A Serendipitous Discovery That in Situ Proteolysis is Essential for the Crystallization of Yeast CPSF-100 (Ydh1p)

Overview

Journal Acta Crystallogr Sect F Struct Biol Cryst Commun

Date 2006 Oct 3

PMID 17012808

Citations 15

Authors

Corey R Mandel

Damara Gebauer

Hailong Zhang

Liang Tong

Affiliations

Soon will be listed here.

Abstract

The cleavage and polyadenylation specificity factor (CPSF) complex is required for the cleavage and polyadenylation of the 3'-end of messenger RNA precursors in eukaryotes. During structural studies of the 100 kDa subunit (CPSF-100, Ydh1p) of the yeast CPSF complex, it was serendipitously discovered that a solution that is infected by a fungus (subsequently identified as Penicillium) is crucial for the crystallization of this protein. Further analyses suggest that the protein has undergone partial proteolysis during crystallization, resulting in the deletion of an internal segment of about 200 highly charged and hydrophilic residues, very likely catalyzed by a protease secreted by the fungus. With the removal of this segment, yeast CPSF-100 (Ydh1p) has greatly reduced solubility and can be crystallized in the presence of a minute amount of precipitant.

Citing Articles

Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin.

Thore S, Raoelijaona F, Talenton V, Fribourg S, Mackereth C Open Biol. 2023; 13(11):230221.

PMID: 37989222 PMC: 10688271. DOI: 10.1098/rsob.230221.

Molecular mechanism for the interaction between human CPSF30 and hFip1.

Hamilton K, Tong L Genes Dev. 2020; 34(23-24):1753-1761.

PMID: 33122294 PMC: 7706699. DOI: 10.1101/gad.343814.120.

Recent molecular insights into canonical pre-mRNA 3'-end processing.

Sun Y, Hamilton K, Tong L Transcription. 2020; 11(2):83-96.

PMID: 32522085 PMC: 7549739. DOI: 10.1080/21541264.2020.1777047.

In Situ Proteolysis Condition-Induced Crystallization of the XcpVWX Complex in Different Lattices.

Zhang Y, Wang S, Jia Z Int J Mol Sci. 2020; 21(1).

PMID: 31906428 PMC: 6981927. DOI: 10.3390/ijms21010308.

Structural Insights into the Human Pre-mRNA 3'-End Processing Machinery.

Zhang Y, Sun Y, Shi Y, Walz T, Tong L Mol Cell. 2019; 77(4):800-809.e6.

PMID: 31810758 PMC: 7036032. DOI: 10.1016/j.molcel.2019.11.005.

References

Zhao J, Hyman L, Moore C . Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev. 1999; 63(2):405-45. PMC: 98971. DOI: 10.1128/MMBR.63.2.405-445.1999. View

Dauter Z, Li M, Wlodawer A . Practical experience with the use of halides for phasing macromolecular structures: a powerful tool for structural genomics. Acta Crystallogr D Biol Crystallogr. 2001; 57(Pt 2):239-49. DOI: 10.1107/s0907444900015249. View

Nolen B, Yun C, Wong C, McCammon J, Fu X, Ghosh G . The structure of Sky1p reveals a novel mechanism for constitutive activity. Nat Struct Biol. 2001; 8(2):176-83. DOI: 10.1038/84178. View

Jogl G, Tao X, Xu Y, Tong L . COMO: a program for combined molecular replacement. Acta Crystallogr D Biol Crystallogr. 2001; 57(Pt 8):1127-34. DOI: 10.1107/s0907444901006783. View

Daiyasu H, Osaka K, Ishino Y, Toh H . Expansion of the zinc metallo-hydrolase family of the beta-lactamase fold. FEBS Lett. 2001; 503(1):1-6. DOI: 10.1016/s0014-5793(01)02686-2. View

Callebaut I, Moshous D, Mornon J, de Villartay J . Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family. Nucleic Acids Res. 2002; 30(16):3592-601. PMC: 134238. DOI: 10.1093/nar/gkf470. View

Mazza C, Segref A, Mattaj I, Cusack S . Co-crystallization of the human nuclear cap-binding complex with a m7GpppG cap analogue using protein engineering. Acta Crystallogr D Biol Crystallogr. 2002; 58(Pt 12):2194-7. DOI: 10.1107/s0907444902015445. View

Calvo O, Manley J . Strange bedfellows: polyadenylation factors at the promoter. Genes Dev. 2003; 17(11):1321-7. DOI: 10.1101/gad.1093603. View

Hamuro Y, Coales S, Southern M, Nemeth-Cawley J, Stranz D, Griffin P . Rapid analysis of protein structure and dynamics by hydrogen/deuterium exchange mass spectrometry. J Biomol Tech. 2003; 14(3):171-82. PMC: 2279949. View

10.

Tong L, Choi H, Minor W, Rossmann M . The structure determination of Sindbis virus core protein using isomorphous replacement and molecular replacement averaging between two crystal forms. Acta Crystallogr A. 1992; 48 ( Pt 4):430-42. DOI: 10.1107/s0108767391014630. View

11.

Terwilliger T . SOLVE and RESOLVE: automated structure solution and density modification. Methods Enzymol. 2003; 374:22-37. DOI: 10.1016/S0076-6879(03)74002-6. View

12.

Nagem R, Polikarpov I, Dauter Z . Phasing on rapidly soaked ions. Methods Enzymol. 2003; 374:120-37. DOI: 10.1016/S0076-6879(03)74005-1. View

13.

Ryan K, Calvo O, Manley J . Evidence that polyadenylation factor CPSF-73 is the mRNA 3' processing endonuclease. RNA. 2004; 10(4):565-73. PMC: 1370546. DOI: 10.1261/rna.5214404. View

14.

Gaur R, Kupper M, Fischer R, Hoffmann K . Preliminary X-ray analysis of a human V(H) fragment at 1.8 A resolution. Acta Crystallogr D Biol Crystallogr. 2004; 60(Pt 5):965-7. DOI: 10.1107/S0907444904004834. View

15.

Zorio D, Bentley D . The link between mRNA processing and transcription: communication works both ways. Exp Cell Res. 2004; 296(1):91-7. DOI: 10.1016/j.yexcr.2004.03.019. View

16.

Proudfoot N . New perspectives on connecting messenger RNA 3' end formation to transcription. Curr Opin Cell Biol. 2004; 16(3):272-8. DOI: 10.1016/j.ceb.2004.03.007. View

17.

Cudney R, Patel S, Weisgraber K, Newhouse Y, McPherson A . Screening and optimization strategies for macromolecular crystal growth. Acta Crystallogr D Biol Crystallogr. 1994; 50(Pt 4):414-23. DOI: 10.1107/S0907444994002660. View

18.

Taneja B, Patel A, Slesarev A, Mondragon A . Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases. EMBO J. 2006; 25(2):398-408. PMC: 1383508. DOI: 10.1038/sj.emboj.7600922. View

19.

Sickmier E, Frato K, Kielkopf C . Crystallization and preliminary X-ray analysis of a U2AF65 variant in complex with a polypyrimidine-tract analogue by use of protein engineering. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006; 62(Pt 5):457-9. PMC: 2219975. DOI: 10.1107/S1744309106012504. View

20.

Johnson S, Roversi P, Espina M, Deane J, Birket S, Picking W . Expression, limited proteolysis and preliminary crystallographic analysis of IpaD, a component of the Shigella flexneri type III secretion system. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006; 62(Pt 9):865-8. PMC: 1894744. DOI: 10.1107/S1744309106027047. View