Mutation prediction by PolyPhen or functional assay, a detailed comparison of CYP27B1 missense mutations
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- 作者：Minjing Zou (1)
Essa Y. Baitei (1)
Ali S. Alzahrani (2)
Ranjit S. Parhar (3)
Futwan A. Al-Mohanna (3)
Brian F. Meyer (1)
Yufei Shi (1) - 关键词：CYP27B1 mutation ; 1α ; hydroxylase ; Vitamin D ; Rickets ; P450c1α
- 刊名：Endocrine
- 出版年：2011
- 出版时间：August 2011
- 年：2011
- 卷：40
- 期：1
- 页码：14-20
- 全文大小：470KB
- 参考文献：1. M.F. Holick, N. Engl. J. Med. 357(3), 266 (2007) CrossRef
2. W.L. Miller, A.A. Portale, Best Pract. Res. Clin. Endocrinol. Metab. 15(1), 95 (2001) CrossRef
3. R.P. Gupta, Y.A. He, K.S. Patrick, J.R. Halpert, N.H. Bell, J. Clin. Endocrinol. Metab. 90(2), 1210 (2005) CrossRef
4. J.B. Cheng, M.A. Levine, N.H. Bell, D.J. Mangelsdorf, D.W. Russell, Proc. Natl. Acad. Sci. USA 101(20), 7711 (2004) CrossRef
5. W.L. Miller, Endocrinology 146(6), 2544 (2005). doi:10.1210/en.2005-0096 CrossRef
6. W.L. Miller, A.A. Portale, Endocr. Dev. 6, 156 (2003) CrossRef
7. G.K. Fu, D. Lin, M.Y. Zhang, D.D. Bikle, C.H. Shackleton, W.L. Miller, A.A. Portale, Mol. Endocrinol. 11(13), 1961 (1997) CrossRef
8. M. Labuda, K. Morgan, F.H. Glorieux, Am. J. Hum. Genet. 47(1), 28 (1990)
9. R. St-Arnaud, S. Messerlian, J.M. Moir, J.L. Omdahl, F.H. Glorieux, J. Bone Miner. Res. 12(10), 1552 (1997) CrossRef
10. T. Monkawa, T. Yoshida, S. Wakino, T. Shinki, H. Anazawa, H.F. Deluca, T. Suda, M. Hayashi, T. Saruta, Biochem. Biophys. Res. Commun. 239(2), 527 (1997) CrossRef
11. G.K. Fu, A.A. Portale, W.L. Miller, DNA Cell Biol. 16(12), 1499 (1997) CrossRef
12. S. Kitanaka, K. Takeyama, A. Murayama, T. Sato, K. Okumura, M. Nogami, Y. Hasegawa, H. Niimi, J. Yanagisawa, T. Tanaka, S. Kato, N. Engl. J. Med. 338(10), 653 (1998) CrossRef
13. A.S. Alzahrani, M. Zou, E.Y. Baitei, O.M. Alshaikh, R.A. Al-Rijjal, B.F. Meyer, Y. Shi, A novel G102E mutation of CYP27B1 in a large family with vitamin D-dependent rickets type 1. J. Clin. Endocrinol. Metab. 95(9), 4176
14. A. Aiyar, Y. Xiang, J. Leis, Methods Mol. Biol. 57, 177 (1996)
15. Y. Shi, M. Zou, K. Collison, E.Y. Baitei, Z. Al-Makhalafi, N.R. Farid, F.A. Al-Mohanna, J. Clin. Endocrinol. Metab. 91(6), 2373 (2006) CrossRef
16. S. Kitanaka, A. Murayama, T. Sakaki, K. Inouye, Y. Seino, S. Fukumoto, M. Shima, S. Yukizane, M. Takayanagi, H. Niimi, K. Takeyama, S. Kato, J. Clin. Endocrinol. Metab. 84(11), 4111 (1999) CrossRef
17. V. Ramensky, P. Bork, S. Sunyaev, Nucleic Acids Res. 30(17), 3894 (2002) CrossRef
18. S. Sunyaev, V. Ramensky, P. Bork, Trends Genet. 16(5), 198 (2000) CrossRef
19. I.A. Adzhubei, S. Schmidt, L. Peshkin, V.E. Ramensky, A. Gerasimova, P. Bork, A.S. Kondrashov, S.R. Sunyaev, Nat. Methods 7(4), 248 (2010) CrossRef
20. K.Bryson, L.J. McGuffin, R.L. Marsden, J.J. Ward, J.S. Sodhi, D.T. Jones, Protein structure prediction servers at University College London. Nucleic Acids Res. 33(Web Server issue), W36 (2005)
21. D.T. Jones, J. Mol. Biol. 292(2), 195 (1999) CrossRef
22. W.L. Miller, A.A. Portale, Endocrinol. Metab. Clin. North Am. 28(4), 825 (1999) CrossRef
23. T. Shinki, H. Shimada, S. Wakino, H. Anazawa, M. Hayashi, T. Saruta, H.F. DeLuca, T. Suda, Proc. Natl. Acad. Sci. USA 94(24), 12920 (1997) CrossRef
24. K. Takeyama, S. Kitanaka, T. Sato, M. Kobori, J. Yanagisawa, S. Kato, Science 277(5333), 1827 (1997) CrossRef
25. C.J. Kim, L.E. Kaplan, F. Perwad, N. Huang, A. Sharma, Y. Choi, W.L. Miller, A.A. Portale, J. Clin. Endocrinol. Metab. 92(8), 3177 (2007) CrossRef
26. K. Yamamoto, E. Uchida, N. Urushino, T. Sakaki, N. Kagawa, N. Sawada, M. Kamakura, S. Kato, K. Inouye, S. Yamada, J. Biol. Chem. 280(34), 30511 (2005) CrossRef
27. J.T. Wang, C.J. Lin, S.M. Burridge, G.K. Fu, M. Labuda, A.A. Portale, W.L. Miller, Am. J. Hum. Genet. 63(6), 1694 (1998) CrossRef
28. N. Sawada, T. Sakaki, S. Kitanaka, S. Kato, K. Inouye, Eur. J. Biochem. 268(24), 6607 (2001) CrossRef
29. C.A. Hasemann, R.G. Kurumbail, S.S. Boddupalli, J.A. Peterson, J. Deisenhofer, Structure 3(1), 41 (1995) CrossRef
30. D.E. Prosser, G. Jones, Trends Biochem. Sci. 29(12), 664 (2004) CrossRef
31. K. Yamamoto, H. Masuno, N. Sawada, T. Sakaki, K. Inouye, M. Ishiguro, S. Yamada, J. Steroid Biochem. Mol. Biol. 89-0(1-), 167 (2004) CrossRef
32. O. Gotoh, J. Biol. Chem. 267(1), 83 (1992)
33. X. Wang, M.Y. Zhang, W.L. Miller, A.A. Portale, J. Clin. Endocrinol. Metab. 87(6), 2424 (2002) CrossRef
34. S.J. Smith, A.K. Rucka, J.L. Berry, M. Davies, S. Mylchreest, C.R. Paterson, D.A. Heath, M. Tassabehji, A.P. Read, A.P. Mee, E.B. Mawer, J. Bone Miner. Res. 14(5), 730 (1999) CrossRef
35. C. Hackel, L.E. Oliveira, L.F. Ferraz, M.M. Tonini, D.N. Silva, M.B. Toralles, E.G. Stuchi-Perez, G. Guerra-Junior, J. Mol. Med. 83(7), 569 (2005) CrossRef
36. F. Vilchis, J.P. Mendez, P. Canto, E. Lieberman, B. Chavez, Clin. Endocrinol. (Oxf) 52(3), 383 (2000) CrossRef
37. P.H. Dixon, P.T. Christie, C. Wooding, D. Trump, M. Grieff, I. Holm, J.M. Gertner, J. Schmidtke, B. Shah, N. Shaw, C. Smith, C. Tau, D. Schlessinger, M.P. Whyte, R.V. Thakker, J. Clin. Endocrinol. Metab. 83(10), 3615 (1998) CrossRef
38. G.N. Gallus, M.T. Dotti, A. Federico, Neurol. Sci. 27(2), 143 (2006) CrossRef - 作者单位：Minjing Zou (1)
Essa Y. Baitei (1)
Ali S. Alzahrani (2)
Ranjit S. Parhar (3)
Futwan A. Al-Mohanna (3)
Brian F. Meyer (1)
Yufei Shi (1)
1. Department of Genetics (MBC-03), King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
2. Department of Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
3. Department of Biological and Medical Research, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
文摘
Vitamin D-dependent rickets type 1 (VDDR-I) is caused by mutation in CYP27B1. The glycine residue at codon 102 is not conserved between human (G102) and rodent (S102). G102E mutation results in 80% reduction in its enzymatic activity but PolyPhen predicts benign change. It is not known whether G102S has any damaging effect on 1α-hydroxylase activity. We investigated the effect of CYP27B1 G102S on its enzymatic activity and compared mutation prediction accuracy for all known CYP27B1 mutations among three free online protein prediction programs: PolyPhen, PolyPhen-2, and PSIPRED. G102S has no damaging effect on 1α-hydroxylase activity. G102D retained 30% enzymatic activity. All three programs correctly predicted damaging change for G102D. PolyPhen predicted benign change for G102S, whereas PolyPhen-2 and PSIPRED indicated possible damaging effect. Among 24 reported damaging mutations, PSIPRED, PolyPhen-2, and PolyPhen achieved 100%, 91.7% (22/24), and 75% (18/24) accuracy rate, respectively. The residues of incorrectly predicted mutations were not conserved. We conclude that G102D resulted in a significant reduction in 1α-hydroxylase activity, whereas G102S did not. PSIPRED and PolyPhen-2 are superior to PolyPhen in predicting damaging mutations.