The energy landscape of adenylate kinase during catalysis
Structural, computation and kinetics approaches reveal the energy landscape of catalysis by adenylate kinase and show that the cofactor Mg 2+ activates two distinct molecular events in the reaction cycle: phosphoryl transfer and lid opening. Kinases perform phosphoryl-transfer reactions in milliseco...
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| Published in | Nature structural & molecular biology Vol. 22; no. 2; pp. 124 - 131 |
|---|---|
| Main Authors | , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Nature Publishing Group US
01.02.2015
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Structural, computation and kinetics approaches reveal the energy landscape of catalysis by adenylate kinase and show that the cofactor Mg
2+
activates two distinct molecular events in the reaction cycle: phosphoryl transfer and lid opening.
Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg
2+
cofactor activates two distinct molecular events: phosphoryl transfer (>10
5
-fold) and lid opening (10
3
-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 10
3
-fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site. |
|---|---|
| AbstractList | Structural, computation and kinetics approaches reveal the energy landscape of catalysis by adenylate kinase and show that the cofactor Mg
2+
activates two distinct molecular events in the reaction cycle: phosphoryl transfer and lid opening.
Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg
2+
cofactor activates two distinct molecular events: phosphoryl transfer (>10
5
-fold) and lid opening (10
3
-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 10
3
-fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site. Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. In this paper, we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg2+ cofactor activates two distinct molecular events: phosphoryl transfer (>105-fold) and lid opening (103-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 103-fold without substantially affecting lid opening. Finally, our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site. Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg(2+) cofactor activates two distinct molecular events: phosphoryl transfer (>10(5)-fold) and lid opening (10(3)-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 10(3)-fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site. Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, MD simulations, and crystallography of active complexes. We find that the Mg 2+ cofactor activates two distinct molecular events, phosphoryl transfer (>10 5 -fold) and lid-opening (10 3 -fold). In contrast, mutation of an essential active-site arginine decelerates phosphoryl transfer 10 3 -fold without substantially affecting lid-opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a pre-organized active site. Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the [Mg.sup.2+] cofactor activates two distinct molecular events: phosphoryl transfer (>[10.sup.5]-fold) and lid opening ([10.sup.3]-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer [10.sup.3]-fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site. Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg2+ cofactor activates two distinct molecular events: phosphoryl transfer (>105 -fold) and lid opening (103 -fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 103 -fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site. |
| Audience | Academic |
| Author | Murphy, Padraig N Thai, Vu Kerns, S Jordan Pachov, Dimitar V Alber, Tom Hagan, Michael F Phung, Lien A Kern, Dorothee Kutter, Steffen Otten, Renee Agafonov, Roman V Pontiggia, Francesco Cho, Young-Jin |
| AuthorAffiliation | 3 Department of Physics, Brandeis University, Waltham, MA, USA 1 Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, MA, USA 2 Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, USA |
| AuthorAffiliation_xml | – name: 3 Department of Physics, Brandeis University, Waltham, MA, USA – name: 1 Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, MA, USA – name: 2 Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, USA |
| Author_xml | – sequence: 1 givenname: S Jordan surname: Kerns fullname: Kerns, S Jordan organization: Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Present addresses: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA (S.J.K.), New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Korea (Y.-J.C.) and Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, USA (V.T.) – sequence: 2 givenname: Roman V surname: Agafonov fullname: Agafonov, Roman V organization: Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University – sequence: 3 givenname: Young-Jin surname: Cho fullname: Cho, Young-Jin organization: Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Present addresses: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA (S.J.K.), New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Korea (Y.-J.C.) and Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, USA (V.T.) – sequence: 4 givenname: Francesco surname: Pontiggia fullname: Pontiggia, Francesco organization: Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University – sequence: 5 givenname: Renee surname: Otten fullname: Otten, Renee organization: Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University – sequence: 6 givenname: Dimitar V surname: Pachov fullname: Pachov, Dimitar V organization: Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University – sequence: 7 givenname: Steffen surname: Kutter fullname: Kutter, Steffen organization: Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University – sequence: 8 givenname: Lien A surname: Phung fullname: Phung, Lien A organization: Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University – sequence: 9 givenname: Padraig N surname: Murphy fullname: Murphy, Padraig N organization: Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University – sequence: 10 givenname: Vu surname: Thai fullname: Thai, Vu organization: Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Present addresses: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA (S.J.K.), New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Korea (Y.-J.C.) and Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, USA (V.T.) – sequence: 11 givenname: Tom surname: Alber fullname: Alber, Tom – sequence: 12 givenname: Michael F surname: Hagan fullname: Hagan, Michael F organization: Department of Physics, Brandeis University – sequence: 13 givenname: Dorothee surname: Kern fullname: Kern, Dorothee email: dkern@brandeis.edu organization: Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/25580578$$D View this record in MEDLINE/PubMed https://www.osti.gov/servlets/purl/1182309$$D View this record in Osti.gov |
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| Copyright | Springer Nature America, Inc. 2014 COPYRIGHT 2015 Nature Publishing Group Copyright Nature Publishing Group Feb 2015 |
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| Snippet | Structural, computation and kinetics approaches reveal the energy landscape of catalysis by adenylate kinase and show that the cofactor Mg
2+
activates two... Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions.... Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8000 years under physiological conditions.... |
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| SubjectTerms | 101/6 631/45/173 631/45/275 631/535/1266 631/535/878/1263 82 Adenylate kinase Adenylate Kinase - chemistry Adenylate Kinase - metabolism Binding Sites Biochemistry Biological Microscopy Biology Catalysis Catalytic Domain Crystallography Crystallography, X-Ray Energy Enzyme mechanisms Enzymes INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY Kinases Life Sciences Ligands Magnetic Resonance Spectroscopy Membrane Biology Models, Molecular Phosphate esters Phosphorylation Physiological aspects Protein Structure Proteins Solution-state NMR Structure X-ray crystallography |
| Title | The energy landscape of adenylate kinase during catalysis |
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