Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping

Journal of Molecular Biology

Volumn 347, Issue 4, 2005, Pages 707-718

  Chen, Nan ^a   Walsh, Martin A ^b   Liu, Yuying ^a   Parker, Roy ^c   Song, Haiwei ^a,d  

^a INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

^b EUROPEAN SYNCHROTRON RADIATION FACILITY   (France)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^d NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

mRNA decapping; mRNA decay; Protein structure; Scavenger mRNA decapping; X ray crystallography

Indexed keywords

DCPS ENZYME; DIMER; ENZYME; GUANOSINE DIPHOSPHATE; LIGAND; MESSENGER RNA; TYROSINE; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; CHEMICAL ANALYSIS; COMPARATIVE STUDY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ENZYME BINDING; ENZYME CONFORMATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; MOLECULAR DYNAMICS; MOLECULAR MIMICRY; MRNA DECAPPING; MUTAGENESIS; PRIORITY JOURNAL; PROTEIN DOMAIN; RNA STRUCTURE; STRUCTURE ANALYSIS;

EUKARYOTA;

EID: 14844359631     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.01.062     Document Type: Article

References (36)

1. R. Parker, and H. Song The enzymes and control of eukaryotic mRNA turnover Nature Struct. Mol. Biol. 11 2004 121 127
2. D. Muhlrad, and R. Parker Premature translational termination triggers mRNA decapping Nature 370 1994 578 581
3. D. Cao, and R. Parker Computational modeling and experimental analysis of nonsense-mediated decay in yeast Cell 113 2003 533 545
4. P. Mitchell, and D. Tollervey An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3′-5′ degradation Mol. Cell. 11 2003 1405 1413
5. S. Takahashi, Y. Araki, T. Sakuno, and T. Katada Interaction between Ski7p and Upf1p is required for nonsense-mediated 3′-to-5′ mRNA decay in yeast EMBO J. 22 2003 3951 3959
6. F. Lejeune, X. Li, and L.E. Maquat Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities Mol. Cell. 12 2003 675 687
7. P.A. Frischmeyer, A. van Hoof, K. O'Donnell, A.L. Guerrerio, R. Parker, and H.C. Dietz An mRNA surveillance mechanism that eliminates transcripts lacking termination codons Science 295 2002 2258 2261
8. A. van Hoof, P.A. Frischmeyer, H.C. Dietz, and R. Parker Exosome-mediated recognition and degradation of mRNAs lacking a termination codon Science 295 2002 2262 2264
9. M.J. Bessman, D.N. Frick, and S.F. O'Handley The MutT proteins or "Nudix" hydrolases, a family of versatile, widely distributed, "housecleaning" enzymes J. Biol. Chem. 271 1996 25059 25062
10. Z. Wang, X. Jiao, A. Carr-Schmid, and M. Kiledjian The hDcp2 protein is a mammalian mRNA decapping enzyme Proc. Natl Acad. Sci. USA 99 2002 12663 12668
11. T. Dunckley, and R. Parker The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif EMBO J. 18 1999 5411 5422
12. E. van Dijk, N. Cougot, S. Meyer, S. Babajko, E. Wahle, and B. Seraphin Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures EMBO J. 21 2002 6915 6924
13. C. Piccirillo, R. Khanna, and M. Kiledjian Functional characterization of the mammalian mRNA decapping enzyme hDcp2 RNA 9 2003 1138 1147
14. M. Steiger, A. Carr-Schmid, D.C. Schwartz, M. Kiledjian, and R. Parker Analysis of recombinant yeast decapping enzyme RNA 9 2003 231 238
15. Z. Wang, and M. Kiledjian Functional link between the mammalian exosome and mRNA decapping Cell 107 2001 751 762
16. H. Liu, N.D. Rodgers, X. Jiao, and M. Kiledjian The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases EMBO J. 21 2002 4699 4708
17. B. Seraphin The HIT protein family: a new family of proteins present in prokaryotes, yeast and mammals DNA Seq. 3 1992 177 179
18. C.D. Lima, M.G. Klein, and W.A. Hendrickson Structure-based analysis of catalysis and substrate definition in the HIT protein family Science 278 1997 286 290
19. H.C. Pace, P.N. Garrison, A.K. Robinson, L.D. Barnes, A. Draganescu, and A. Rosler Genetic, biochemical, and crystallographic characterization of Fhit-substrate complexes as the active signaling form of Fhit Proc. Natl Acad. Sci. USA 95 1998 5484 5489
20. C. Brenner, P. Garrison, J. Gilmour, D. Peisach, D. Ringe, G.A. Petsko, and J.M. Lowenstein Crystal structures of HINT demonstrate that histidine triad proteins are GalT-related nucleotide-binding proteins Nature Struct. Biol. 4 1997 231 238
21. E. van Dijk, H. Le Hir, and B. Seraphin DcpS can act in the 5′-3′ mRNA decay pathway in addition to the 3′-5′ pathway Proc. Natl Acad. Sci. USA 100 2003 12081 12086
22. M. Gu, C. Fabrega, S.W. Liu, H. Liu, M. Kiledjian, and C.D. Lima Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity Mol. Cell. 14 2004 67 80
23. J.R. Schnell, H.J. Dyson, and P.E. Wright Structure, dynamics, and catalytic function of dihydrofolate reductase Annu. Rev. Biophys. Biomol. Struct. 33 2004 119 140
24. M. Karplus Aspects of protein reaction dynamics: deviations from simple behavior J. Phys. Chem. B 104 2000 11 27
25. G.G. Hammes Mechanism of enzyme catalysis Nature 204 1964 342 343
26. B. Somogyi, G.R. Welch, and S. Damjanovich The dynamic basis of energy transduction in enzymes Biochim. Biophys. Acta 768 1984 81 112
27. S.W. Liu, X. Jiao, H. Liu, M. Gu, C.D. Lima, and M. Kiledjian Functional analysis of mRNA scavenger decapping enzymes RNA 10 2004 1412 1422
28. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
29. CCP4 (Collaborative Computational Project No.4) The CCP4 suite: programs for protein crystallography Acta Crystallog. sect. D 50 1994 760 763
30. A. Vagin, and A. Teplyakov MOLREP: an automated program for molecular replacement J. Appl. Crystallog. 30 1997 1022 1025
31. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallog. sect. A 47 1991 110 119
32. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, and R.W. Grosse-Kunstleve Crystallography and NMR system: a new software suite for macromolecular structure determination Acta Crystallog. sect. D 54 1998 905 921
33. G.N. Murshudov, A.A. Vagin, and E.J. Dodson Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallog. sect. D 53 1997 240 255
34. A. Perrakis, R. Morris, and V.S. Lamzin Automated protein model building combined with iterative structure refinement Nature Struct. Biol 6 1999 458 463
35. P.J. Kraulis MOLSCRIPT:a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950
36. A. Nicholls, K.A. Sharp, and B. Honig Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons Proteins: Struct. Funct. Genet. 11 1991 281 296