Structure and Mechanism of the RNA Triphosphatase Component of Mammalian MRNA Capping Enzyme

Overview

Journal EMBO J

Specialties Biotechnology
Molecular Biology

Date 2001 May 15

PMID 11350947

Citations 39

Authors

A Changela

C K Ho

A Martins

S Shuman

A Mondragon

Affiliations

Soon will be listed here.

Abstract

The 5' capping of mammalian pre-mRNAs is initiated by RNA triphosphatase, a member of the cysteine phosphatase superfamily. Here we report the 1.65 A crystal structure of mouse RNA triphosphatase, which reveals a deep, positively charged active site pocket that can fit a 5' triphosphate end. Structural, biochemical and mutational results show that despite sharing an HCxxxxxR(S/T) motif, a phosphoenzyme intermediate and a core alpha/beta-fold with other cysteine phosphatases, the mechanism of phosphoanhydride cleavage by mammalian capping enzyme differs from that used by protein phosphatases to hydrolyze phosphomonoesters. The most significant difference is the absence of a carboxylate general acid catalyst in RNA triphosphatase. Residues conserved uniquely among the RNA phosphatase subfamily are important for function in cap formation and are likely to play a role in substrate recognition.

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References

Martins A, Shuman S . Mechanism of phosphoanhydride cleavage by baculovirus phosphatase. J Biol Chem. 2000; 275(45):35070-6. DOI: 10.1074/jbc.M005748200. View

Takagi T, Taylor G, Kusakabe T, Charbonneau H, Buratowski S . A protein tyrosine phosphatase-like protein from baculovirus has RNA 5'-triphosphatase and diphosphatase activities. Proc Natl Acad Sci U S A. 1998; 95(17):9808-12. PMC: 21418. DOI: 10.1073/pnas.95.17.9808. View

Shuman S . Structure, mechanism, and evolution of the mRNA capping apparatus. Prog Nucleic Acid Res Mol Biol. 2000; 66:1-40. DOI: 10.1016/s0079-6603(00)66025-7. View

Zhang Z, Dixon J . Active site labeling of the Yersinia protein tyrosine phosphatase: the determination of the pKa of the active site cysteine and the function of the conserved histidine 402. Biochemistry. 1993; 32(36):9340-5. DOI: 10.1021/bi00087a012. View

Nicholls A, Sharp K, Honig B . Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 1991; 11(4):281-96. DOI: 10.1002/prot.340110407. View

Van Duyne G, Standaert R, Karplus P, Schreiber S, Clardy J . Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J Mol Biol. 1993; 229(1):105-24. DOI: 10.1006/jmbi.1993.1012. View

Lohse D, Denu J, Santoro N, Dixon J . Roles of aspartic acid-181 and serine-222 in intermediate formation and hydrolysis of the mammalian protein-tyrosine-phosphatase PTP1. Biochemistry. 1997; 36(15):4568-75. DOI: 10.1021/bi963094r. View

Flint A, Tiganis T, Barford D, Tonks N . Development of "substrate-trapping" mutants to identify physiological substrates of protein tyrosine phosphatases. Proc Natl Acad Sci U S A. 1997; 94(5):1680-5. PMC: 19976. DOI: 10.1073/pnas.94.5.1680. View

Becker K, Savvides S, Keese M, Schirmer R, Karplus P . Enzyme inactivation through sulfhydryl oxidation by physiologic NO-carriers. Nat Struct Biol. 1998; 5(4):267-71. DOI: 10.1038/nsb0498-267. View

10.

Nam H, POY F, Krueger N, Saito H, Frederick C . Crystal structure of the tandem phosphatase domains of RPTP LAR. Cell. 1999; 97(4):449-57. DOI: 10.1016/s0092-8674(00)80755-2. View

11.

Ho C, Schwer B, Shuman S . Genetic, physical, and functional interactions between the triphosphatase and guanylyltransferase components of the yeast mRNA capping apparatus. Mol Cell Biol. 1998; 18(9):5189-98. PMC: 109104. DOI: 10.1128/MCB.18.9.5189. View

12.

Barford D, Flint A, Tonks N . Crystal structure of human protein tyrosine phosphatase 1B. Science. 1994; 263(5152):1397-404. View

13.

Gross C, Shuman S . Characterization of a baculovirus-encoded RNA 5'-triphosphatase. J Virol. 1998; 72(9):7057-63. PMC: 109926. DOI: 10.1128/JVI.72.9.7057-7063.1998. View

14.

Evans B, Tishmack P, Pokalsky C, Zhang M, Van Etten R . Site-directed mutagenesis, kinetic, and spectroscopic studies of the P-loop residues in a low molecular weight protein tyrosine phosphatase. Biochemistry. 1996; 35(42):13609-17. DOI: 10.1021/bi9605651. View

15.

Stuckey J, Schubert H, Fauman E, Zhang Z, Dixon J, Saper M . Crystal structure of Yersinia protein tyrosine phosphatase at 2.5 A and the complex with tungstate. Nature. 1994; 370(6490):571-5. DOI: 10.1038/370571a0. View

16.

Brunger A, Adams P, Clore G, DeLano W, Gros P, Grosse-Kunstleve R . Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998; 54(Pt 5):905-21. DOI: 10.1107/s0907444998003254. View

17.

Jones T, Zou J, Cowan S, Kjeldgaard M . Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A. 1991; 47 ( Pt 2):110-9. DOI: 10.1107/s0108767390010224. View

18.

Wen Y, Yue Z, Shatkin A . Mammalian capping enzyme binds RNA and uses protein tyrosine phosphatase mechanism. Proc Natl Acad Sci U S A. 1998; 95(21):12226-31. PMC: 22813. DOI: 10.1073/pnas.95.21.12226. View

19.

Denu J, Dixon J . A catalytic mechanism for the dual-specific phosphatases. Proc Natl Acad Sci U S A. 1995; 92(13):5910-4. PMC: 41611. DOI: 10.1073/pnas.92.13.5910. View

20.

Fauman E, Cogswell J, Lovejoy B, Rocque W, Holmes W, Montana V . Crystal structure of the catalytic domain of the human cell cycle control phosphatase, Cdc25A. Cell. 1998; 93(4):617-25. DOI: 10.1016/s0092-8674(00)81190-3. View