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Ren Q, Guo X, Yang D, Zhao C, Zhang X, Xia X. A wide survey of heavy metals-induced in-vitro DNA replication stress characterized by rate-limited replication. Curr Res Toxicol 2024; 6:100152. [PMID: 38327637 PMCID: PMC10848000 DOI: 10.1016/j.crtox.2024.100152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/12/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024] Open
Abstract
Heavy metals (HMs) are environmental pollutants that pose a threat to human health and have been accepted to cause various diseases, including cancer and developmental disorders. DNA replication stress has been identified to be associated with such diseases. However, the effect of HMs exclusively on DNA replication stress is still not well understood. In this study, DNA replication stress induced by thirteen HMs was assessed using a simplified in-vitro DNA replication model. Two parameters, Cte/Ctc reflecting the cycle threshold value alteration and Ke/Kc reflecting the linear phase slope change, were calculated based on the DNA replication amplification curve to evaluate the rate of exponential and linear phases. These parameters were used to detect the replication rate reflecting in-vitro DNA replication stress induced by tested HMs. According to the effective concentrations and rate-limiting degree, HMs were ranked as follows: Hg, Ce > Pb > Zn > Cr > Cd > Co > Fe > Mn, Cu, Bi, Sr, Ni. Additionally, EDTA could relieve the DNA replication stress induced by some HMs. In conclusion, this study highlights the potential danger of HMs themselves on DNA replication and provides new insight into the possible links between HMs and DNA replication-related diseases.
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Affiliation(s)
- Qidong Ren
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Key Laboratory of Agro-Products Processing Technology of Shandong Province/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, 23788 Gongye North Road, Jinan 250100, China
- State Key Laboratory of Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xuejun Guo
- State Key Laboratory of Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Dong Yang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Chuanfang Zhao
- State Key Laboratory of Environmental Chemistry and Eco-Toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xiangyuan Zhang
- State Key Laboratory of Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xinghui Xia
- State Key Laboratory of Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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2
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Vergara S, Zhou X, Santiago U, Conway JF, Sluis-Cremer N, Calero G. Structures of kinetic intermediate states of HIV-1 reverse transcriptase DNA synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572243. [PMID: 38187617 PMCID: PMC10769260 DOI: 10.1101/2023.12.18.572243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Reverse transcription of the retroviral single-stranded RNA into double-stranded DNA is an integral step during HIV-1 replication, and reverse transcriptase (RT) is a primary target for antiviral therapy. Despite a wealth of structural information on RT, we lack critical insight into the intermediate kinetic states of DNA synthesis. Using catalytically active substrates, and a novel blot/diffusion cryo-electron microscopy approach, we captured 11 structures that define the substrate binding, reactant, transition and product states of dATP addition by RT at 1.9 to 2.4 Å resolution in the active site. Initial dATP binding to RT-template/primer complex involves a single Mg 2+ (site B), and promotes partial closure of the active site pocket by a large conformational change in the β3-β4 loop in the Fingers domain, and formation of a negatively charged pocket where a second "drifting" Mg 2+ can bind (site A). During the transition state, the α-phosphate oxygen from a previously unobserved dATP conformer aligns with the site A Mg 2+ and the primer 3'-OH for nucleophilic attack. In the product state, we captured two substrate conformations in the active site: 1) dATP that had yet to be incorporated into the nascent DNA, and 2) an incorporated dAMP with the pyrophosphate leaving group coordinated by metal B and stabilized through H- bonds in the active site of RT. This study provides insights into a fundamental chemical reaction that impacts polymerase fidelity, nucleoside inhibitor drug design, and mechanisms of drug resistance.
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3
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Qin T, Hu B, Zhao Q, Wang Y, Wang S, Luo D, Lyu J, Chen Y, Gan J, Huang Z. Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom. Int J Mol Sci 2023; 24:15758. [PMID: 37958741 PMCID: PMC10647396 DOI: 10.3390/ijms242115758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
DNA synthesis catalyzed by DNA polymerase is essential for all life forms, and phosphodiester bond formation with phosphorus center inversion is a key step in this process. Herein, by using a single-selenium-atom-modified dNTP probe, we report a novel strategy to visualize the reaction stereochemistry and catalysis. We capture the before- and after-reaction states and provide explicit evidence of the center inversion and in-line attacking SN2 mechanism of DNA polymerization, while solving the diastereomer absolute configurations. Further, our kinetic and thermodynamic studies demonstrate that in the presence of Mg2+ ions (or Mn2+), the binding affinity (Km) and reaction selectivity (kcat/Km) of dGTPαSe-Rp were 51.1-fold (or 19.5-fold) stronger and 21.8-fold (or 11.3-fold) higher than those of dGTPαSe-Sp, respectively, indicating that the diastereomeric Se-Sp atom was quite disruptive of the binding and catalysis. Our findings reveal that the third metal ion is much more critical than the other two metal ions in both substrate recognition and bond formation, providing insights into how to better design the polymerase inhibitors and discover the therapeutics.
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Affiliation(s)
- Tong Qin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; (T.Q.); (B.H.); (Q.Z.); (S.W.); (J.L.)
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; (T.Q.); (B.H.); (Q.Z.); (S.W.); (J.L.)
| | - Qianwei Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; (T.Q.); (B.H.); (Q.Z.); (S.W.); (J.L.)
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Yali Wang
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin 644000, China;
| | - Shaoxin Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; (T.Q.); (B.H.); (Q.Z.); (S.W.); (J.L.)
| | - Danyan Luo
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acid Institute, Chengdu 618000, China;
| | - Jiazhen Lyu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; (T.Q.); (B.H.); (Q.Z.); (S.W.); (J.L.)
| | - Yiqing Chen
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China;
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China;
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; (T.Q.); (B.H.); (Q.Z.); (S.W.); (J.L.)
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acid Institute, Chengdu 618000, China;
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 610000, China
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4
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Nelson-Rigg R, Fagan SP, Jaremko WJ, Pata JD. Pre-Steady-State Kinetic Characterization of an Antibiotic-Resistant Mutant of Staphylococcus aureus DNA Polymerase PolC. Antimicrob Agents Chemother 2023; 67:e0157122. [PMID: 37222615 PMCID: PMC10269047 DOI: 10.1128/aac.01571-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/17/2023] [Indexed: 05/25/2023] Open
Abstract
The emergence and spread of antibiotic resistance in bacterial pathogens are serious and ongoing threats to public health. Since chromosome replication is essential to cell growth and pathogenesis, the essential DNA polymerases in bacteria have long been targets of antimicrobial development, although none have yet advanced to the market. Here, we use transient-state kinetic methods to characterize the inhibition of the PolC replicative DNA polymerase from Staphylococcus aureus by 2-methoxyethyl-6-(3'-ethyl-4'-methylanilino)uracil (ME-EMAU), a member of the 6-anilinouracil compounds that specifically target PolC enzymes, which are found in low-GC content Gram-positive bacteria. We find that ME-EMAU binds to S. aureus PolC with a dissociation constant of 14 nM, more than 200-fold tighter than the previously reported inhibition constant, which was determined using steady-state kinetic methods. This tight binding is driven by a very slow off rate of 0.006 s-1. We also characterized the kinetics of nucleotide incorporation by PolC containing a mutation of phenylalanine 1261 to leucine (F1261L). The F1261L mutation decreases ME-EMAU binding affinity by at least 3,500-fold but also decreases the maximal rate of nucleotide incorporation by 11.5-fold. This suggests that bacteria acquiring this mutation would be likely to replicate slowly and be unable to out-compete wild-type strains in the absence of inhibitors, reducing the likelihood of the resistant bacteria propagating and spreading resistance.
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Affiliation(s)
- Rachel Nelson-Rigg
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - Sean P. Fagan
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - William J. Jaremko
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Janice D. Pata
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
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5
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Prabhu D, Rajamanikandan S, Amala M, Saritha P, Jeyakanthan J, Ramasamy P. Functional Characterization, Mechanism, and Mode of Action of Putative Streptomycin Adenylyltransferase from Serratia marcescens. Antibiotics (Basel) 2022; 11:antibiotics11121722. [PMID: 36551379 PMCID: PMC9774460 DOI: 10.3390/antibiotics11121722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Nosocomial infections are serious threats to the entire world in healthcare settings. The major causative agents of nosocomial infections are bacterial pathogens, among which Enterobacteriaceae family member Serratia marcescens plays a crucial role. It is a gram-negative opportunistic pathogen, predominantly affecting patients in intensive-care units. The presence of intrinsic genes in S. marcescens led to the development of resistance to antibiotics for survival. Complete scanning of the proteome, including hypothetical and partially annotated proteins, paves the way for a better understanding of potential drug targets. The targeted protein expressed in E. coli BL21 (DE3) pLysS cells has shown complete resistance to aminoglycoside antibiotic streptomycin (>256 MCG). The recombinant protein was purified using affinity and size-exclusion chromatography and characterized using SDS-PAGE, western blotting, and MALDI-TOF analysis. Free phosphate bound to malachite green was detected at 620 nm, evident of the conversion of adenosine triphosphate to adenosine monophosphate during the adenylation process. Similarly, in the chromatographic assay, adenylated streptomycin absorbed at 260 nm in AKTA (FPLC), confirming the enzyme-catalyzed adenylation of streptomycin. Further, the adenylated product of streptomycin was confirmed through HPLC and mass spectrometry analysis. In conclusion, our characterization studies identified the partially annotated hypothetical protein as streptomycin adenylyltransferase.
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Affiliation(s)
- Dhamodharan Prabhu
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education and Research (BIHER), Chennai 600 044, Tamil Nadu, India
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
- Correspondence: (D.P.); (J.J.); (P.R.)
| | - Sundararaj Rajamanikandan
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education and Research (BIHER), Chennai 600 044, Tamil Nadu, India
| | - Mathimaran Amala
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - Poopandi Saritha
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
- Correspondence: (D.P.); (J.J.); (P.R.)
| | - Palaniappan Ramasamy
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education and Research (BIHER), Chennai 600 044, Tamil Nadu, India
- Correspondence: (D.P.); (J.J.); (P.R.)
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6
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Ahlqvist J, Linares-Pastén JA, Jasilionis A, Welin M, Håkansson M, Svensson LA, Wang L, Watzlawick H, Ævarsson A, Friðjónsson ÓH, Hreggviðsson GÓ, Ketelsen Striberny B, Glomsaker E, Lanes O, Al-Karadaghi S, Nordberg Karlsson E. Crystal structure of DNA polymerase I from Thermus phage G20c. Acta Crystallogr D Struct Biol 2022; 78:1384-1398. [PMID: 36322421 PMCID: PMC9629493 DOI: 10.1107/s2059798322009895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
This study describes the structure of DNA polymerase I from Thermus phage G20c, termed PolI_G20c. This is the first structure of a DNA polymerase originating from a group of related thermophilic bacteriophages infecting Thermus thermophilus, including phages G20c, TSP4, P74-26, P23-45 and phiFA and the novel phage Tth15-6. Sequence and structural analysis of PolI_G20c revealed a 3'-5' exonuclease domain and a DNA polymerase domain, and activity screening confirmed that both domains were functional. No functional 5'-3' exonuclease domain was present. Structural analysis also revealed a novel specific structure motif, here termed SβαR, that was not previously identified in any polymerase belonging to the DNA polymerases I (or the DNA polymerase A family). The SβαR motif did not show any homology to the sequences or structures of known DNA polymerases. The exception was the sequence conservation of the residues in this motif in putative DNA polymerases encoded in the genomes of a group of thermophilic phages related to Thermus phage G20c. The structure of PolI_G20c was determined with the aid of another structure that was determined in parallel and was used as a model for molecular replacement. This other structure was of a 3'-5' exonuclease termed ExnV1. The cloned and expressed gene encoding ExnV1 was isolated from a thermophilic virus metagenome that was collected from several hot springs in Iceland. The structure of ExnV1, which contains the novel SβαR motif, was first determined to 2.19 Å resolution. With these data at hand, the structure of PolI_G20c was determined to 2.97 Å resolution. The structures of PolI_G20c and ExnV1 are most similar to those of the Klenow fragment of DNA polymerase I (PDB entry 2kzz) from Escherichia coli, DNA polymerase I from Geobacillus stearothermophilus (PDB entry 1knc) and Taq polymerase (PDB entry 1bgx) from Thermus aquaticus.
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Affiliation(s)
- Josefin Ahlqvist
- Division of Biotechnology, Department of Chemistry, Lund University, PO Box 124, 221 00 Lund, Sweden
| | - Javier A. Linares-Pastén
- Division of Biotechnology, Department of Chemistry, Lund University, PO Box 124, 221 00 Lund, Sweden
| | - Andrius Jasilionis
- Division of Biotechnology, Department of Chemistry, Lund University, PO Box 124, 221 00 Lund, Sweden
| | - Martin Welin
- SARomics Biostructures (Sweden), Medicon Village, 223 81 Lund, Sweden
| | - Maria Håkansson
- SARomics Biostructures (Sweden), Medicon Village, 223 81 Lund, Sweden
| | | | - Lei Wang
- Institute of Biomedical Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Hildegard Watzlawick
- Institute of Biomedical Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | | | | | - Guðmundur Ó. Hreggviðsson
- Matís, Vínlandsleið 12, 113 Reykjavík, Iceland
- Department of Biology, School of Engineering and Natural Sciences, University of Iceland, Sturlugata 7, 102 Reykjavík, Iceland
| | | | | | - Olav Lanes
- ArcticZymes Technologies, PO Box 6463, 9294 Tromsø, Norway
| | | | - Eva Nordberg Karlsson
- Division of Biotechnology, Department of Chemistry, Lund University, PO Box 124, 221 00 Lund, Sweden
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7
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Pata JD, Yin YW, Lahiri I. Editorial: Nucleic Acid Polymerases: The Two-Metal-Ion Mechanism and Beyond. Front Mol Biosci 2022; 9:948326. [PMID: 35911968 PMCID: PMC9332193 DOI: 10.3389/fmolb.2022.948326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Janice D. Pata
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, United States
- *Correspondence: Janice D. Pata,
| | - Y. Whitney Yin
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Indrajit Lahiri
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab, India
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8
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Structural and Molecular Kinetic Features of Activities of DNA Polymerases. Int J Mol Sci 2022; 23:ijms23126373. [PMID: 35742812 PMCID: PMC9224347 DOI: 10.3390/ijms23126373] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 02/01/2023] Open
Abstract
DNA polymerases catalyze DNA synthesis during the replication, repair, and recombination of DNA. Based on phylogenetic analysis and primary protein sequences, DNA polymerases have been categorized into seven families: A, B, C, D, X, Y, and RT. This review presents generalized data on the catalytic mechanism of action of DNA polymerases. The structural features of different DNA polymerase families are described in detail. The discussion highlights the kinetics and conformational dynamics of DNA polymerases from all known polymerase families during DNA synthesis.
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Li X, Jin J, Xu W, Wang M, Liu L. Abortive ligation intermediate blocks seamless repair of double-stranded breaks. Int J Biol Macromol 2022; 209:1498-1503. [PMID: 35469952 DOI: 10.1016/j.ijbiomac.2022.04.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022]
Abstract
Because indel results in frame-shift mutations, seamless repair of double-stranded break (DSB)s plays a pivotal role in synthetic biology, molecular biology, and genome integrity. However, DSB repair is not well documented. T4 DNA ligase (T4lig) served to ligate intra-molecularly a zero bp break-apart DSB linear plasmid DNA pET22b(28a)-xylanase. An ATP T4lig ligation reaction joined one single-stranded break (SSB) into a phosphodiester-bond, whereas the opposite SSB into an abortive ligation intermediate blocking the DSB sequential repair. The intermediate proved to be fluorescent Cy5-AMP-SSB by a T4lig ligation reaction in the aid of Alexa Fluor 647 ATP having Cy5-AMP fluorescence. The fluorescent Cy5-AMP-SSB was de-adenylated into SSB by an ATP-free T4lig or Mg2+-free T4ligL159L reaction. The de-adenylated SSB was re-joined into another phosphodiester-bond by a sequential ATP T4lig re-ligation reaction. Thereby, DSB repair proceeds an abortive ligation, a reverse de-adenylation, and a sequential re-ligation reaction. The result has a potential usage in synthetic biology, molecular biology, and cancer-curing.
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Affiliation(s)
- Xuegang Li
- The Life Science College, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiacheng Jin
- The Life Science College, Henan Agricultural University, Zhengzhou 450002, China
| | - Wenxuan Xu
- The Life Science College, Henan Agricultural University, Zhengzhou 450002, China
| | - Mingdao Wang
- The Life Science College, Henan Agricultural University, Zhengzhou 450002, China
| | - Liangwei Liu
- The Life Science College, Henan Agricultural University, Zhengzhou 450002, China; The Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Henan Agricultural University, Zhengzhou 450002, China.
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10
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The Role of Natural Polymorphic Variants of DNA Polymerase β in DNA Repair. Int J Mol Sci 2022; 23:ijms23042390. [PMID: 35216513 PMCID: PMC8877055 DOI: 10.3390/ijms23042390] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 11/17/2022] Open
Abstract
DNA polymerase β (Polβ) is considered the main repair DNA polymerase involved in the base excision repair (BER) pathway, which plays an important part in the repair of damaged DNA bases usually resulting from alkylation or oxidation. In general, BER involves consecutive actions of DNA glycosylases, AP endonucleases, DNA polymerases, and DNA ligases. It is known that protein-protein interactions of Polβ with enzymes from the BER pathway increase the efficiency of damaged base repair in DNA. However natural single-nucleotide polymorphisms can lead to a substitution of functionally significant amino acid residues and therefore affect the catalytic activity of the enzyme and the accuracy of Polβ action. Up-to-date databases contain information about more than 8000 SNPs in the gene of Polβ. This review summarizes data on the in silico prediction of the effects of Polβ SNPs on DNA repair efficacy; available data on cancers associated with SNPs of Polβ; and experimentally tested variants of Polβ. Analysis of the literature indicates that amino acid substitutions could be important for the maintenance of the native structure of Polβ and contacts with DNA; others affect the catalytic activity of the enzyme or play a part in the precise and correct attachment of the required nucleotide triphosphate. Moreover, the amino acid substitutions in Polβ can disturb interactions with enzymes involved in BER, while the enzymatic activity of the polymorphic variant may not differ significantly from that of the wild-type enzyme. Therefore, investigation regarding the effect of Polβ natural variants occurring in the human population on enzymatic activity and protein-protein interactions is an urgent scientific task.
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11
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Amare B, Mo A, Khan N, Sowa DJ, Warner MM, Tetenych A, Andres SN. LigD: A Structural Guide to the Multi-Tool of Bacterial Non-Homologous End Joining. Front Mol Biosci 2021; 8:787709. [PMID: 34901162 PMCID: PMC8656161 DOI: 10.3389/fmolb.2021.787709] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/08/2021] [Indexed: 11/27/2022] Open
Abstract
DNA double-strand breaks are the most lethal form of damage for living organisms. The non-homologous end joining (NHEJ) pathway can repair these breaks without the use of a DNA template, making it a critical repair mechanism when DNA is not replicating, but also a threat to genome integrity. NHEJ requires proteins to anchor the DNA double-strand break, recruit additional repair proteins, and then depending on the damage at the DNA ends, fill in nucleotide gaps or add or remove phosphate groups before final ligation. In eukaryotes, NHEJ uses a multitude of proteins to carry out processing and ligation of the DNA double-strand break. Bacterial NHEJ, though, accomplishes repair primarily with only two proteins-Ku and LigD. While Ku binds the initial break and recruits LigD, it is LigD that is the primary DNA end processing machinery. Up to three enzymatic domains reside within LigD, dependent on the bacterial species. These domains are a polymerase domain, to fill in nucleotide gaps with a preference for ribonucleotide addition; a phosphoesterase domain, to generate a 3'-hydroxyl DNA end; and the ligase domain, to seal the phosphodiester backbone. To date, there are no experimental structures of wild-type LigD, but there are x-ray and nuclear magnetic resonance structures of the individual enzymatic domains from different bacteria and archaea, along with structural predictions of wild-type LigD via AlphaFold. In this review, we will examine the structures of the independent domains of LigD from different bacterial species and the contributions these structures have made to understanding the NHEJ repair mechanism. We will then examine how the experimental structures of the individual LigD enzymatic domains combine with structural predictions of LigD from different bacterial species and postulate how LigD coordinates multiple enzymatic activities to carry out DNA double-strand break repair in bacteria.
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Affiliation(s)
- Benhur Amare
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Anthea Mo
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Noorisah Khan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Dana J. Sowa
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Monica M. Warner
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Andriana Tetenych
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Sara N. Andres
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
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12
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Fagan SP, Mukherjee P, Jaremko WJ, Nelson-Rigg R, Wilson RC, Dangerfield TL, Johnson KA, Lahiri I, Pata JD. Pyrophosphate release acts as a kinetic checkpoint during high-fidelity DNA replication by the Staphylococcus aureus replicative polymerase PolC. Nucleic Acids Res 2021; 49:8324-8338. [PMID: 34302475 PMCID: PMC8373059 DOI: 10.1093/nar/gkab613] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/29/2021] [Accepted: 07/21/2021] [Indexed: 12/22/2022] Open
Abstract
Bacterial replication is a fast and accurate process, with the bulk of genome duplication being catalyzed by the α subunit of DNA polymerase III within the bacterial replisome. Structural and biochemical studies have elucidated the overall properties of these polymerases, including how they interact with other components of the replisome, but have only begun to define the enzymatic mechanism of nucleotide incorporation. Using transient-state methods, we have determined the kinetic mechanism of accurate replication by PolC, the replicative polymerase from the Gram-positive pathogen Staphylococcus aureus. Remarkably, PolC can recognize the presence of the next correct nucleotide prior to completing the addition of the current nucleotide. By modulating the rate of pyrophosphate byproduct release, PolC can tune the speed of DNA synthesis in response to the concentration of the next incoming nucleotide. The kinetic mechanism described here would allow PolC to perform high fidelity replication in response to diverse cellular environments.
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Affiliation(s)
- Sean P Fagan
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY, USA
| | - Purba Mukherjee
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY, USA
| | - William J Jaremko
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Rachel Nelson-Rigg
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY, USA
| | - Ryan C Wilson
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Tyler L Dangerfield
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Kenneth A Johnson
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Indrajit Lahiri
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY, USA.,Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Punjab, India
| | - Janice D Pata
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY, USA
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13
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Winston DS, Boehr DD. Allosteric and dynamic control of RNA-dependent RNA polymerase function and fidelity. Enzymes 2021; 49:149-193. [PMID: 34696831 DOI: 10.1016/bs.enz.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
All RNA viruses encode an RNA-dependent RNA polymerase (RdRp) responsible for genome replication. It is now recognized that enzymes in general, and RdRps specifically, are dynamic macromolecular machines such that their moving parts, including active site loops, play direct functional roles. While X-ray crystallography has provided deep insight into structural elements important for RdRp function, this methodology generally provides only static snapshots, and so is limited in its ability to report on dynamic fluctuations away from the lowest energy conformation. Nuclear magnetic resonance (NMR), molecular dynamics (MD) simulations and other biophysical techniques have brought new insight into RdRp function by their ability to characterize the trajectories, kinetics and thermodynamics of conformational motions. In particular, these methodologies have identified coordinated motions among conserved structural motifs necessary for nucleotide selection and incorporation. Disruption of these motions through amino acid substitutions or inhibitor binding impairs RdRp function. Understanding and re-engineering these motions thus provides exciting new avenues for anti-viral strategies. This chapter outlines the basics of these methodologies, summarizes the dynamic motions observed in different RdRps important for nucleotide selection and incorporation, and illustrates how this information can be leveraged towards rational vaccine strain development and anti-viral drug design.
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Affiliation(s)
- Dennis S Winston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States.
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14
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Pintér G, Hohmann K, Grün J, Wirmer-Bartoschek J, Glaubitz C, Fürtig B, Schwalbe H. Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:291-320. [PMID: 37904763 PMCID: PMC10539803 DOI: 10.5194/mr-2-291-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/07/2021] [Indexed: 11/01/2023]
Abstract
The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.
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Affiliation(s)
- György Pintér
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
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15
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Narzi D, van Keulen SC, Röthlisberger U. Gαi1 inhibition mechanism of ATP-bound adenylyl cyclase type 5. PLoS One 2021; 16:e0245197. [PMID: 33493164 PMCID: PMC7833170 DOI: 10.1371/journal.pone.0245197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/25/2020] [Indexed: 01/17/2023] Open
Abstract
Conversion of adenosine triphosphate (ATP) to the second messenger cyclic adenosine monophosphate (cAMP) is an essential reaction mechanism that takes place in eukaryotes, triggering a variety of signal transduction pathways. ATP conversion is catalyzed by the enzyme adenylyl cyclase (AC), which can be regulated by binding inhibitory, Gαi, and stimulatory, Gαs subunits. In the past twenty years, several crystal structures of AC in isolated form and complexed to Gαs subunits have been resolved. Nevertheless, the molecular basis of the inhibition mechanism of AC, induced by Gαi, is still far from being fully understood. Here, classical molecular dynamics simulations of the isolated holo AC protein type 5 and the holo binary complex AC5:Gαi have been analyzed to investigate the conformational impact of Gαi association on ATP-bound AC5. The results show that Gαi appears to inhibit the activity of AC5 by preventing the formation of a reactive ATP conformation.
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Affiliation(s)
- Daniele Narzi
- Institut des Sciences et Ingénierie Chimiques, École Polytechnicque Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Siri C. van Keulen
- Institut des Sciences et Ingénierie Chimiques, École Polytechnicque Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ursula Röthlisberger
- Institut des Sciences et Ingénierie Chimiques, École Polytechnicque Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- * E-mail:
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16
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Ouaray Z, Benner SA, Georgiadis MM, Richards NGJ. Building better polymerases: Engineering the replication of expanded genetic alphabets. J Biol Chem 2020; 295:17046-17059. [PMID: 33004440 PMCID: PMC7863901 DOI: 10.1074/jbc.rev120.013745] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/30/2020] [Indexed: 11/30/2022] Open
Abstract
DNA polymerases are today used throughout scientific research, biotechnology, and medicine, in part for their ability to interact with unnatural forms of DNA created by synthetic biologists. Here especially, natural DNA polymerases often do not have the "performance specifications" needed for transformative technologies. This creates a need for science-guided rational (or semi-rational) engineering to identify variants that replicate unnatural base pairs (UBPs), unnatural backbones, tags, or other evolutionarily novel features of unnatural DNA. In this review, we provide a brief overview of the chemistry and properties of replicative DNA polymerases and their evolved variants, focusing on the Klenow fragment of Taq DNA polymerase (Klentaq). We describe comparative structural, enzymatic, and molecular dynamics studies of WT and Klentaq variants, complexed with natural or noncanonical substrates. Combining these methods provides insight into how specific amino acid substitutions distant from the active site in a Klentaq DNA polymerase variant (ZP Klentaq) contribute to its ability to replicate UBPs with improved efficiency compared with Klentaq. This approach can therefore serve to guide any future rational engineering of replicative DNA polymerases.
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Affiliation(s)
- Zahra Ouaray
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
| | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom; Foundation for Applied Molecular Evolution, Alachua, Florida, USA.
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17
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Structural Recognition of Spectinomycin by Resistance Enzyme ANT(9) from Enterococcus faecalis. Antimicrob Agents Chemother 2020; 64:AAC.00371-20. [PMID: 32253216 DOI: 10.1128/aac.00371-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 03/25/2020] [Indexed: 11/20/2022] Open
Abstract
Spectinomycin is a ribosome-binding antibiotic that blocks the translocation step of translation. A prevalent resistance mechanism is modification of the drug by aminoglycoside nucleotidyl transferase (ANT) enzymes of the spectinomycin-specific ANT(9) family or by enzymes of the dual-specificity ANT(3")(9) family, which also acts on streptomycin. We previously reported the structural mechanism of streptomycin modification by the ANT(3")(9) AadA from Salmonella enterica ANT(9) from Enterococcus faecalis adenylates the 9-hydroxyl of spectinomycin. Here, we present the first structures of spectinomycin bound to an ANT enzyme. Structures were solved for ANT(9) in apo form, in complex with ATP, spectinomycin, and magnesium, or in complex with only spectinomycin. ANT(9) shows an overall structure similar to that of AadA, with an N-terminal nucleotidyltransferase domain and a C-terminal α-helical domain. Spectinomycin binds close to the entrance of the interdomain cleft, while ATP is buried at the bottom. Upon drug binding, the C-terminal domain rotates 14 degrees to close the cleft, allowing contacts of both domains with the drug. Comparison with AadA shows that spectinomycin specificity is explained by a straight α5 helix and a shorter α5-α6 loop, which would clash with the larger streptomycin substrate. In the active site, we observed two magnesium ions, one of them in a previously unobserved position that may activate the 9-hydroxyl for deprotonation by the catalytic base Glu-86. The observed binding mode for spectinomycin suggests that spectinamides and aminomethyl spectinomycins, recent spectinomycin analogues with expansions in position 4 of the C ring, are also subjected to modification by ANT(9) and ANT(3")(9) enzymes.
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18
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Gao W, Xu J, Lian G, Wang X, Gong X, Zhou D, Chang J. A novel analytical principle using AP site-mediated T7 RNA polymerase transcription regulation for sensing uracil-DNA glycosylase activity. Analyst 2020; 145:4321-4327. [DOI: 10.1039/d0an00509f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
udgactivity could regulateT7 RNApolymerase transcription ability by the heteroduplex substrates with chemical modifications.
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Affiliation(s)
- Weichen Gao
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin)
- Tianjin 300072
- China
| | - Jin Xu
- Tianjin Hospital
- Tianjin 300211
- China
| | - Guowei Lian
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin)
- Tianjin 300072
- China
| | - Xiaojun Wang
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Xiaoqun Gong
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin)
- Tianjin 300072
- China
| | - Dianming Zhou
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Jin Chang
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin)
- Tianjin 300072
- China
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19
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Boehr AK, Arnold JJ, Oh HS, Cameron CE, Boehr DD. 2'-C-methylated nucleotides terminate virus RNA synthesis by preventing active site closure of the viral RNA-dependent RNA polymerase. J Biol Chem 2019; 294:16897-16907. [PMID: 31575662 PMCID: PMC6851289 DOI: 10.1074/jbc.ra119.010214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/28/2019] [Indexed: 01/25/2023] Open
Abstract
The 2'-C-methyl ribonucleosides are nucleoside analogs representing an important class of antiviral agents, especially against positive-strand RNA viruses. Their value is highlighted by the highly successful anti-hepatitis C drug sofosbuvir. When appropriately phosphorylated, these nucleotides are successfully incorporated into RNA by the virally encoded RNA-dependent RNA polymerase (RdRp). This activity prevents further RNA extension, but the mechanism is poorly characterized. Previously, we had identified NMR signatures characteristic of formation of RdRp-RNA binary and RdRp-RNA-NTP ternary complexes for the poliovirus RdRp, including an open-to-closed conformational change necessary to prepare the active site for catalysis of phosphoryl transfer. Here we used these observations as a framework for interpreting the effects of 2'-C-methyl adenosine analogs on RNA chain extension in solution-state NMR spectroscopy experiments, enabling us to gain additional mechanistic insights into 2'-C-methyl ribonucleoside-mediated RNA chain termination. Contrary to what has been proposed previously, poliovirus RdRp that was bound to RNA with an incorporated 2'-C-methyl nucleotide could still bind to the next incoming NTP. Our results also indicated that incorporation of the 2'-C-methyl nucleotide does not disrupt RdRp-RNA interactions and does not prevent translocation. Instead, incorporation of the 2'-C-methyl nucleotide blocked closure of the RdRp active site upon binding of the next correct incoming NTP, which prevented further nucleotide addition. We propose that other nucleotide analogs that act as nonobligate chain terminators may operate through a similar mechanism.
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Affiliation(s)
- Alyson K Boehr
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Hyung S Oh
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - David D Boehr
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
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20
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Bruce NJ, Narzi D, Trpevski D, van Keulen SC, Nair AG, Röthlisberger U, Wade RC, Carloni P, Hellgren Kotaleski J. Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals. PLoS Comput Biol 2019; 15:e1007382. [PMID: 31665146 PMCID: PMC6821081 DOI: 10.1371/journal.pcbi.1007382] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/05/2019] [Indexed: 02/04/2023] Open
Abstract
Long-term potentiation and depression of synaptic activity in response to stimuli is a key factor in reinforcement learning. Strengthening of the corticostriatal synapses depends on the second messenger cAMP, whose synthesis is catalysed by the enzyme adenylyl cyclase 5 (AC5), which is itself regulated by the stimulatory Gαolf and inhibitory Gαi proteins. AC isoforms have been suggested to act as coincidence detectors, promoting cellular responses only when convergent regulatory signals occur close in time. However, the mechanism for this is currently unclear, and seems to lie in their diverse regulation patterns. Despite attempts to isolate the ternary complex, it is not known if Gαolf and Gαi can bind to AC5 simultaneously, nor what activity the complex would have. Using protein structure-based molecular dynamics simulations, we show that this complex is stable and inactive. These simulations, along with Brownian dynamics simulations to estimate protein association rates constants, constrain a kinetic model that shows that the presence of this ternary inactive complex is crucial for AC5's ability to detect coincident signals, producing a synergistic increase in cAMP. These results reveal some of the prerequisites for corticostriatal synaptic plasticity, and explain recent experimental data on cAMP concentrations following receptor activation. Moreover, they provide insights into the regulatory mechanisms that control signal processing by different AC isoforms.
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Affiliation(s)
- Neil J. Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Heidelberg, Germany
| | - Daniele Narzi
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Daniel Trpevski
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Siri C. van Keulen
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Anu G. Nair
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ursula Röthlisberger
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Rebecca C. Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Heidelberg, Germany
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Paolo Carloni
- Department of Physics and Department of Neurobiology, RWTH Aachen University,Aachen, Germany
- Institute for Neuroscience and Medicine (INM)-11, Forschungszentrum Jülich, Jülich, Germany
- Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Jülich, Jülich, Germany
- Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich, Jülich, Germany
| | - Jeanette Hellgren Kotaleski
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, Solna, Sweden
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21
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Deshpande S, Yang Y, Chilkoti A, Zauscher S. Enzymatic synthesis and modification of high molecular weight DNA using terminal deoxynucleotidyl transferase. Methods Enzymol 2019; 627:163-188. [PMID: 31630739 PMCID: PMC7241426 DOI: 10.1016/bs.mie.2019.07.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The recognition that nucleic acids can be used as polymeric materials led to the blossoming of the field of DNA nanotechnology, with a broad range of applications in biotechnology, biosensors, diagnostics, and drug delivery. These applications require efficient methods to synthesize and chemically modify high molecular weight DNA. Here, we discuss terminal deoxynucleotidyl transferase (TdT)-catalyzed enzymatic polymerization (TcEP) as an alternative to conventional enzymatic and solid-phase DNA synthesis. We describe biochemical requirements for TcEP and provide step-by-step protocols to carry out TcEP in solution and from surfaces.
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Affiliation(s)
- Sonal Deshpande
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Yunqi Yang
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, United States; Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, United States.
| | - Stefan Zauscher
- Department of Biomedical Engineering, Duke University, Durham, NC, United States; Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, United States.
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22
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Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Elisa Donati
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
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23
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Genna V, Carloni P, De Vivo M. A Strategically Located Arg/Lys Residue Promotes Correct Base Paring During Nucleic Acid Biosynthesis in Polymerases. J Am Chem Soc 2018; 140:3312-3321. [PMID: 29424536 DOI: 10.1021/jacs.7b12446] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Polymerases (Pols) synthesize the double-stranded nucleic acids in the Watson-Crick (W-C) conformation, which is critical for DNA and RNA functioning. Yet, the molecular basis to catalyze the W-C base pairing during Pol-mediated nucleic acids biosynthesis remains unclear. Here, through bioinformatics analyses on a large data set of Pol/DNA structures, we first describe the conserved presence of one positively charged residue (Lys or Arg), which is similarly located near the enzymatic two-metal active site, always interacting directly with the incoming substrate (d)NTP. Incidentally, we noted that some Pol/DNA structures showing the alternative Hoogsteen base pairing were often solved with this specific residue either mutated, displaced, or missing. We then used quantum and classical simulations coupled to free-energy calculations to illustrate how, in human DNA Pol-η, the conserved Arg61 favors W-C base pairing through defined interactions with the incoming nucleotide. Taken together, these structural observations and computational results suggest a structural framework in which this specific residue is critical for stabilizing the incoming (d)NTP nucleotide and base pairing during Pol-mediated nucleic acid biosynthesis. These results may benefit enzyme engineering for nucleic acid processing and encourage new drug discovery strategies to modulate Pols function.
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Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genoa , Italy.,Computational Biophysics, German Research School for Simulation Sciences, and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich , 52425 Jülich , Germany
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich , 52425 Jülich , Germany
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genoa , Italy.,Computational Biophysics, German Research School for Simulation Sciences, and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich , 52425 Jülich , Germany
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24
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Raper AT, Reed AJ, Gadkari VV, Suo Z. Advances in Structural and Single-Molecule Methods for Investigating DNA Lesion Bypass and Repair Polymerases. Chem Res Toxicol 2016; 30:260-269. [PMID: 28092942 DOI: 10.1021/acs.chemrestox.6b00342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Innovative advances in X-ray crystallography and single-molecule biophysics have yielded unprecedented insight into the mechanisms of DNA lesion bypass and damage repair. Time-dependent X-ray crystallography has been successfully applied to view the bypass of 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), a major oxidative DNA lesion, and the incorporation of the triphosphate form, 8-oxo-dGTP, catalyzed by human DNA polymerase β. Significant findings of these studies are highlighted here, and their contributions to the current mechanistic understanding of mutagenic translesion DNA synthesis (TLS) and base excision repair are discussed. In addition, single-molecule Förster resonance energy transfer (smFRET) techniques have recently been adapted to investigate nucleotide binding and incorporation opposite undamaged dG and 8-oxoG by Sulfolobus solfataricus DNA polymerase IV (Dpo4), a model Y-family DNA polymerase. The mechanistic response of Dpo4 to a DNA lesion and the complex smFRET technique are described here. In this perspective, we also describe how time-dependent X-ray crystallography and smFRET can be used to achieve the spatial and temporal resolutions necessary to answer some of the mechanistic questions that remain in the fields of TLS and DNA damage repair.
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Affiliation(s)
- Austin T Raper
- Department of Chemistry and Biochemistry and The Ohio State Biochemistry Program, The Ohio State University , Columbus, Ohio 43210, United States
| | - Andrew J Reed
- Department of Chemistry and Biochemistry and The Ohio State Biochemistry Program, The Ohio State University , Columbus, Ohio 43210, United States
| | - Varun V Gadkari
- Department of Chemistry and Biochemistry and The Ohio State Biochemistry Program, The Ohio State University , Columbus, Ohio 43210, United States
| | - Zucai Suo
- Department of Chemistry and Biochemistry and The Ohio State Biochemistry Program, The Ohio State University , Columbus, Ohio 43210, United States
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25
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Chamorro C, Camarasa MJ, Pérez-Pérez MJ, de Clercq E, Balzarini J, Félix AS. An Approach towards the Synthesis of Potential Metal-Chelating TSAO-T Derivatives as Bidentate Inhibitors of Human Immunodeficiency virus Type 1 Reverse Transcriptase. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029800900505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Novel derivatives of the potent human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) inhibitor TSAO-T have been designed, synthesized and tested for their in vitro antiretro-viral activity against HIV. These TSAO-T derivatives have been designed as potential bidentate inhibitors of HIV-1 RT, which combine in their structure the functionality of a non-nucleoside RT inhibitor (TSAO-T) and a bivalent ion-chelating moiety (a β-diketone moiety) linked through an appropriate spacer to the N-3 of thymine of TSAO-T . Some of the new compounds have an anti-HIV-1 activity comparable to that of the parent compound TSAO-T, but display a markedly increased antiviral selectivity. There was a clear relationship between antiviral activity and the length of the spacer group that links the TSAO molecule with the chelating moiety. A shorter spacer invariably resulted in increased antiviral potency. None of the TSAO-T derivatives were endowed with anti-HIV-2 activity.
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Affiliation(s)
- C Chamorro
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - M-J Camarasa
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - M-J Pérez-Pérez
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - E de Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - J Balzarini
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - A San Félix
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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Genna V, Vidossich P, Ippoliti E, Carloni P, De Vivo M. A Self-Activated Mechanism for Nucleic Acid Polymerization Catalyzed by DNA/RNA Polymerases. J Am Chem Soc 2016; 138:14592-14598. [PMID: 27530537 DOI: 10.1021/jacs.6b05475] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The enzymatic polymerization of DNA and RNA is the basis for genetic inheritance for all living organisms. It is catalyzed by the DNA/RNA polymerase (Pol) superfamily. Here, bioinformatics analysis reveals that the incoming nucleotide substrate always forms an H-bond between its 3'-OH and β-phosphate moieties upon formation of the Michaelis complex. This previously unrecognized H-bond implies a novel self-activated mechanism (SAM), which synergistically connects the in situ nucleophile formation with subsequent nucleotide addition and, importantly, nucleic acid translocation. Thus, SAM allows an elegant and efficient closed-loop sequence of chemical and physical steps for Pol catalysis. This is markedly different from previous mechanistic hypotheses. Our proposed mechanism is corroborated via ab initio QM/MM simulations on a specific Pol, the human DNA polymerase-η, an enzyme involved in repairing damaged DNA. The structural conservation of DNA and RNA Pols supports the possible extension of SAM to Pol enzymes from the three domains of life.
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Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia , Via Morego 30, 16163, Genoa, Italy.,IAS-5/INM-9 Computational Biomedicine and JARA-HPC, Forschungszentrum Jülich , Wilhelm-Johnen-Strasse, 52428 Jülich, Germany
| | - Pietro Vidossich
- IAS-5/INM-9 Computational Biomedicine and JARA-HPC, Forschungszentrum Jülich , Wilhelm-Johnen-Strasse, 52428 Jülich, Germany
| | - Emiliano Ippoliti
- IAS-5/INM-9 Computational Biomedicine and JARA-HPC, Forschungszentrum Jülich , Wilhelm-Johnen-Strasse, 52428 Jülich, Germany
| | - Paolo Carloni
- IAS-5/INM-9 Computational Biomedicine and JARA-HPC, Forschungszentrum Jülich , Wilhelm-Johnen-Strasse, 52428 Jülich, Germany
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia , Via Morego 30, 16163, Genoa, Italy.,IAS-5/INM-9 Computational Biomedicine and JARA-HPC, Forschungszentrum Jülich , Wilhelm-Johnen-Strasse, 52428 Jülich, Germany
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27
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Benzaria S, Maury G, Gosselin G, Rittinger K, Divita G, Goody RS, Imbach JL. Synthesis of 2′,3′,5′-trideoxyuridine-5′-methylphosphonic Acid and its Diphosphate Derivative. Study of the Interaction with HIV-1 reverse Transcriptase. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029400500403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
2′,3′,5′-Trideoxyuridine-5′-methylphosphonate, [8], was synthesized from ddU. The 5′,6′ carbon-carbon bond was formed by condensing the 5′-aldehyde of ddU and a Wittig reagent. The binding interaction of the diphosphate derivative [10] of the phosphonate [8] with HIV-1 reverse transcriptase (RT) was studied using methods based primarily on fluorescence spectroscopy. From the quenching of intrinsic tryptophan fluorescence of RT during its titration against [10], a dissociation constant of 24 μm was calculated at 25°C. In the presence of a DNA/DNA template/primer of defined sequence and RT, [10] and a fluorescent derivative of ddTTP competed for binding to RT without incorporation of ddU-5′-methylphosphonate. In the presence of a 0.5 mm concentration of [10], the RT activity measured with Poly(rA)/(dT)15 and [3H] dTTP was lowered to 65%. All our observations are consistent with suppression of the catalysis of bond formation between the OH at the primer 3′-end and α-P of [10] after formation of the complex between RT, template/primer and [10].
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Affiliation(s)
- S. Benzaria
- Université Montpellier II, URA 488 du CNRS, Place E. Bataillon, 34095 Montpellier Cedex 5, France
| | - G. Maury
- Université Montpellier II, URA 488 du CNRS, Place E. Bataillon, 34095 Montpellier Cedex 5, France
| | - G. Gosselin
- Université Montpellier II, URA 488 du CNRS, Place E. Bataillon, 34095 Montpellier Cedex 5, France
| | - K. Rittinger
- Abteilung Biophysik, Max-Planck Institut für medizinische Forschung, Jahnstrasse 29, 69028 Heidelberg, Germany
| | - G. Divita
- Abteilung Biophysik, Max-Planck Institut für medizinische Forschung, Jahnstrasse 29, 69028 Heidelberg, Germany
| | - R. S. Goody
- Abteilung Biophysik, Max-Planck Institut für medizinische Forschung, Jahnstrasse 29, 69028 Heidelberg, Germany
| | - J.-L. Imbach
- Université Montpellier II, URA 488 du CNRS, Place E. Bataillon, 34095 Montpellier Cedex 5, France
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Abstract
DNA replication in Escherichia coli initiates at oriC, the origin of replication and proceeds bidirectionally, resulting in two replication forks that travel in opposite directions from the origin. Here, we focus on events at the replication fork. The replication machinery (or replisome), first assembled on both forks at oriC, contains the DnaB helicase for strand separation, and the DNA polymerase III holoenzyme (Pol III HE) for DNA synthesis. DnaB interacts transiently with the DnaG primase for RNA priming on both strands. The Pol III HE is made up of three subassemblies: (i) the αɛθ core polymerase complex that is present in two (or three) copies to simultaneously copy both DNA strands, (ii) the β2 sliding clamp that interacts with the core polymerase to ensure its processivity, and (iii) the seven-subunit clamp loader complex that loads β2 onto primer-template junctions and interacts with the α polymerase subunit of the core and the DnaB helicase to organize the two (or three) core polymerases. Here, we review the structures of the enzymatic components of replisomes, and the protein-protein and protein-DNA interactions that ensure they remain intact while undergoing substantial dynamic changes as they function to copy both the leading and lagging strands simultaneously during coordinated replication.
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Affiliation(s)
- J S Lewis
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - S Jergic
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - N E Dixon
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
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29
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Dahl JM, Lieberman KR, Wang H. Modulation of DNA Polymerase Noncovalent Kinetic Transitions by Divalent Cations. J Biol Chem 2016; 291:6456-70. [PMID: 26797125 PMCID: PMC4813572 DOI: 10.1074/jbc.m115.701797] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/02/2016] [Indexed: 11/06/2022] Open
Abstract
Replicative DNA polymerases (DNAPs) require divalent metal cations for phosphodiester bond formation in the polymerase site and for hydrolytic editing in the exonuclease site. Me(2+) ions are intimate architectural components of each active site, where they are coordinated by a conserved set of amino acids and functional groups of the reaction substrates. Therefore Me(2+) ions can influence the noncovalent transitions that occur during each nucleotide addition cycle. Using a nanopore, transitions in individual Φ29 DNAP complexes are resolved with single-nucleotide spatial precision and sub-millisecond temporal resolution. We studied Mg(2+) and Mn(2+), which support catalysis, and Ca(2+), which supports deoxynucleoside triphosphate (dNTP) binding but not catalysis. We examined their effects on translocation, dNTP binding, and primer strand transfer between the polymerase and exonuclease sites. All three metals cause a concentration-dependent shift in the translocation equilibrium, predominantly by decreasing the forward translocation rate. Me(2+) also promotes an increase in the backward translocation rate that is dependent upon the primer terminal 3'-OH group. Me(2+) modulates the translocation rates but not their response to force, suggesting that Me(2+) does not affect the distance to the transition state of translocation. Absent Me(2+), the primer strand transfer pathway between the polymerase and exonuclease sites displays additional kinetic states not observed at >1 mm Me(2+). Complementary dNTP binding is affected by Me(2+) identity, with Ca(2+) affording the highest affinity, followed by Mn(2+), and then Mg(2+). Both Ca(2+) and Mn(2+) substantially decrease the dNTP dissociation rate relative to Mg(2+), while Ca(2+) also increases the dNTP association rate.
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Affiliation(s)
- Joseph M Dahl
- From the Departments of Biomolecular Engineering and
| | | | - Hongyun Wang
- Applied Mathematics and Statistics, University of California, Santa Cruz, California 95064
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30
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Hahn DK, Tusell JR, Sprang SR, Chu X. Catalytic Mechanism of Mammalian Adenylyl Cyclase: A Computational Investigation. Biochemistry 2015; 54:6252-62. [PMID: 26393535 PMCID: PMC5156327 DOI: 10.1021/acs.biochem.5b00655] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenylyl cyclase (AC) catalyzes the synthesis of cyclic AMP, an important intracellular regulatory molecule, from ATP. We propose a catalytic mechanism for class III mammalian AC based on density functional theory calculations. We employ a model of the AC active site derived from a crystal structure of mammalian AC activated by Gα·GTP and forskolin at separate allosteric sites. We compared the calculated activation free energies for 13 possible reaction sequences involving proton transfer, nucleophilic attack, and elimination of pyrophosphate. The proposed most probable mechanism is initiated by deprotonation of 3'OH and water-mediated transfer of the 3'H to the γ-phosphate. Proton transfer is followed by changes in coordination of the two magnesium ion cofactors and changes in the conformation of ATP to enhance the role of 3'O as a nucleophile and to bring 3'O close to Pα. The subsequent phosphoryl transfer step is concerted and rate-limiting. Comparison of the enzyme-catalyzed and nonenzymatic reactions reveals that the active site residues lower the free energy barrier for both phosphoryl transfer and proton transfer and significantly shift the proton transfer equilibrium. Calculations for mutants K1065A and R1029A demonstrate that K1065 plays a significant role in shifting the proton transfer equilibrium, whereas R1029 is important for making the transition state of concerted phosphoryl transfer tight rather than loose.
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Affiliation(s)
- David K. Hahn
- Center for Biomolecular Structure and Dynamics and Department of Chemistry and Biochemistry, The University of Montana, Missoula, Montana 59812
| | - Jose R Tusell
- Center for Biomolecular Structure and Dynamics and Department of Chemistry and Biochemistry, The University of Montana, Missoula, Montana 59812
| | - Stephen R. Sprang
- Center for Biomolecular Structure and Dynamics and Department of Chemistry and Biochemistry, The University of Montana, Missoula, Montana 59812
| | - Xi Chu
- Center for Biomolecular Structure and Dynamics and Department of Chemistry and Biochemistry, The University of Montana, Missoula, Montana 59812
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31
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Ernst FGM, Rickert C, Bluschke A, Betat H, Steinhoff HJ, Mörl M. Domain movements during CCA-addition: a new function for motif C in the catalytic core of the human tRNA nucleotidyltransferases. RNA Biol 2015; 12:435-46. [PMID: 25849199 PMCID: PMC4615804 DOI: 10.1080/15476286.2015.1018502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/06/2015] [Accepted: 02/07/2015] [Indexed: 10/23/2022] Open
Abstract
CCA-adding enzymes are highly specific RNA polymerases that synthesize and maintain the sequence CCA at the tRNA 3'-end. This nucleotide triplet is a prerequisite for tRNAs to be aminoacylated and to participate in protein biosynthesis. During CCA-addition, a set of highly conserved motifs in the catalytic core of these enzymes is responsible for accurate sequential nucleotide incorporation. In the nucleotide binding pocket, three amino acid residues form Watson-Crick-like base pairs to the incoming CTP and ATP. A reorientation of these templating amino acids switches the enzyme's specificity from CTP to ATP recognition. However, the mechanism underlying this essential structural rearrangement is not understood. Here, we show that motif C, whose actual function has not been identified yet, contributes to the switch in nucleotide specificity during polymerization. Biochemical characterization as well as EPR spectroscopy measurements of the human enzyme reveal that mutating the highly conserved amino acid position D139 in this motif interferes with AMP incorporation and affects interdomain movements in the enzyme. We propose a model of action, where motif C forms a flexible spring element modulating the relative orientation of the enzyme's head and body domains to accommodate the growing 3'-end of the tRNA. Furthermore, these conformational transitions initiate the rearranging of the templating amino acids to switch the specificity of the nucleotide binding pocket from CTP to ATP during CCA-synthesis.
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Affiliation(s)
- Felix G M Ernst
- Institute for Biochemistry; University of Leipzig; Leipzig, Germany
| | | | | | - Heike Betat
- Institute for Biochemistry; University of Leipzig; Leipzig, Germany
| | | | - Mario Mörl
- Institute for Biochemistry; University of Leipzig; Leipzig, Germany
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32
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Liu X, Yin Y, Wu J, Liu Z. Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis. Nat Commun 2014; 5:4244. [PMID: 24968740 PMCID: PMC4083444 DOI: 10.1038/ncomms5244] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/28/2014] [Indexed: 11/09/2022] Open
Abstract
Phospholipids are elemental building-block molecules for biological membranes. Biosynthesis of phosphatidylinositol, phosphatidylglycerol and phosphatidylserine requires a central liponucleotide intermediate named cytidine-diphosphate diacylglycerol (CDP-DAG). The CDP-DAG synthetase (Cds) is an integral membrane enzyme catalysing the formation of CDP-DAG, an essential step for phosphoinositide recycling during signal transduction. Here we report the structure of the Cds from Thermotoga maritima (TmCdsA) at 3.4 Å resolution. TmCdsA forms a homodimer and each monomer contains nine transmembrane helices arranged into a novel fold with three domains. An unusual funnel-shaped cavity penetrates half way into the membrane, allowing the enzyme to simultaneously accept hydrophilic substrate (cytidine 5'-triphosphate (CTP)/deoxy-CTP) from cytoplasm and hydrophobic substrate (phosphatidic acid) from membrane. Located at the bottom of the cavity, a Mg(2+)-K(+) hetero-di-metal centre coordinated by an Asp-Asp dyad serves as the cofactor of TmCdsA. The results suggest a two-metal-ion catalytic mechanism for the Cds-mediated synthesis of CDP-DAG at the membrane-cytoplasm interface.
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Affiliation(s)
- Xiuying Liu
- 1] National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China [2]
| | - Yan Yin
- 1] National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100049, China [3]
| | - Jinjun Wu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Zhenfeng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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33
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Beck JL, Urathamakul T, Watt SJ, Sheil MM, Schaeffer PM, Dixon NE. Proteomic dissection of DNA polymerization. Expert Rev Proteomics 2014; 3:197-211. [PMID: 16608433 DOI: 10.1586/14789450.3.2.197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA polymerases replicate the genome by associating with a range of other proteins that enable rapid, high-fidelity copying of DNA. This complex of proteins and nucleic acids is termed the replisome. Proteins of the replisome must interact with other networks of proteins, such as those involved in DNA repair. Many of the proteins involved in DNA polymerization and the accessory proteins are known, but the array of proteins they interact with, and the spatial and temporal arrangement of these interactions, are current research topics. Mass spectrometry is a technique that can be used to identify the sites of these interactions and to determine the precise stoichiometries of binding partners in a functional complex. A complete understanding of the macromolecular interactions involved in DNA replication and repair may lead to discovery of new targets for antibiotics against bacteria and biomarkers for diagnosis of diseases, such as cancer, in humans.
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Affiliation(s)
- Jennifer L Beck
- Department of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia.
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34
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35
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Shen H, Sun H, Li G. What is the role of motif D in the nucleotide incorporation catalyzed by the RNA-dependent RNA polymerase from poliovirus? PLoS Comput Biol 2012; 8:e1002851. [PMID: 23300428 PMCID: PMC3531290 DOI: 10.1371/journal.pcbi.1002851] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 11/07/2012] [Indexed: 12/13/2022] Open
Abstract
Poliovirus (PV) is a well-characterized RNA virus, and the RNA-dependent RNA polymerase (RdRp) from PV (3Dpol) has been widely employed as an important model for understanding the structure-function relationships of RNA and DNA polymerases. Many experimental studies of the kinetics of nucleotide incorporation by RNA and DNA polymerases suggest that each nucleotide incorporation cycle basically consists of six sequential steps: (1) an incoming nucleotide binds to the polymerase-primer/template complex; (2) the ternary complex (nucleotide-polymerase-primer/template) undergoes a conformational change; (3) phosphoryl transfer occurs (the chemistry step); (4) a post-chemistry conformational change occurs; (5) pyrophosphate is released; (6) RNA or DNA translocation. Recently, the importance of structural motif D in nucleotide incorporation has been recognized, but the functions of motif D are less well explored so far. In this work, we used two computational techniques, molecular dynamics (MD) simulation and quantum mechanics (QM) method, to explore the roles of motif D in nucleotide incorporation catalyzed by PV 3Dpol. We discovered that the motif D, exhibiting high flexibility in either the presence or the absence of RNA primer/template, might facilitate the transportation of incoming nucleotide or outgoing pyrophosphate. We observed that the dynamic behavior of motif A, which should be essential to the polymerase function, was greatly affected by the motions of motif D. In the end, through QM calculations, we attempted to investigate the proton transfer in enzyme catalysis associated with a few amino acid residues of motifs F and D. The missing link between dynamics and structure or between dynamics and function of a protein has recently been paid much attention by many scientists since it has been recognized that a folded protein should be considered as an ensemble of conformations fluctuating in the neighborhood of its native state, instead of being pictured as a single static structure. Thus, to completely understand a protein and its functions, the dynamic features of the protein under a certain condition are required to be known. In this study, we performed atomistic MD simulations and QM calculations on the RNA-dependent RNA polymerase (RdRp) from poliovirus (PV), which is an important model system for gaining insight into the features of RNA and DNA polymerases. Through the computational studies of PV 3Dpol, we aim at finding out valuable information about the dynamic properties of the enzyme and exploring the molecular mechanism of the phosphoryl transfer in nucleotide incorporation.
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Affiliation(s)
- Hujun Shen
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Hui Sun
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- * E-mail:
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36
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Arnold JJ, Smidansky ED, Moustafa IM, Cameron CE. Human mitochondrial RNA polymerase: structure-function, mechanism and inhibition. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:948-60. [PMID: 22551784 DOI: 10.1016/j.bbagrm.2012.04.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 04/09/2012] [Accepted: 04/11/2012] [Indexed: 11/29/2022]
Abstract
Transcription of the human mitochondrial genome is required for the expression of 13 subunits of the respiratory chain complexes involved in oxidative phosphorylation, which is responsible for meeting the cells' energy demands in the form of ATP. Also transcribed are the two rRNAs and 22 tRNAs required for mitochondrial translation. This process is accomplished, with the help of several accessory proteins, by the human mitochondrial RNA polymerase (POLRMT, also known as h-mtRNAP), a nuclear-encoded single-subunit DNA-dependent RNA polymerase (DdRp or RNAP) that is distantly related to the bacteriophage T7 class of single-subunit RNAPs. In addition to its role in transcription, POLRMT serves as the primase for mitochondrial DNA replication. Therefore, this enzyme is of fundamental importance for both expression and replication of the human mitochondrial genome. Over the past several years rapid progress has occurred in understanding POLRMT and elucidating the molecular mechanisms of mitochondrial transcription. Important accomplishments include development of recombinant systems that reconstitute human mitochondrial transcription in vitro, determination of the X-ray crystal structure of POLRMT, identification of distinct mechanisms for promoter recognition and transcription initiation, elucidation of the kinetic mechanism for POLRMT-catalyzed nucleotide incorporation and discovery of unique mechanisms of mitochondrial transcription inhibition including the realization that POLRMT is an off target for antiviral ribonucleoside analogs. This review summarizes the current understanding of POLRMT structure-function, mechanism and inhibition. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Jamie J Arnold
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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37
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Abstract
DNA polymerase ε (Pol ε) is one of three replicative DNA polymerases in eukaryotic cells. Pol ε is a multi-subunit DNA polymerase with many functions. For example, recent studies in yeast have suggested that Pol ε is essential during the initiation of DNA replication and also participates during leading strand synthesis. In this chapter, we will discuss the structure of Pol ε, the individual subunits and their function.
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Affiliation(s)
- Matthew Hogg
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden
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38
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Xia S, Wang M, Blaha G, Konigsberg WH, Wang J. Structural insights into complete metal ion coordination from ternary complexes of B family RB69 DNA polymerase. Biochemistry 2011; 50:9114-24. [PMID: 21923197 PMCID: PMC3760225 DOI: 10.1021/bi201260h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We have captured a preinsertion ternary complex of RB69 DNA polymerase (RB69pol) containing the 3' hydroxyl group at the terminus of an extendable primer (ptO3') and a nonhydrolyzable 2'-deoxyuridine 5'-α,β-substituted triphosphate, dUpXpp, where X is either NH or CH(2), opposite a complementary templating dA nucleotide residue. Here we report four structures of these complexes formed by three different RB69pol variants with catalytically inert Ca(2+) and four other structures with catalytically competent Mn(2+) or Mg(2+). These structures provide new insights into why the complete divalent metal-ion coordination complexes at the A and B sites are required for nucleotidyl transfer. They show that the metal ion in the A site brings ptO3' close to the α-phosphorus atom (Pα) of the incoming dNTP to enable phosphodiester bond formation through simultaneous coordination of both ptO3' and the nonbridging Sp oxygen of the dNTP's α-phosphate. The coordination bond length of metal ion A as well as its ionic radius determines how close ptO3' can approach Pα. These variables are expected to affect the rate of bond formation. The metal ion in the B site brings the pyrophosphate product close enough to Pα to enable pyrophosphorolysis and assist in the departure of the pyrophosphate. In these dUpXpp-containing complexes, ptO3' occupies the vertex of a distorted metal ion A coordination octahedron. When ptO3' is placed at the vertex of an undistorted, idealized metal ion A octahedron, it is within bond formation distance to Pα. This geometric relationship appears to be conserved among DNA polymerases of known structure.
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Affiliation(s)
- Shuangluo Xia
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT96520-8114, USA
| | - Mina Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT96520-8114, USA
| | - Gregor Blaha
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT96520-8114, USA
| | - William H. Konigsberg
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT96520-8114, USA
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT96520-8114, USA,Corresponding Author: Jimin Wang, Phone: (203)-432-5737; Fax: (203)-432-3282.
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39
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Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Proc Natl Acad Sci U S A 2011; 108:17644-8. [PMID: 22006298 DOI: 10.1073/pnas.1114496108] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that catalyzes replication in crystals, we observe that a C • A mismatch can mimic the shape of cognate base pairs at the site of incorporation. This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such that a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. These observations provide structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis, a long-standing concept that has been difficult to demonstrate directly.
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Slack GS, Low J, Kaminski G, Yirrell D. Optimising PCR reactions; remember magnesium? J Clin Virol 2011; 52:63-4. [DOI: 10.1016/j.jcv.2011.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 06/06/2011] [Accepted: 06/10/2011] [Indexed: 10/18/2022]
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Chaudret R, Piquemal JP, Cisneros GA. Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations. Phys Chem Chem Phys 2011; 13:11239-47. [PMID: 21566841 DOI: 10.1039/c0cp02550j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA polymerases require two divalent metal ions in the active site for catalysis. Mg(2+) has been confirmed to be the most probable cation utilized by most polymerases in vivo. Other metal ions are either potent mutagens or inhibitors. We used structural and topological analyses based on ab initio QM/MM calculations to study human DNA polymerase λ (Polλ) with different metals in the active site. Our results indicate a slightly longer O3'-Pα distance (∼3.6 Å) for most inhibitor cations compared to the natural and mutagenic metals (∼3.3-3.4 Å). Optimization with a larger basis set for the previously reported transition state (TS) structures (Cisneros et al., DNA Repair, 2008, 7, 1824.) gives barriers of 17.4 kcal mol(-1) and 15.1 kcal mol(-1) for the Mg(2+) and Mn(2+) catalyzed reactions respectively. Relying on the key relation between the topological signature of a metal cation and its selectivity within biological systems (de Courcy et al., J. Chem. Theor. Comput., 2010, 6, 1048.) we have performed electron localization function (ELF) topological analyses. These analyses show that all inhibitor and mutagenic metals considered, except Na(+), present a "split" of the outer-shell density of the metal. This "splitting" is not observed for the non-mutagenic Mg(2+) metal. Population and multipole analyses on the ELF basins reveal that the electronic dipolar and quadrupolar polarization is significantly different with Mg(2+) compared to all other cations. Our results shed light at the atomic level on the subtle differences between Mg(2+), mutagenic, and inhibitor metals in DNA polymerases. These results provide a correlation between the electronic distribution of the cations in the active site and the possible consequences on DNA synthesis.
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Affiliation(s)
- Robin Chaudret
- UPMC Université Paris 06, UMR 7616 Laboratoire de Chimie Théorique, Paris, France
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42
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Hemsworth GR, Moroz OV, Fogg MJ, Scott B, Bosch-Navarrete C, González-Pacanowska D, Wilson KS. The crystal structure of the Leishmania major deoxyuridine triphosphate nucleotidohydrolase in complex with nucleotide analogues, dUMP, and deoxyuridine. J Biol Chem 2011; 286:16470-81. [PMID: 21454646 DOI: 10.1074/jbc.m111.224873] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the Leishmania genus are the causative agents of the life-threatening disease leishmaniasis. New drugs are being sought due to increasing resistance and adverse side effects with current treatments. The knowledge that dUTPase is an essential enzyme and that the all α-helical dimeric kinetoplastid dUTPases have completely different structures compared with the trimeric β-sheet type dUTPase possessed by most organisms, including humans, make the dimeric enzymes attractive drug targets. Here, we present crystal structures of the Leishmania major dUTPase in complex with substrate analogues, the product dUMP and a substrate fragment, and of the homologous Campylobacter jejuni dUTPase in complex with a triphosphate substrate analogue. The metal-binding properties of both enzymes are shown to be dependent upon the ligand identity, a previously unseen characteristic of this family. Furthermore, structures of the Leishmania enzyme in the presence of dUMP and deoxyuridine coupled with tryptophan fluorescence quenching indicate that occupation of the phosphate binding region is essential for induction of the closed conformation and hence for substrate binding. These findings will aid in the development of dUTPase inhibitors as potential new lead anti-trypanosomal compounds.
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Affiliation(s)
- Glyn R Hemsworth
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, United Kingdom
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43
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Ho MH, De Vivo M, Dal Peraro M, Klein ML. Understanding the effect of magnesium ion concentration on the catalytic activity of ribonuclease H through computation: does a third metal binding site modulate endonuclease catalysis? J Am Chem Soc 2011; 132:13702-12. [PMID: 20731347 DOI: 10.1021/ja102933y] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase superfamily and hydrolyzes the phosphodiester linkage on the RNA strand of a DNA/RNA hybrid duplex. Due to its activity in HIV reverse transcription, it represents a promising target for anti-HIV drug design. While crystallographic data have located two ions in the catalytic site, there is ongoing debate concerning just how many metal ions bound at the active site are optimal for catalysis. Indeed, experiments have shown a dependency of the catalytic activity on the Mg(2+) concentration. Moreover, in RNase H, the glutamate residue E188 has been shown to be essential for full enzymatic activation, regardless of the Mg(2+) concentration. The catalytic center is known to contain two Mg(2+) ions, and E188 is not one of the primary metal ligands. Herein, classical molecular dynamics (MD) simulations are employed to study the metal-ligand coordination in RNase H at different concentration of Mg(2+). Importantly, the presence of a third Mg(2+) ion, bound to the second-shell ligand E188, is a persistent feature of the MD simulations. Free energy calculations have identified two distinct conformations, depending on the concentration of Mg(2+). At standard concentration, a third Mg(2+) is found in the catalytic pocket, but it does not perturb the optimal RNase H active conformation. However, at higher concentration, the third Mg(2+) ion heavily perturbs the nucleophilic water and thereby influences the catalytic efficiency of RNase H. In addition, the E188A mutant shows no ability to engage additional Mg(2+) ions near the catalytic pocket. This finding likely explains the decrease in catalytic activity of E188A and also supports the key role of E188 in localizing the third Mg(2+) ion at the active site. Glutamate residues are commonly found surrounding the metal center in the endonuclease family, which suggests that this structural motif may be an important feature to enhance catalytic activity. The present MD calculations support the hypothesis that RNase H can accommodate three divalent metal ions in its catalytic pocket and provide an in-depth understanding of their dynamic role for catalysis.
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Affiliation(s)
- Ming-Hsun Ho
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania, 19104, USA
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44
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Brown JA, Zhang L, Sherrer SM, Taylor JS, Burgers PMJ, Suo Z. Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase Eta. J Nucleic Acids 2010; 2010:871939. [PMID: 20798853 PMCID: PMC2925389 DOI: 10.4061/2010/871939] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 04/30/2010] [Indexed: 11/23/2022] Open
Abstract
Understanding polymerase fidelity is an important objective towards ascertaining the overall stability of an organism's genome. Saccharomyces cerevisiae DNA polymerase eta (yPoleta), a Y-family DNA polymerase, is known to efficiently bypass DNA lesions (e.g., pyrimidine dimers) in vivo. Using pre-steady-state kinetic methods, we examined both full-length and a truncated version of yPoleta which contains only the polymerase domain. In the absence of yPoleta's C-terminal residues 514-632, the DNA binding affinity was weakened by 2-fold and the base substitution fidelity dropped by 3-fold. Thus, the C-terminus of yPoleta may interact with DNA and slightly alter the conformation of the polymerase domain during catalysis. In general, yPoleta discriminated between a correct and incorrect nucleotide more during the incorporation step (50-fold on average) than the ground-state binding step (18-fold on average). Blunt-end additions of dATP or pyrene nucleotide 5'-triphosphate revealed the importance of base stacking during the binding of incorrect incoming nucleotides.
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Affiliation(s)
- Jessica A. Brown
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Likui Zhang
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Shanen M. Sherrer
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | | | - Peter M. J. Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zucai Suo
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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45
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Giambasu GM, Lee TS, Sosa CP, Robertson MP, Scott WG, York DM. Identification of dynamical hinge points of the L1 ligase molecular switch. RNA (NEW YORK, N.Y.) 2010; 16:769-780. [PMID: 20167653 PMCID: PMC2844624 DOI: 10.1261/rna.1897810] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 12/19/2009] [Indexed: 05/28/2023]
Abstract
The L1 ligase is an in vitro selected ribozyme that uses a noncanonically base-paired ligation site to catalyze regioselectively and regiospecifically the 5' to 3' phosphodiester bond ligation, a reaction relevant to origin of life hypotheses that invoke an RNA world scenario. The L1 ligase crystal structure revealed two different conformational states that were proposed to represent the active and inactive forms. It remains an open question as to what degree these two conformers persist as stable conformational intermediates in solution, and along what pathway are they able to interconvert. To explore these questions, we have performed a series of molecular dynamics simulations in explicit solvent of the inactive-active conformational switch in L1 ligase. Four simulations were performed departing from both conformers in both the reactant and product states, in addition to a simulation where local unfolding in the active state was induced. From these simulations, along with crystallographic data, a set of four virtual torsion angles that span two evolutionarily conserved and restricted regions were identified as dynamical hinge points in the conformational switch transition. The ligation site visits three distinct states characterized by hydrogen bond patterns that are correlated with the formation of specific contacts that may promote catalysis. The insights gained from these simulations contribute to a more detailed understanding of the coupled catalytic/conformational switch mechanism of L1 ligase that may facilitate the design and engineering of new catalytic riboswitches.
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Affiliation(s)
- George M Giambasu
- Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455, USA
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46
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Lansdon EB, Samuel D, Lagpacan L, Brendza KM, White KL, Hung M, Liu X, Boojamra CG, Mackman RL, Cihlar T, Ray AS, McGrath ME, Swaminathan S. Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex. J Mol Biol 2010; 397:967-78. [PMID: 20156454 DOI: 10.1016/j.jmb.2010.02.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 02/05/2010] [Accepted: 02/10/2010] [Indexed: 11/30/2022]
Abstract
GS-9148 ([5-(6-amino-purin-9-yl)-4-fluoro-2,5-dihydro-furan-2-yloxymethyl]-phosphonic acid) is a dAMP (2'-deoxyadenosine monophosphate) analog that maintains its antiviral activity against drug-resistant HIV. Crystal structures for HIV-1 reverse transcriptase (RT) bound to double-stranded DNA, ternary complexes with either GS-9148-diphosphate or 2'-deoxyadenosine triphosphate (dATP), and a post-incorporation structure with GS-9148 translocated to the priming site were obtained to gain insight into the mechanism of RT inhibition. The binding of either GS-9148-diphosphate or dATP to the binary RT-DNA complex resulted in the fingers subdomain closing around the incoming substrate. This produced up to a 9 A shift in the tips of the fingers subdomain as it closed toward the palm and thumb subdomains. GS-9148-diphosphate shows a similar binding mode as dATP in the nucleotide-binding site. Residues whose mutations confer resistance to nucleotide/nucleoside RT inhibitors, such as M184, Y115, L74, and K65, show little to no shift in orientation whether GS-9148-diphosphate or dATP is bound. One difference observed in binding is the position of the central ring. The dihydrofuran ring of GS-9148-diphosphate interacts with the aromatic side chain of Y115 more than does the ribose ring of dATP, possibly picking up a favorable pi-pi interaction. The ability of GS-9148-diphosphate to mimic the active-site contacts of dATP may explain its effective inhibition of RT and maintained activity against resistance mutations. Interestingly, the 2'-fluoro moiety of GS-9148-diphosphate was found in close proximity to the Q151 side chain, potentially explaining the observed moderately reduced susceptibly to GS-9148 conferred by Q151M mutation.
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Affiliation(s)
- Eric B Lansdon
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA.
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47
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Pata JD. Structural diversity of the Y-family DNA polymerases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1124-35. [PMID: 20123134 DOI: 10.1016/j.bbapap.2010.01.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 12/11/2009] [Accepted: 01/25/2010] [Indexed: 11/17/2022]
Abstract
The Y-family translesion DNA polymerases enable cells to tolerate many forms of DNA damage, yet these enzymes have the potential to create genetic mutations at high rates. Although this polymerase family was defined less than a decade ago, more than 90 structures have already been determined so far. These structures show that the individual family members bypass damage and replicate DNA with either error-free or mutagenic outcomes, depending on the polymerase, the lesion and the sequence context. Here, these structures are reviewed and implications for polymerase function are discussed.
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Affiliation(s)
- Janice D Pata
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA.
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48
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Single-molecule study of DNA polymerization activity of HIV-1 reverse transcriptase on DNA templates. J Mol Biol 2009; 395:995-1006. [PMID: 19968999 DOI: 10.1016/j.jmb.2009.11.072] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 11/12/2009] [Accepted: 11/30/2009] [Indexed: 11/20/2022]
Abstract
HIV-1 RT (human immunodeficiency virus-1 reverse transcriptase) is a multifunctional polymerase responsible for reverse transcription of the HIV genome, including DNA replication on both RNA and DNA templates. During reverse transcription in vivo, HIV-1 RT replicates through various secondary structures on RNA and single-stranded DNA (ssDNA) templates without the need for a nucleic acid unwinding protein, such as a helicase. In order to understand the mechanism of polymerization through secondary structures, we investigated the DNA polymerization activity of HIV-1 RT on long ssDNA templates using a multiplexed single-molecule DNA flow-stretching assay. We observed that HIV-1 RT performs fast primer extension DNA synthesis on single-stranded regions of DNA (18.7 nt/s) and switches its activity to slow strand displacement synthesis at DNA hairpin locations (2.3 nt/s). Furthermore, we found that the rate of strand displacement synthesis is dependent on the GC content in hairpin stems and template stretching force. This indicates that the strand displacement synthesis occurs through a mechanism that is neither completely active nor passive: that is, the opening of the DNA hairpin is driven by a combination of free energy released during dNTP (deoxyribonucleotide triphosphate) hydrolysis and thermal fraying of base pairs. Our experimental observations provide new insight into the interchanging modes of DNA replication by HIV-1 RT on long ssDNA templates.
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49
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Probing conformational changes of human DNA polymerase lambda using mass spectrometry-based protein footprinting. J Mol Biol 2009; 390:368-79. [PMID: 19467241 DOI: 10.1016/j.jmb.2009.05.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 05/12/2009] [Accepted: 05/20/2009] [Indexed: 11/24/2022]
Abstract
Crystallographic studies of the C-terminal DNA polymerase-beta-like domain of full-length human DNA polymerase lambda (fPollambda) suggested that the catalytic cycle might not involve a large protein domain rearrangement as observed with several replicative DNA polymerases and DNA polymerase beta. To examine solution-phase protein conformational changes in fPollambda, which also contains a breast cancer susceptibility gene 1 C-terminal domain and a proline-rich domain at its N-terminus, we used a mass spectrometry-based protein footprinting approach. In parallel experiments, surface accessibility maps for Arg residues were compared for the free fPollambda versus the binary complex of enzyme*gapped DNA and the ternary complex of enzyme*gapped DNA*dNTP (2'-deoxynucleotide triphosphate). These experiments suggested that fPollambda does not undergo major conformational changes during the catalysis in the solution phase. Furthermore, the mass spectrometry-based protein footprinting experiments revealed that active site residue R386 was shielded from the surface only in the presence of both a gapped DNA substrate and an incoming nucleotide. Site-directed mutagenesis and pre-steady-state kinetic studies confirmed the importance of R386 for the enzyme activity and indicated the key role for its guanidino group in stabilizing the negative charges of an incoming nucleotide and the leaving pyrophosphate product. We suggest that such interactions could be shared by and important for catalytic functions of other DNA polymerases.
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50
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Mou T, Masada N, Cooper DMF, Sprang SR. Structural basis for inhibition of mammalian adenylyl cyclase by calcium. Biochemistry 2009; 48:3387-97. [PMID: 19243146 PMCID: PMC2680196 DOI: 10.1021/bi802122k] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Type V and VI mammalian adenylyl cyclases (AC5, AC6) are inhibited by Ca(2+) at both sub- and supramicromolar concentration. This inhibition may provide feedback in situations where cAMP promotes opening of Ca(2+) channels, allowing fine control of cardiac contraction and rhythmicity in cardiac tissue where AC5 and AC6 predominate. Ca(2+) inhibits the soluble AC core composed of the C1 domain of AC5 (VC1) and the C2 domain of AC2 (IIC2). As observed for holo-AC5, inhibition is biphasic, showing "high-affinity" (K(i) = approximately 0.4 microM) and "low-affinity" (K(i) = approximately 100 microM) modes of inhibition. At micromolar concentration, Ca(2+) inhibition is nonexclusive with respect to pyrophosphate (PP(i)), a noncompetitive inhibitor with respect to ATP, but at >100 microM Ca(2+), inhibition appears to be exclusive with respect to PP(i). The 3.0 A resolution structure of Galphas.GTPgammaS/forskolin-activated VC1:IIC2 crystals soaked in the presence of ATPalphaS and 8 microM free Ca(2+) contains a single, loosely coordinated metal ion. ATP soaked into VC1:IIC2 crystals in the presence of 1.5 mM Ca(2+) is not cyclized, and two calcium ions are observed in the 2.9 A resolution structure of the complex. In both of the latter complexes VC1:IIC2 adopts the "open", catalytically inactive conformation characteristic of the apoenzyme, in contrast to the "closed", active conformation seen in the presence of ATP analogues and Mg(2+) or Mn(2+). Structures of the pyrophosphate (PP(i)) complex with 10 mM Mg(2+) (2.8 A) or 2 mM Ca(2+) (2.7 A) also adopt the open conformation, indicating that the closed to open transition occurs after cAMP release. In the latter complexes, Ca(2+) and Mg(2+) bind only to the high-affinity "B" metal site associated with substrate/product stabilization. Ca(2+) thus stabilizes the inactive conformation in both ATP- and PP(i)-bound states.
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Affiliation(s)
- Tung—Chung Mou
- Center for Biomolecular Structure and Dynamics and the Division of Biological Sciences, The University of Montana, Missoula, MT 59812
| | - Nanako Masada
- Department of Pharmacology, University of Cambridge, Cambridge, CB2 1PD, United Kingdom
| | - Dermot M. F. Cooper
- Center for Biomolecular Structure and Dynamics and the Division of Biological Sciences, The University of Montana, Missoula, MT 59812
| | - Stephen R. Sprang
- Center for Biomolecular Structure and Dynamics and the Division of Biological Sciences, The University of Montana, Missoula, MT 59812
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