBD1-MSD2 (membrane-spanning domain 2) interface stabilization are required for wild-type-like folding, processing, and transport function, suggesting a synergistic role of NBD1 energetics and topology in CFTR-coupled domain assembly. Identification of distinct structural deficiencies may explain the limited success of DeltaF508 CFTR corrector molecules and suggests structure-based combination corrector therapies. These results may serve as a framework for understanding the mechanism of interface mutation in multidomain membrane proteins.

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69 These results in concert with the effect of F508E, F508R, F508G, F508S, F508D, and F508N mutations revealed that the CD4T-NBD1 PM density was proportional to the domain stability if the NBD1 Tm was >38 C (Figures 3D and S4D). Login to comment

[hide] F508 CFTR interactome remodelling promotes rescue ... Nature. 2015 Dec 24;528(7583):510-6. doi: 10.1038/nature15729. Epub 2015 Nov 30. Pankow S, Bamberger C, Calzolari D, Martinez-Bartolome S, Lavallee-Adam M, Balch WE, Yates JR 3rd
F508 CFTR interactome remodelling promotes rescue of cystic fibrosis.
Nature. 2015 Dec 24;528(7583):510-6. doi: 10.1038/nature15729. Epub 2015 Nov 30., [PMID:26618866]

Abstract [show]
Deletion of phenylalanine 508 of the cystic fibrosis transmembrane conductance regulator (F508 CFTR) is the major cause of cystic fibrosis, one of the most common inherited childhood diseases. The mutated CFTR anion channel is not fully glycosylated and shows minimal activity in bronchial epithelial cells of patients with cystic fibrosis. Low temperature or inhibition of histone deacetylases can partly rescue F508 CFTR cellular processing defects and function. A favourable change of F508 CFTR protein-protein interactions was proposed as a mechanism of rescue; however, CFTR interactome dynamics during temperature shift and inhibition of histone deacetylases are unknown. Here we report the first comprehensive analysis of the CFTR and F508 CFTR interactome and its dynamics during temperature shift and inhibition of histone deacetylases. By using a novel deep proteomic analysis method, we identify 638 individual high-confidence CFTR interactors and discover a F508 deletion-specific interactome, which is extensively remodelled upon rescue. Detailed analysis of the interactome remodelling identifies key novel interactors, whose loss promote F508 CFTR channel function in primary cystic fibrosis epithelia or which are critical for CFTR biogenesis. Our results demonstrate that global remodelling of F508 CFTR interactions is crucial for rescue, and provide comprehensive insight into the molecular disease mechanisms of cystic fibrosis caused by deletion of F508.

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561 d, CFTR co-IPs confirm CFTR interaction with TRIM21, PTPLAD1 and LGALS3BP in primary lung epithelial cells carrying either the ࢞F508 or the F508S mutation from a patient with CF. Login to comment