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Nam K, Thodika ARA, Tischlik S, Phoeurk C, Nagy TM, Schierholz L, Ådén J, Rogne P, Drescher M, Sauer-Eriksson AE, Wolf-Watz M. Magnesium induced structural reorganization in the active site of adenylate kinase. SCIENCE ADVANCES 2024; 10:eado5504. [PMID: 39121211 PMCID: PMC11313852 DOI: 10.1126/sciadv.ado5504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 07/08/2024] [Indexed: 08/11/2024]
Abstract
Phosphoryl transfer is a fundamental reaction in cellular signaling and metabolism that requires Mg2+ as an essential cofactor. While the primary function of Mg2+ is electrostatic activation of substrates, such as ATP, the full spectrum of catalytic mechanisms exerted by Mg2+ is not known. In this study, we integrate structural biology methods, molecular dynamic (MD) simulations, phylogeny, and enzymology assays to provide molecular insights into Mg2+-dependent structural reorganization in the active site of the metabolic enzyme adenylate kinase. Our results demonstrate that Mg2+ induces a conformational rearrangement of the substrates (ATP and ADP), resulting in a 30° adjustment of the angle essential for reversible phosphoryl transfer, thereby optimizing it for catalysis. MD simulations revealed transitions between conformational substates that link the fluctuation of the angle to large-scale enzyme dynamics. The findings contribute detailed insight into Mg2+ activation of enzymes and may be relevant for reversible and irreversible phosphoryl transfer reactions.
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Affiliation(s)
- Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX 76019, USA
| | | | - Sonja Tischlik
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Chanrith Phoeurk
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
- Department of Bio-Engineering, Royal University of Phnom Penh, Phnom Penh, Cambodia
| | | | - Léon Schierholz
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Jörgen Ådén
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Per Rogne
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Malte Drescher
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78464 Konstanz, Germany
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2
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Kim J, Moon S, Romo TD, Yang Y, Bae E, Phillips GN. Conformational dynamics of adenylate kinase in crystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:014702. [PMID: 38389978 PMCID: PMC10883716 DOI: 10.1063/4.0000205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/14/2023] [Indexed: 02/24/2024]
Abstract
Adenylate kinase is a ubiquitous enzyme in living systems and undergoes dramatic conformational changes during its catalytic cycle. For these reasons, it is widely studied by genetic, biochemical, and biophysical methods, both experimental and theoretical. We have determined the basic crystal structures of three differently liganded states of adenylate kinase from Methanotorrus igneus, a hyperthermophilic organism whose adenylate kinase is a homotrimeric oligomer. The multiple copies of each protomer in the asymmetric unit of the crystal provide a unique opportunity to study the variation in the structure and were further analyzed using advanced crystallographic refinement methods and analysis tools to reveal conformational heterogeneity and, thus, implied dynamic behaviors in the catalytic cycle.
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Affiliation(s)
- Junhyung Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Sojin Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Tod D Romo
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Yifei Yang
- Departments of BioSciences, Rice University, Houston, Texas 77005, USA
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Gault S, Jaworek MW, Winter R, Cockell CS. Perchlorate salts confer psychrophilic characteristics in α-chymotrypsin. Sci Rep 2021; 11:16523. [PMID: 34400699 PMCID: PMC8367967 DOI: 10.1038/s41598-021-95997-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
Studies of salt effects on enzyme activity have typically been conducted at standard temperatures and pressures, thus missing effects which only become apparent under non-standard conditions. Here we show that perchlorate salts, which are found pervasively on Mars, increase the activity of α-chymotrypsin at low temperatures. The low temperature activation is facilitated by a reduced enthalpy of activation owing to the destabilising effects of perchlorate salts. By destabilising α-chymotrypsin, the perchlorate salts also cause an increasingly negative entropy of activation, which drives the reduction of enzyme activity at higher temperatures. We have also shown that α-chymotrypsin activity appears to exhibit an altered pressure response at low temperatures while also maintaining stability at high pressures and sub-zero temperatures. As the effects of perchlorate salts on the thermodynamics of α-chymotrypsin's activity closely resemble those of psychrophilic adaptations, it suggests that the presence of chaotropic molecules may be beneficial to life operating in low temperature environments.
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Affiliation(s)
- Stewart Gault
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Michel W Jaworek
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227, Dortmund, Germany
| | - Charles S Cockell
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
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Miller MD, Phillips GN. Moving beyond static snapshots: Protein dynamics and the Protein Data Bank. J Biol Chem 2021; 296:100749. [PMID: 33961840 PMCID: PMC8164045 DOI: 10.1016/j.jbc.2021.100749] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 01/02/2023] Open
Abstract
Proteins are the molecular machines of living systems. Their dynamics are an intrinsic part of their evolutionary selection in carrying out their biological functions. Although the dynamics are more difficult to observe than a static, average structure, we are beginning to observe these dynamics and form sound mechanistic connections between structure, dynamics, and function. This progress is highlighted in case studies from myoglobin and adenylate kinase to the ribosome and molecular motors where these molecules are being probed with a multitude of techniques across many timescales. New approaches to time-resolved crystallography are allowing simple “movies” to be taken of proteins in action, and new methods of mapping the variations in cryo-electron microscopy are emerging to reveal a more complete description of life’s machines. The results of these new methods are aided in their dissemination by continual improvements in curation and distribution by the Protein Data Bank and their partners around the world.
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Affiliation(s)
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas, USA; Department of Chemistry, Rice University, Houston, Texas, USA.
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Dong S, Luo S, Huang K, Zhao X, Duan L, Li H. Insights into four helical proteins folding via self-guided Langevin dynamics simulation. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1874558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Shuheng Dong
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Song Luo
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Kaifang Huang
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Xiaoyu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Hao Li
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
- Department of Science and Technology, Shandong Normal University, Jinan, People’s Republic of China
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Rogne P, Dulko-Smith B, Goodman J, Rosselin M, Grundström C, Hedberg C, Nam K, Sauer-Eriksson AE, Wolf-Watz M. Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3. Biochemistry 2020; 59:3570-3581. [PMID: 32822537 DOI: 10.1021/acs.biochem.0c00549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
ATP and GTP are exceptionally important molecules in biology with multiple, and often discrete, functions. Therefore, enzymes that bind to either of them must develop robust mechanisms to selectively utilize one or the other. Here, this specific problem is addressed by molecular studies of the human NMP kinase AK3, which uses GTP to phosphorylate AMP. AK3 plays an important role in the citric acid cycle, where it is responsible for GTP/GDP recycling. By combining a structural biology approach with functional experiments, we present a comprehensive structural and mechanistic understanding of the enzyme. We discovered that AK3 functions by recruitment of GTP to the active site, while ATP is rejected and nonproductively bound to the AMP binding site. Consequently, ATP acts as an inhibitor with respect to GTP and AMP. The overall features with specific recognition of the correct substrate and nonproductive binding by the incorrect substrate bear a strong similarity to previous findings for the ATP specific NMP kinase adenylate kinase. Taken together, we are now able to provide the fundamental principles for GTP and ATP selectivity in the large NMP kinase family. As a side-result originating from nonlinearity of chemical shifts in GTP and ATP titrations, we find that protein surfaces offer a general and weak binding affinity for both GTP and ATP. These nonspecific interactions likely act to lower the available intracellular GTP and ATP concentrations and may have driven evolution of the Michaelis constants of NMP kinases accordingly.
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Affiliation(s)
- Per Rogne
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Beata Dulko-Smith
- Department of Chemistry and Biochemistry, University of Texas at Alington, Arlington, Texas 76019-0065, United States
| | - Jack Goodman
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Marie Rosselin
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | | | | | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Alington, Arlington, Texas 76019-0065, United States
| | | | - Magnus Wolf-Watz
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
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Saavedra HG, Wrabl JO, Anderson JA, Li J, Hilser VJ. Dynamic allostery can drive cold adaptation in enzymes. Nature 2018; 558:324-328. [PMID: 29875414 PMCID: PMC6033628 DOI: 10.1038/s41586-018-0183-2] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 05/01/2018] [Indexed: 11/19/2022]
Abstract
Adaptation of organisms to environmental niches is a hallmark of evolution. One prevalent example is that of thermal adaptation, wherein two descendants evolve at different temperature extremes1,2. Underlying the physiological differences between such organisms are changes in enzymes catalyzing essential reactions3, with orthologues from each organism undergoing adaptive mutations that preserve similar catalytic rates at their respective physiological temperatures 4,5. The sequence changes responsible for these adaptive differences, however, are often at surface exposed sites distant from the substrate binding site, leaving the active site of the enzyme structurally unperturbed6,7. How such changes are allosterically propagated to the active site, to modulate activity, is not known. Here we show that entropy-tuning changes can be engineered into distal sites of Escherichia coli adenylate kinase (AK) to quantitatively assess the role of dynamics in determining affinity, turnover, and the role in driving adaptation. The results not only reveal a dynamics-based allosteric tuning mechanism, but also uncover a spatial separation of the control of key enzymatic parameters. Fluctuations in one mobile domain (i.e. the LID) control substrate affinity, while dynamic attenuation in the other (i.e. the AMPbd) affects rate-limiting conformational changes governing enzyme turnover. Dynamics-based regulation may thus represent an elegant, widespread, and previously unrealized evolutionary adaptation mechanism that fine-tunes biological function without altering the ground state structure. Furthermore, because rigid-body conformational changes in both domains were thought to be rate limiting for turnover8,9, these adaptation studies reveal a new paradigm for understanding the relationship between dynamics and turnover in AK.
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Affiliation(s)
- Harry G Saavedra
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - James O Wrabl
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Jeremy A Anderson
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Jing Li
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA. .,T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
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Molecular mechanism of ATP versus GTP selectivity of adenylate kinase. Proc Natl Acad Sci U S A 2018; 115:3012-3017. [PMID: 29507216 DOI: 10.1073/pnas.1721508115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Enzymatic substrate selectivity is critical for the precise control of metabolic pathways. In cases where chemically related substrates are present inside cells, robust mechanisms of substrate selectivity are required. Here, we report the mechanism utilized for catalytic ATP versus GTP selectivity during adenylate kinase (Adk) -mediated phosphorylation of AMP. Using NMR spectroscopy we found that while Adk adopts a catalytically competent and closed structural state in complex with ATP, the enzyme is arrested in a catalytically inhibited and open state in complex with GTP. X-ray crystallography experiments revealed that the interaction interfaces supporting ATP and GTP recognition, in part, are mediated by coinciding residues. The mechanism provides an atomic view on how the cellular GTP pool is protected from Adk turnover, which is important because GTP has many specialized cellular functions. In further support of this mechanism, a structure-function analysis enabled by synthesis of ATP analogs suggests that a hydrogen bond between the adenine moiety and the backbone of the enzyme is vital for ATP selectivity. The importance of the hydrogen bond for substrate selectivity is likely general given the conservation of its location and orientation across the family of eukaryotic protein kinases.
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