ABCMdb

ABCC7 p.Phe508Arg

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Publications

PMID: 15619636 [PubMed] Thibodeau PH et al: "Side chain and backbone contributions of Phe508 to CFTR folding."

No. Sentence Comment

18 genet.sickkids.on.ca/cftr), and F508R, a maturation-deficient mutation5, were determined. 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
63 This rotation is observed in only one of two monomers in the asymmetric unit when the phenylalanine is replaced by the larger arginine side chain in the F508R structure (Fig.2c).In both mutants,like the wild type,the side chain of the residue at position 508 is largely surface-exposed and accessible (Fig.2d). 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
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
85 (c) The 2Fo - Fc map (contoured at 1 σ) calculated from the F508R data at a resolution of 3.1 Å superposed on the final F508R model. 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
178 The structure of F508R was determined using the molecular replacement protocols available in CNS version 1.1 (ref. 48). 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

PMID: 18080175 [PubMed] Mendoza JL et al: "Building an understanding of cystic fibrosis on the foundation of ABC transporter structures."

No. Sentence Comment

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

PMID: 18304008 [PubMed] Riordan JR et al: "CFTR function and prospects for therapy."

No. Sentence Comment

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

PMID: 19944699 [PubMed] Lewis HA et al: "Structure and dynamics of NBD1 from CFTR characterized using crystallography and hydrogen/deuterium exchange mass spectrometry."

No. Sentence Comment

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

PMID: 20667826 [PubMed] Thibodeau PH et al: "The cystic fibrosis-causing mutation deltaF508 affects multiple steps in cystic fibrosis transmembrane conductance regulator biogenesis."

No. Sentence Comment

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

PMID: 22265408 [PubMed] Rabeh WM et al: "Correction of both NBD1 energetics and domain interface is required to restore DeltaF508 CFTR folding and function."

No. Sentence Comment

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

PMID: 18215773 [PubMed] Pissarra LS et al: "Solubilizing mutations used to crystallize one CFTR domain attenuate the trafficking and channel defects caused by the major cystic fibrosis mutation."

No. Sentence Comment

146 However, the effect produced by F494N is not completely unexpected, as structural crosstalk between the side chain of the F508 residue (e.g., F508R) and the Q loop or g-phosphate switch (e.g., residues W496 and M498) has been previously shown to occur (Massiah et al., 1999). Login to comment

PMID: 9401049 [PubMed] Goldman BS et al: "Comparison of the bacterial HelA protein to the F508 region of the cystic fibrosis transmembrane regulator."

No. Sentence Comment

7 Previous studies have established that CFTR F508⌬ or F508R proteins are defective but F508C is functional. Login to comment
43 It has been demonstrated that the CFTR F508⌬ and a site-directed mutant, CFTR F508R, are defective in intracellular transport and processing, and thus folding (4). Login to comment
55 It is particularly intriguing that the HelA F88R and the CFTR F508R mutants are both defective, whereas with other substitutions (e.g., cysteine) function is retained. Login to comment
63 The CFTR mutation F508R (marked with a asterisk) was found to be defective in COS-7 cells (4) and was not associated with a CF patient. Login to comment

PMID: 1699669 [PubMed] Cheng SH et al: "Defective intracellular transport and processing of CFTR is the molecular basis of most cystic fibrosis."

No. Sentence Comment

130 Also included is F508R, in which we changed the residue at 508 rather than deleting it. Login to comment
132 The mutation of phenylalanine 508 to arginine also results in CFTR that does not mature. Login to comment
137 CFTR Mutants Mutant CF Exon CFTR Domain A B C Wild type R334W K464M Al507 AF508 F508R s5491 G551 D N894,900Q K1250M Tthllll Y 7 N 9 Y 10 Y 10 N 10 Y 11 Y 11 N 15 N 20 N 22 TM6 NBDl NBDl NBDl NBDl NBDl NBDl ECD4 NBD2 Term - + ++ - + ++ - + - - + - - + - - + - - + - - + ++ + - - - + ++ - + - The known association with CF (Y, yes; N, no), exon localization, domain location, and presence (+ ) or absence (- ) of bands A, B, and C of mutant CFTR species is shown. Login to comment
169 All the mutations around 508 studied here (AF508, Al507, F508R) fail to generate mature CFTR, whereas of mutations at the second site, S549l does not produce mature CFTR but G551D does. Login to comment

PMID: 16678395 [PubMed] Munthe-Kaas MC et al: "CFTR gene mutations and asthma in the Norwegian Environment and Childhood Asthma study."

No. Sentence Comment

46 PCR and fragment analysis for the 394delTT and delF508 were performed in a multiplex reaction with the following primers: 394F (forward) 50 -FAM-GCAGAGAATGGGATAGA- GAGC-, 394R (reverse) 50 -ATTCACCAGATTTCGTA- GTC- and F508F (forward) 50 -HEX-GCCTGGCACCAT- TAAAGAA-and F508R (reverse) 50 -AGTTGGCATGC- TTTGATGAC-. Login to comment

PMID: 22265409 [PubMed] Mendoza JL et al: "Requirements for efficient correction of DeltaF508 CFTR revealed by analyses of evolved sequences."

No. Sentence Comment

187 See also Table S2. (C) F508K, F508R, and F508K in combination with I539T, G550E, R553M, R555K, and 3M mutations increase folding yield of NBD1, but exhibit no corresponding increase in CFTR maturation yield (dark blue circles and line, m = 0.03, R = 0.40) (&#b1;SEM, n = 9 along x axis and n = 3 along y axis). Login to comment