Literature DB >> 15178760

Kinetic isotope effects in Ras-catalyzed GTP hydrolysis: evidence for a loose transition state.

Xinlin Du1, Gavin E Black, Paolo Lecchi, Fred P Abramson, Stephen R Sprang.   

Abstract

A remote labeling method has been developed to determine (18)O kinetic isotope effects (KIEs) in Ras-catalyzed GTP hydrolysis. Substrate mixtures consist of (13)C-depleted GTP and [(18)O,(13)C]GTP that contains (18)O at phosphoryl positions of mechanistic interest and (13)C at all carbon positions of the guanosine moiety. Isotope ratios of the nonvolatile substrates and products are measured by using a chemical reaction interface/isotope ratio mass spectrometer. The isotope effects are 1.0012 (0.0026) in the gamma nonbridge oxygens, 1.0194 (0.0025) in the leaving group oxygens (the beta-gamma oxygen and the two beta nonbridge oxygens), and 1.0105 (0.0016) in the two beta nonbridge oxygens. The KIE in the beta-gamma bridge oxygen was computed to be 1.0116 or 1.0088 by two different methods. The significant KIE in the leaving group reveals that chemistry is largely rate-limiting whereas the KIEs in the gamma nonbridge oxygens and the leaving group indicate a loose transition state that approaches a metaphosphate. The KIE in the two beta nonbridge oxygens is roughly equal to that in the beta-gamma bridge oxygen. This indicates that, in the transition state, Ras shifts one-half of the negative charge that arises from P(gamma)-O(beta-gamma) fission from the beta-gamma bridge oxygen to the two beta nonbridge oxygens. The KIE effects, interpreted in light of structural and spectroscopic data, suggest that Ras promotes a loose transition state by stabilizing negative charge in the beta-gamma bridge and beta nonbridge oxygens of GTP.

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Year:  2004        PMID: 15178760      PMCID: PMC428437          DOI: 10.1073/pnas.0401675101

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  43 in total

Review 1.  Isotope effects in the study of enzymatic phosphoryl transfer reactions.

Authors:  A C Hengge
Journal:  FEBS Lett       Date:  2001-07-20       Impact factor: 4.124

2.  Application of high-performance liquid chromatography with isotope-ratio mass spectrometry for measuring low levels of enrichment of underivatized materials.

Authors:  F P Abramson; G E Black; P Lecchi
Journal:  J Chromatogr A       Date:  2001-04-13       Impact factor: 4.759

3.  How does GAP catalyze the GTPase reaction of Ras? A computer simulation study.

Authors:  T M Glennon; J Villà; A Warshel
Journal:  Biochemistry       Date:  2000-08-15       Impact factor: 3.162

4.  Effects on general acid catalysis from mutations of the invariant tryptophan and arginine residues in the protein tyrosine phosphatase from Yersinia.

Authors:  R H Hoff; A C Hengge; L Wu; Y F Keng; Z Y Zhang
Journal:  Biochemistry       Date:  2000-01-11       Impact factor: 3.162

Review 5.  Understanding Ras: 'it ain't over 'til it's over'.

Authors:  J M Shields; K Pruitt; A McFall; A Shaub; C J Der
Journal:  Trends Cell Biol       Date:  2000-04       Impact factor: 20.808

6.  Nature of the transition state of the protein-tyrosine phosphatase-catalyzed reaction.

Authors:  A C Hengge; G A Sowa; L Wu; Z Y Zhang
Journal:  Biochemistry       Date:  1995-10-31       Impact factor: 3.162

Review 7.  Mechanisms of phosphoryl and acyl transfer.

Authors:  W W Cleland; A C Hengge
Journal:  FASEB J       Date:  1995-12       Impact factor: 5.191

8.  Ras catalyzes GTP hydrolysis by shifting negative charges from gamma- to beta-phosphate as revealed by time-resolved FTIR difference spectroscopy.

Authors:  C Allin; K Gerwert
Journal:  Biochemistry       Date:  2001-03-13       Impact factor: 3.162

9.  The mechanism of GTP hydrolysis by Ras probed by Fourier transform infrared spectroscopy.

Authors:  X Du; H Frei; S H Kim
Journal:  J Biol Chem       Date:  2000-03-24       Impact factor: 5.157

10.  Raman difference studies of GDP and GTP binding to c-Harvey ras.

Authors:  J H Wang; D G Xiao; H Deng; M R Webb; R Callender
Journal:  Biochemistry       Date:  1998-08-04       Impact factor: 3.162

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  15 in total

Review 1.  Biological phosphoryl-transfer reactions: understanding mechanism and catalysis.

Authors:  Jonathan K Lassila; Jesse G Zalatan; Daniel Herschlag
Journal:  Annu Rev Biochem       Date:  2011       Impact factor: 23.643

2.  Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis.

Authors:  Jesse G Zalatan; Daniel Herschlag
Journal:  J Am Chem Soc       Date:  2006-02-01       Impact factor: 15.419

3.  Allosteric modulation of Ras-GTP is linked to signal transduction through RAF kinase.

Authors:  Greg Buhrman; V S Senthil Kumar; Murat Cirit; Jason M Haugh; Carla Mattos
Journal:  J Biol Chem       Date:  2010-11-22       Impact factor: 5.157

4.  Mechanistic evidence for a front-side, SNi-type reaction in a retaining glycosyltransferase.

Authors:  Seung Seo Lee; Sung You Hong; James C Errey; Atsushi Izumi; Gideon J Davies; Benjamin G Davis
Journal:  Nat Chem Biol       Date:  2011-08-07       Impact factor: 15.040

5.  Neutron Crystal Structure of RAS GTPase Puts in Question the Protonation State of the GTP γ-Phosphate.

Authors:  Ryan Knihtila; Genevieve Holzapfel; Kevin Weiss; Flora Meilleur; Carla Mattos
Journal:  J Biol Chem       Date:  2015-10-29       Impact factor: 5.157

6.  Proton shuttles and phosphatase activity in soluble epoxide hydrolase.

Authors:  Marco De Vivo; Bernd Ensing; Matteo Dal Peraro; German A Gomez; David W Christianson; Michael L Klein
Journal:  J Am Chem Soc       Date:  2007-01-17       Impact factor: 15.419

7.  Transition states of uncatalyzed hydrolysis and aminolysis reactions of a ribosomal P-site substrate determined by kinetic isotope effects.

Authors:  David A Hiller; Minghong Zhong; Vipender Singh; Scott A Strobel
Journal:  Biochemistry       Date:  2010-05-11       Impact factor: 3.162

8.  A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.

Authors:  Lihua Wang; Xinyun Yu; Po Hu; Suse Broyde; Yingkai Zhang
Journal:  J Am Chem Soc       Date:  2007-03-22       Impact factor: 15.419

Review 9.  Why nature really chose phosphate.

Authors:  Shina C L Kamerlin; Pankaz K Sharma; Ram B Prasad; Arieh Warshel
Journal:  Q Rev Biophys       Date:  2013-01-15       Impact factor: 5.318

10.  Transition state structures and the roles of catalytic residues in GAP-facilitated GTPase of Ras as elucidated by (18)O kinetic isotope effects.

Authors:  Xinlin Du; Stephen R Sprang
Journal:  Biochemistry       Date:  2009-06-02       Impact factor: 3.162

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