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Jin Y, Molt RW, Pellegrini E, Cliff MJ, Bowler MW, Richards NGJ, Blackburn GM, Waltho JP. Assessing the Influence of Mutation on GTPase Transition States by Using X-ray Crystallography, 19 F NMR, and DFT Approaches. Angew Chem Int Ed Engl 2017; 56:9732-9735. [PMID: 28498638 PMCID: PMC5575484 DOI: 10.1002/anie.201703074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Indexed: 11/08/2022]
Abstract
We report X-ray crystallographic and 19 F NMR studies of the G-protein RhoA complexed with MgF3- , GDP, and RhoGAP, which has the mutation Arg85'Ala. When combined with DFT calculations, these data permit the identification of changes in transition state (TS) properties. The X-ray data show how Tyr34 maintains solvent exclusion and the core H-bond network in the active site by relocating to replace the missing Arg85' sidechain. The 19 F NMR data show deshielding effects that indicate the main function of Arg85' is electronic polarization of the transferring phosphoryl group, primarily mediated by H-bonding to O3G and thence to PG . DFT calculations identify electron-density redistribution and pinpoint why the TS for guanosine 5'-triphosphate (GTP) hydrolysis is higher in energy when RhoA is complexed with RhoGAPArg85'Ala relative to wild-type (WT) RhoGAP. This study demonstrates that 19 F NMR measurements, in combination with X-ray crystallography and DFT calculations, can reliably dissect the response of small GTPases to site-specific modifications.
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Affiliation(s)
- Yi Jin
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK.,School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Robert W Molt
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,ENSCO, Inc., Melbourne, FL, 32940, USA
| | - Erika Pellegrini
- Structural Biology Group, ESRF-The European Synchrotron, CS40220, 38043, Grenoble, Cedex 9, France
| | - Matthew J Cliff
- Manchester Institute of Biotechnology, Manchester, M1 7DN, UK
| | - Matthew W Bowler
- Structural Biology Group, ESRF-The European Synchrotron, CS40220, 38043, Grenoble, Cedex 9, France.,European Molecular Biology Laboratory, Grenoble Outstation CS90181, 38042, Grenoble, Cedex 9, France
| | | | - G Michael Blackburn
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK.,Manchester Institute of Biotechnology, Manchester, M1 7DN, UK
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Jin Y, Molt RW, Pellegrini E, Cliff MJ, Bowler MW, Richards NGJ, Blackburn GM, Waltho JP. Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography,
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F NMR, and DFT Approaches. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yi Jin
- Department of Molecular Biology and BiotechnologyKrebs InstituteUniversity of Sheffield Sheffield S10 2TN UK
- School of ChemistryCardiff University Cardiff CF10 3AT UK
| | - Robert W. Molt
- School of ChemistryCardiff University Cardiff CF10 3AT UK
- Department of Biochemistry and Molecular BiologyIndiana University School of Medicine Indianapolis IN 46202 USA
- ENSCO, Inc. Melbourne FL 32940 USA
| | - Erika Pellegrini
- Structural Biology GroupESRF-The European Synchrotron, CS40220 38043 Grenoble, Cedex 9 France
| | | | - Matthew W. Bowler
- Structural Biology GroupESRF-The European Synchrotron, CS40220 38043 Grenoble, Cedex 9 France
- European Molecular Biology Laboratory, Grenoble Outstation CS90181 38042 Grenoble, Cedex 9 France
| | | | - G. Michael Blackburn
- Department of Molecular Biology and BiotechnologyKrebs InstituteUniversity of Sheffield Sheffield S10 2TN UK
| | - Jonathan P. Waltho
- Department of Molecular Biology and BiotechnologyKrebs InstituteUniversity of Sheffield Sheffield S10 2TN UK
- Manchester Institute of Biotechnology Manchester M1 7DN UK
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Jin Y, Richards NG, Waltho JP, Blackburn GM. Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes. Angew Chem Int Ed Engl 2017; 56:4110-4128. [PMID: 27862756 DOI: 10.1002/anie.201606474] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Indexed: 12/27/2022]
Abstract
The 1994 structure of a transition-state analogue with AlF4- and GDP complexed to G1α, a small G protein, heralded a new field of research into the structure and mechanism of enzymes that manipulate the transfer of phosphoryl (PO3- ) groups. The number of enzyme structures in the PDB containing metal fluorides (MFx ) as ligands that imitate either a phosphoryl or a phosphate group was 357 at the end of 2016. They fall into three distinct geometrical classes: 1) Tetrahedral complexes based on BeF3- that mimic ground-state phosphates; 2) octahedral complexes, primarily based on AlF4- , which mimic "in-line" anionic transition states for phosphoryl transfer; and 3) trigonal bipyramidal complexes, represented by MgF3- and putative AlF30 moieties, which mimic the geometry of the transition state. The interpretation of these structures provides a deeper mechanistic understanding into the behavior and manipulation of phosphate monoesters in molecular biology. This Review provides a comprehensive overview of these structures, their uses, and their computational development.
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Affiliation(s)
- Yi Jin
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | | | | | - G Michael Blackburn
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
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Jin Y, Richards NG, Waltho JP, Blackburn GM. Metallfluoride als Analoga für Studien an Phosphoryltransferenzymen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201606474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yi Jin
- Department of Chemistry; University of York; York YO10 5DD Großbritannien
| | - Nigel G. Richards
- School of Chemistry; Cardiff University; Cardiff CF10 3AT Großbritannien
| | | | - G. Michael Blackburn
- Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN Großbritannien
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Jin Y, Molt RW, Waltho JP, Richards NGJ, Blackburn GM. (19)F NMR and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA-Catalyzed GTP Hydrolysis. Angew Chem Int Ed Engl 2016; 55:3318-22. [PMID: 26822702 PMCID: PMC4770445 DOI: 10.1002/anie.201509477] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/14/2016] [Indexed: 11/13/2022]
Abstract
Molecular details for RhoA/GAP catalysis of the hydrolysis of GTP to GDP are poorly understood. We use (19)F NMR chemical shifts in the MgF3(-) transition state analogue (TSA) complex as a spectroscopic reporter to indicate electron distribution for the γ-PO3(-) oxygens in the corresponding TS, implying that oxygen coordinated to Mg has the greatest electron density. This was validated by QM calculations giving a picture of the electronic properties of the transition state (TS) for nucleophilic attack of water on the γ-PO3(-) group based on the structure of a RhoA/GAP-GDP-MgF3(-) TSA complex. The TS model displays a network of 20 hydrogen bonds, including the GAP Arg85' side chain, but neither phosphate torsional strain nor general base catalysis is evident. The nucleophilic water occupies a reactive location different from that in multiple ground state complexes, arising from reorientation of the Gln-63 carboxamide by Arg85' to preclude direct hydrogen bonding from water to the target γ-PO3(-) group.
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Affiliation(s)
- Yi Jin
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Robert W Molt
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jonathan P Waltho
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK.
- Manchester Institute of Biotechnology, Manchester, M1 7DN, UK.
| | - Nigel G J Richards
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA.
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.
| | - G Michael Blackburn
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK.
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Jin Y, Molt RW, Waltho JP, Richards NGJ, Blackburn GM. 19F NMR and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA-Catalyzed GTP Hydrolysis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509477] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yi Jin
- Krebs Institute, Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN UK
| | - Robert W. Molt
- Department of Chemistry and Chemical Biology; Indiana University Purdue University Indianapolis; Indianapolis IN 46202 USA
| | - Jonathan P. Waltho
- Krebs Institute, Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN UK
- Manchester Institute of Biotechnology; Manchester M1 7DN UK
| | - Nigel G. J. Richards
- Department of Chemistry and Chemical Biology; Indiana University Purdue University Indianapolis; Indianapolis IN 46202 USA
- School of Chemistry; Cardiff University; Cardiff CF10 3AT UK
| | - G. Michael Blackburn
- Krebs Institute, Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN UK
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