5kfp › Citations

Capture of a third Mg²⁺ is essential for catalyzing DNA synthesis.

Gao Y, Yang W
Science 352 1334-7 (2016)

Cited: 85 times
EuropePMC logo PMID: 27284197

Abstract

It is generally assumed that an enzyme-substrate (ES) complex contains all components necessary for catalysis and that conversion to products occurs by rearrangement of atoms, protons, and electrons. However, we find that DNA synthesis does not occur in a fully assembled DNA polymerase-DNA-deoxynucleoside triphosphate complex with two canonical metal ions bound. Using time-resolved x-ray crystallography, we show that the phosphoryltransfer reaction takes place only after the ES complex captures a third divalent cation that is not coordinated by the enzyme. Binding of the third cation is incompatible with the basal ES complex and requires thermal activation of the ES for entry. It is likely that the third cation provides the ultimate boost over the energy barrier to catalysis of DNA synthesis.

Reviews citing this publication (18)

  1. Translesion and Repair DNA Polymerases: Diverse Structure and Mechanism. Yang W, Gao Y. Annu Rev Biochem 87 239-261 (2018)
  2. Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases. Vashishtha AK, Wang J, Konigsberg WH. J Biol Chem 291 20869-20875 (2016)
  3. A new paradigm of DNA synthesis: three-metal-ion catalysis. Yang W, Weng PJ, Gao Y. Cell Biosci 6 51 (2016)
  4. Magnesium Is a Key Player in Neuronal Maturation and Neuropathology. Yamanaka R, Shindo Y, Oka K. Int J Mol Sci 20 E3439 (2019)
  5. Structure and function relationships in mammalian DNA polymerases. Hoitsma NM, Whitaker AM, Schaich MA, Smith MR, Fairlamb MS, Freudenthal BD. Cell Mol Life Sci 77 35-59 (2020)
  6. Two-Metal-Ion Catalysis: Inhibition of DNA Polymerase Activity by a Third Divalent Metal Ion. Wang J, Konigsberg WH. Front Mol Biosci 9 824794 (2022)
  7. Catalytic mechanism of DNA polymerases-Two metal ions or three? Tsai MD. Protein Sci 28 288-291 (2019)
  8. The Role of 3' to 5' Reverse RNA Polymerization in tRNA Fidelity and Repair. Chen AW, Jayasinghe MI, Chung CZ, Rao BS, Kenana R, Heinemann IU, Jackman JE. Genes (Basel) 10 E250 (2019)
  9. Building better polymerases: Engineering the replication of expanded genetic alphabets. Ouaray Z, Benner SA, Georgiadis MM, Richards NGJ. J Biol Chem 295 17046-17059 (2020)
  10. The Role of Natural Polymorphic Variants of DNA Polymerase β in DNA Repair. Kladova OA, Fedorova OS, Kuznetsov NA. Int J Mol Sci 23 2390 (2022)
  11. Cystoviral RNA-directed RNA polymerases: Regulation of RNA synthesis on multiple time and length scales. Alphonse S, Ghose R. Virus Res 234 135-152 (2017)
  12. Nucleotide addition and cleavage by RNA polymerase II: Coordination of two catalytic reactions using a single active site. Unarta IC, Goonetilleke EC, Wang D, Huang X. J Biol Chem 299 102844 (2023)
  13. Structural and Molecular Kinetic Features of Activities of DNA Polymerases. Kuznetsova AA, Fedorova OS, Kuznetsov NA. Int J Mol Sci 23 6373 (2022)
  14. Determining translocation orientations of nucleic acid helicases. Perera HM, Trakselis MA. Methods 204 160-171 (2022)
  15. For the Better or for the Worse? The Effect of Manganese on the Activity of Eukaryotic DNA Polymerases. Balint E, Unk I. Int J Mol Sci 25 363 (2023)
  16. New insights into DNA polymerase mechanisms provided by time-lapse crystallography. Weaver TM, Washington MT, Freudenthal BD. Curr Opin Struct Biol 77 102465 (2022)
  17. Recent progress in dissecting molecular recognition by DNA polymerases with non-native substrates. Pugliese KM, Weiss GA. Curr Opin Chem Biol 41 43-49 (2017)
  18. The catalytic mechanism, metal dependence, substrate specificity, and biodiversity of ribonuclease H. Pang J, Guo Q, Lu Z. Front Microbiol 13 1034811 (2022)

Articles citing this publication (67)

  1. Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM, Grasby JA, Tainer JA. Nat Commun 8 15855 (2017)
  2. Time-lapse crystallography snapshots of a double-strand break repair polymerase in action. Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH. Nat Commun 8 253 (2017)
  3. Cation trafficking propels RNA hydrolysis. Samara NL, Yang W. Nat Struct Mol Biol 25 715-721 (2018)
  4. Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction. Kottur J, Nair DT. Nucleic Acids Res 46 5875-5885 (2018)
  5. Human DNA polymerase θ harbors DNA end-trimming activity critical for DNA repair. Zahn KE, Jensen RB, Wood RD, Doublié S. Mol Cell 81 1534-1547.e4 (2021)
  6. Revealing the role of the product metal in DNA polymerase β catalysis. Perera L, Freudenthal BD, Beard WA, Pedersen LG, Wilson SH. Nucleic Acids Res 45 2736-2745 (2017)
  7. Modulating the DNA polymerase β reaction equilibrium to dissect the reverse reaction. Shock DD, Freudenthal BD, Beard WA, Wilson SH. Nat Chem Biol 13 1074-1080 (2017)
  8. Crystal structures of ternary complexes of archaeal B-family DNA polymerases. Kropp HM, Betz K, Wirth J, Diederichs K, Marx A. PLoS One 12 e0188005 (2017)
  9. Crystallographic Snapshots of Class A β-Lactamase Catalysis Reveal Structural Changes That Facilitate β-Lactam Hydrolysis. Pan X, He Y, Lei J, Huang X, Zhao Y. J Biol Chem 292 4022-4033 (2017)
  10. Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase. Wu J, Samara NL, Kuraoka I, Yang W. Mol Cell 76 44-56.e3 (2019)
  11. Crystallographic observation of nonenzymatic RNA primer extension. Zhang W, Walton T, Li L, Szostak JW. Elife 7 e36422 (2018)
  12. Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis. Yoon H, Warshel A. Proteins 85 1446-1453 (2017)
  13. Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage. Schiltz CJ, Lee A, Partlow EA, Hosford CJ, Chappie JS. Nucleic Acids Res 47 9448-9463 (2019)
  14. Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase. Jackson LN, Chim N, Shi C, Chaput JC. Nucleic Acids Res 47 6973-6983 (2019)
  15. Detection of Reaction Intermediates in Mg2+-Dependent DNA Synthesis and RNA Degradation by Time-Resolved X-Ray Crystallography. Samara NL, Gao Y, Wu J, Yang W. Methods Enzymol 592 283-327 (2017)
  16. Visualizing Rev1 catalyze protein-template DNA synthesis. Weaver TM, Cortez LM, Khoang TH, Washington MT, Agarwal PK, Freudenthal BD. Proc Natl Acad Sci U S A 117 25494-25504 (2020)
  17. Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. Reed AJ, Vyas R, Raper AT, Suo Z. J Am Chem Soc 139 465-471 (2017)
  18. Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase η at atomic resolution. Weng PJ, Gao Y, Gregory MT, Wang P, Wang Y, Yang W. Proc Natl Acad Sci U S A 115 10660-10665 (2018)
  19. Iron mediates catalysis of nucleic acid processing enzymes: support for Fe(II) as a cofactor before the great oxidation event. Okafor CD, Lanier KA, Petrov AS, Athavale SS, Bowman JC, Hud NV, Williams LD. Nucleic Acids Res 45 3634-3642 (2017)
  20. Calcium-driven DNA synthesis by a high-fidelity DNA polymerase. Ralec C, Henry E, Lemor M, Killelea T, Henneke G. Nucleic Acids Res 45 12425-12440 (2017)
  21. Extensive free-energy simulations identify water as the base in nucleotide addition by DNA polymerase. Roston D, Demapan D, Cui Q. Proc Natl Acad Sci U S A 116 25048-25056 (2019)
  22. A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors. Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z. Cell 185 4347-4360.e17 (2022)
  23. Mg2+ improves the thermotolerance of probiotic Lactobacillus rhamnosus GG, Lactobacillus casei Zhang and Lactobacillus plantarum P-8. Yang Y, Huang S, Wang J, Jan G, Jeantet R, Chen XD. Lett Appl Microbiol 64 283-288 (2017)
  24. Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes. Genna V, Colombo M, De Vivo M, Marcia M. Structure 26 40-50.e2 (2018)
  25. Structural basis for proficient oxidized ribonucleotide insertion in double strand break repair. Jamsen JA, Sassa A, Perera L, Shock DD, Beard WA, Wilson SH. Nat Commun 12 5055 (2021)
  26. Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase. Rechkoblit O, Johnson RE, Gupta YK, Prakash L, Prakash S, Aggarwal AK. Nat Commun 12 4020 (2021)
  27. Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis. Hwang W, Yoo J, Lee Y, Park S, Hoang PL, Cho H, Yu J, Hoa Vo TM, Shin M, Jin MS, Park D, Hyeon C, Lee G. Nat Commun 9 4404 (2018)
  28. Probing DNA Base-Dependent Leaving Group Kinetic Effects on the DNA Polymerase Transition State. Oertell K, Kashemirov BA, Negahbani A, Minard C, Haratipour P, Alnajjar KS, Sweasy JB, Batra VK, Beard WA, Wilson SH, McKenna CE, Goodman MF. Biochemistry 57 3925-3933 (2018)
  29. Determination of chemical identity and occupancy from experimental density maps. Wang J. Protein Sci 27 411-420 (2018)
  30. Following replicative DNA synthesis by time-resolved X-ray crystallography. Chim N, Meza RA, Trinh AM, Yang K, Chaput JC. Nat Commun 12 2641 (2021)
  31. Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase. Rechkoblit O, Kolbanovskiy A, Landes H, Geacintov NE, Aggarwal AK. Nat Commun 8 965 (2017)
  32. Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction. Gregory MT, Gao Y, Cui Q, Yang W. Proc Natl Acad Sci U S A 118 e2103990118 (2021)
  33. Crystallographic evidence for two-metal-ion catalysis in human pol η. Wang J, Smithline ZB. Protein Sci 28 439-447 (2019)
  34. In crystallo observation of three metal ion promoted DNA polymerase misincorporation. Chang C, Lee Luo C, Gao Y. Nat Commun 13 2346 (2022)
  35. Recruiting Mechanism and Functional Role of a Third Metal Ion in the Enzymatic Activity of 5' Structure-Specific Nucleases. Donati E, Genna V, De Vivo M. J Am Chem Soc 142 2823-2834 (2020)
  36. Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide. Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH. Nat Commun 12 2059 (2021)
  37. Characterization of six recombinant human RNase H2 bearing Aicardi-Goutiéres syndrome causing mutations. Nishimura T, Baba M, Ogawa S, Kojima K, Takita T, Crouch RJ, Yasukawa K. J Biochem 166 537-545 (2019)
  38. Interlocking activities of DNA polymerase β in the base excision repair pathway. Kumar A, Reed AJ, Zahurancik WJ, Daskalova SM, Hecht SM, Suo Z. Proc Natl Acad Sci U S A 119 e2118940119 (2022)
  39. Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate. Ka Man Tse C, Xu J, Xu L, Sheong FK, Wang S, Chow HY, Gao X, Li X, Cheung PP, Wang D, Zhang Y, Huang X. Nat Energy 2 228-235 (2019)
  40. Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase ι. Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M, Guengerich FP. J Biol Chem 291 21063-21073 (2016)
  41. New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1. Zong G, Jork N, Hostachy S, Fiedler D, Jessen HJ, Shears SB, Wang H. FASEB J 35 e21275 (2021)
  42. Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase. Lelyveld VS, Zhang W, Szostak JW. Proc Natl Acad Sci U S A 117 7276-7283 (2020)
  43. 2.0 Å resolution crystal structure of human polκ reveals a new catalytic function of N-clasp in DNA replication. Jha V, Ling H. Sci Rep 8 15125 (2018)
  44. A Transition-State Perspective on Y-Family DNA Polymerase η Fidelity in Comparison with X-Family DNA Polymerases λ and β. Oertell K, Florián J, Haratipour P, Crans DC, Kashemirov BA, Wilson SH, McKenna CE, Goodman MF. Biochemistry 58 1764-1773 (2019)
  45. Insights into DNA polymerase δ's mechanism for accurate DNA replication. Foley MC, Couto L, Rauf S, Boyke A. J Mol Model 25 80 (2019)
  46. Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1. Cui R, Li H, Zhao J, Li X, Gan J, Ma J. Nucleic Acids Res 50 10169-10186 (2022)
  47. Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase. Nakamura T, Yamagata Y. Proc Natl Acad Sci U S A 119 e2203118119 (2022)
  48. Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints. Jamsen JA, Shock DD, Wilson SH. Nat Commun 13 3193 (2022)
  49. Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations. Hix MA, Leddin EM, Cisneros GA. J Chem Theory Comput 17 4524-4537 (2021)
  50. DNA processing by the MOBH family relaxase TraI encoded within the gonococcal genetic island. Heilers JH, Reiners J, Heller EM, Golzer A, Smits SHJ, van der Does C. Nucleic Acids Res 47 8136-8153 (2019)
  51. HIV Reverse Transcriptase Pre-Steady-State Kinetic Analysis of Chain Terminators and Translocation Inhibitors Reveals Interactions between Magnesium and Nucleotide 3'-OH. Dilmore CR, DeStefano JJ. ACS Omega 6 14621-14628 (2021)
  52. Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign. Aggarwal T, Hansen WA, Hong J, Ganguly A, York DM, Khare SD, Izgu EC. ACS Chem Biol 17 1924-1936 (2022)
  53. Selective Metal Ion Utilization Contributes to the Transformation of the Activity of Yeast Polymerase η from DNA Polymerization toward RNA Polymerization. Balint E, Unk I. Int J Mol Sci 21 E8248 (2020)
  54. Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis. Manigrasso J, De Vivo M, Palermo G. ACS Catal 11 8786-8797 (2021)
  55. Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase. Ilic S, Akabayov SR, Froimovici R, Meiry R, Vilenchik D, Hernandez A, Arthanari H, Akabayov B. Sci Rep 7 5797 (2017)
  56. Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity. Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y. J Biol Chem 299 102938 (2023)
  57. Advances in Structural and Single-Molecule Methods for Investigating DNA Lesion Bypass and Repair Polymerases. Raper AT, Reed AJ, Gadkari VV, Suo Z. Chem Res Toxicol 30 260-269 (2017)
  58. Bifurcation and oscillatory dynamics of delayed CDK1-APC feedback loop. Zhou S, Zhang W, Zhang Y, Ni X, Li Z. IET Syst Biol 14 297-306 (2020)
  59. Bioinspired Active Site with a Coordination-Adaptive Organosulfonate Ligand for Catalytic Water Oxidation at Neutral pH. Liu T, Zhan S, Shen N, Wang L, Szabó Z, Yang H, Ahlquist MSG, Sun L. J Am Chem Soc 145 11818-11828 (2023)
  60. Editorial Editorial: Nucleic Acid Polymerases: The Two-Metal-Ion Mechanism and Beyond. Pata JD, Yin YW, Lahiri I. Front Mol Biosci 9 948326 (2022)
  61. In crystallo observation of active site dynamics and transient metal ion binding within DNA polymerases. Chang C, Zhou G, Gao Y. Struct Dyn 10 034702 (2023)
  62. Insights into DNA cleavage by MutL homologs from analysis of conserved motifs in eukaryotic Mlh1. Putnam CD, Kolodner RD. Bioessays 45 e2300031 (2023)
  63. Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase β. Varela FA, Freudenthal BD. Biochemistry 60 373-380 (2021)
  64. Molecular Characterization of a DNA Polymerase from Thermus thermophilus MAT72 Phage vB_Tt72: A Novel Type-A Family Enzyme with Strong Proofreading Activity. Dorawa S, Werbowy O, Plotka M, Kaczorowska AK, Makowska J, Kozlowski LP, Fridjonsson OH, Hreggvidsson GO, Aevarsson A, Kaczorowski T. Int J Mol Sci 23 7945 (2022)
  65. Slowing Development Facilitates Arabidopsis mgt Mutants to Accumulate Enough Magnesium for Pollen Formation and Fertility Restoration. Xu XF, Qian XX, Wang KQ, Yu YH, Guo YY, Zhao X, Wang B, Yang NY, Huang JR, Yang ZN. Front Plant Sci 11 621338 (2020)
  66. Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom. Qin T, Hu B, Zhao Q, Wang Y, Wang S, Luo D, Lyu J, Chen Y, Gan J, Huang Z. Int J Mol Sci 24 15758 (2023)
  67. Visualizing the three-metal-ion-dependent cleavage of a mutagenic nucleotide. Samara NL. Proc Natl Acad Sci U S A 119 e2207180119 (2022)


Quick links