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For: Li CL, Hor LI, Chang ZF, Tsai LC, Yang WZ, Yuan HS. DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site. EMBO J 2003;22:4014-25. [PMID: 12881435 PMCID: PMC169050 DOI: 10.1093/emboj/cdg377] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
Number Cited by Other Article(s)
1
Nikkel DJ, Kaur R, Wetmore SD. How Can One Metal Power Nucleic Acid Phosphodiester Bond Cleavage by a Nuclease? Multiscale Computational Studies Highlight a Diverse Mechanistic Landscape. J Phys Chem B 2025;129:3-18. [PMID: 39720842 DOI: 10.1021/acs.jpcb.4c05875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2024]
2
Kaur R, Nikkel DJ, Wetmore SD. Mechanism of Nucleic Acid Phosphodiester Bond Cleavage by Human Endonuclease V: MD and QM/MM Calculations Reveal a Versatile Metal Dependence. J Phys Chem B 2024;128:9455-9469. [PMID: 39359137 DOI: 10.1021/acs.jpcb.4c05846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
3
Chang C, Zhou G, Gao Y. Observing one-divalent-metal-ion-dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo. eLife 2024;13:RP99960. [PMID: 39141555 PMCID: PMC11325842 DOI: 10.7554/elife.99960] [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: 08/16/2024]  Open
4
Chang C, Zhou G, Gao Y. Observing one-divalent-metal-ion dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592236. [PMID: 38746211 PMCID: PMC11092635 DOI: 10.1101/2024.05.02.592236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
5
Kaur R, Frederickson A, Wetmore SD. Elucidation of the catalytic mechanism of a single-metal dependent homing endonuclease using QM and QM/MM approaches: the case study of I-PpoI. Phys Chem Chem Phys 2024;26:8919-8931. [PMID: 38426850 DOI: 10.1039/d3cp06201e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
6
Kaur R, Wetmore SD. Is Metal Stabilization of the Leaving Group Required or Can Lysine Facilitate Phosphodiester Bond Cleavage in Nucleic Acids? A Computational Study of EndoV. J Chem Inf Model 2024;64:944-959. [PMID: 38253321 DOI: 10.1021/acs.jcim.3c01775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
7
Maghsoud Y, Jayasinghe-Arachchige VM, Kumari P, Cisneros GA, Liu J. Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects. J Chem Inf Model 2023;63:6834-6850. [PMID: 37877218 DOI: 10.1021/acs.jcim.3c01284] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
8
Antao AM, Karapurkar JK, Lee DR, Kim KS, Ramakrishna S. Disease modeling and stem cell immunoengineering in regenerative medicine using CRISPR/Cas9 systems. Comput Struct Biotechnol J 2020;18:3649-3665. [PMID: 33304462 PMCID: PMC7710510 DOI: 10.1016/j.csbj.2020.11.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022]  Open
9
Wu CC, Lin JL, Yuan HS. Structures, Mechanisms, and Functions of His-Me Finger Nucleases. Trends Biochem Sci 2020;45:935-946. [DOI: 10.1016/j.tibs.2020.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/30/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
10
Park KH, Yoon SM, Song HN, Yang JH, Ryu SE, Woo EJ. Crystal structure of the mouse endonuclease G. Biochem Biophys Res Commun 2020;526:35-40. [PMID: 32192768 DOI: 10.1016/j.bbrc.2020.03.060] [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: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
11
Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L, Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y. Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States. Mol Cell 2019;76:938-952.e5. [PMID: 31668930 PMCID: PMC6934045 DOI: 10.1016/j.molcel.2019.09.025] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/13/2019] [Accepted: 09/20/2019] [Indexed: 12/21/2022]
12
Chu CH, Yen CY, Chen BW, Lin MG, Wang LH, Tang KZ, Hsiao CD, Sun YJ. Crystal structures of HpSoj-DNA complexes and the nucleoid-adaptor complex formation in chromosome segregation. Nucleic Acids Res 2019;47:2113-2129. [PMID: 30544248 PMCID: PMC6393308 DOI: 10.1093/nar/gky1251] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 08/10/2018] [Accepted: 12/11/2018] [Indexed: 01/05/2023]  Open
13
Pseudomonas aeruginosa Requires the DNA-Specific Endonuclease EndA To Degrade Extracellular Genomic DNA To Disperse from the Biofilm. J Bacteriol 2019;201:JB.00059-19. [PMID: 30988033 DOI: 10.1128/jb.00059-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/08/2019] [Indexed: 01/16/2023]  Open
14
Genna V, Marcia M, De Vivo M. A Transient and Flexible Cation-π Interaction Promotes Hydrolysis of Nucleic Acids in DNA and RNA Nucleases. J Am Chem Soc 2019;141:10770-10776. [PMID: 31251587 DOI: 10.1021/jacs.9b03663] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
15
Yoon H, Zhao LN, Warshel A. Exploring the Catalytic Mechanism of Cas9 Using Information Inferred from Endonuclease VII. ACS Catal 2019;9:1329-1336. [PMID: 34046245 PMCID: PMC8153514 DOI: 10.1021/acscatal.8b04324] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
16
New Nuclease from Extremely Psychrophilic Microorganism Psychromonas ingrahamii 37: Identification and Characterization. Mol Biotechnol 2018;61:122-133. [PMID: 30539415 DOI: 10.1007/s12033-018-0142-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
17
Binnenkade L, Kreienbaum M, Thormann KM. Characterization of ExeM, an Extracellular Nuclease of Shewanella oneidensis MR-1. Front Microbiol 2018;9:1761. [PMID: 30123203 PMCID: PMC6085458 DOI: 10.3389/fmicb.2018.01761] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/13/2018] [Indexed: 01/08/2023]  Open
18
Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM. Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 2018;557:503-509. [PMID: 29769716 DOI: 10.1038/s41586-018-0124-0] [Citation(s) in RCA: 343] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 04/09/2018] [Indexed: 01/25/2023]
19
Anton T, Karg E, Bultmann S. Applications of the CRISPR/Cas system beyond gene editing. Biol Methods Protoc 2018;3:bpy002. [PMID: 32161796 PMCID: PMC6994046 DOI: 10.1093/biomethods/bpy002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/28/2018] [Accepted: 04/03/2018] [Indexed: 12/26/2022]  Open
20
Baslé A, Hewitt L, Koh A, Lamb HK, Thompson P, Burgess JG, Hall MJ, Hawkins AR, Murray H, Lewis RJ. Crystal structure of NucB, a biofilm-degrading endonuclease. Nucleic Acids Res 2018;46:473-484. [PMID: 29165717 PMCID: PMC5758888 DOI: 10.1093/nar/gkx1170] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/13/2017] [Indexed: 01/23/2023]  Open
21
Wang Y, Jia P, Sharif R, Li Z, Li Y, Chen P. High-Level Production of DNA-Specific Endonuclease AsEndI with Synonymous Codon and its Potential Utilization for Removing DNA Contamination. Appl Biochem Biotechnol 2017;185:641-654. [PMID: 29250754 DOI: 10.1007/s12010-017-2672-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/30/2017] [Indexed: 12/19/2022]
22
Jablonska J, Matelska D, Steczkiewicz K, Ginalski K. Systematic classification of the His-Me finger superfamily. Nucleic Acids Res 2017;45:11479-11494. [PMID: 29040665 PMCID: PMC5714182 DOI: 10.1093/nar/gkx924] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/29/2017] [Indexed: 02/06/2023]  Open
23
Oliva C, Sánchez-Murcia PA, Rico E, Bravo A, Menéndez M, Gago F, Jiménez-Ruiz A. Structure-based domain assignment in Leishmania infantum EndoG: characterization of a pH-dependent regulatory switch and a C-terminal extension that largely dictates DNA substrate preferences. Nucleic Acids Res 2017;45:9030-9045. [PMID: 28911117 PMCID: PMC5587815 DOI: 10.1093/nar/gkx629] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/11/2017] [Indexed: 11/28/2022]  Open
24
The chemistry of Cas9 and its CRISPR colleagues. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0078] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
25
Flenker KS, Burghardt EL, Dutta N, Burns WJ, Grover JM, Kenkel EJ, Weaver TM, Mills J, Kim H, Huang L, Owczarzy R, Musselman CA, Behlke MA, Ford B, McNamara JO. Rapid Detection of Urinary Tract Infections via Bacterial Nuclease Activity. Mol Ther 2017;25:1353-1362. [PMID: 28391960 DOI: 10.1016/j.ymthe.2017.03.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 12/27/2022]  Open
26
Zhang L, Xu D, Huang Y, Zhu X, Rui M, Wan T, Zheng X, Shen Y, Chen X, Ma K, Gong Y. Structural and functional characterization of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease. Sci Rep 2017;7:42542. [PMID: 28211904 PMCID: PMC5304195 DOI: 10.1038/srep42542] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/10/2017] [Indexed: 01/26/2023]  Open
27
Batebi H, Imhof P. Phosphodiester hydrolysis computed for cluster models of enzymatic active sites. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2020-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
28
Lin JLJ, Wu CC, Yang WZ, Yuan HS. Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer. Nucleic Acids Res 2016;44:10480-10490. [PMID: 27738134 PMCID: PMC5137453 DOI: 10.1093/nar/gkw931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 01/20/2023]  Open
29
Moon AF, Krahn JM, Lu X, Cuneo MJ, Pedersen LC. Structural characterization of the virulence factor Sda1 nuclease from Streptococcus pyogenes. Nucleic Acids Res 2016;44:3946-57. [PMID: 26969731 PMCID: PMC4856990 DOI: 10.1093/nar/gkw143] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/25/2016] [Indexed: 11/22/2022]  Open
30
Machnicka MA, Kaminska KH, Dunin-Horkawicz S, Bujnicki JM. Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes. BMC Bioinformatics 2015;16:336. [PMID: 26493560 PMCID: PMC4619093 DOI: 10.1186/s12859-015-0773-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/13/2015] [Indexed: 01/09/2023]  Open
31
de Buhr N, Stehr M, Neumann A, Naim HY, Valentin-Weigand P, von Köckritz-Blickwede M, Baums CG. Identification of a novel DNase of Streptococcus suis (EndAsuis) important for neutrophil extracellular trap degradation during exponential growth. MICROBIOLOGY-SGM 2015;161:838-50. [PMID: 25667008 DOI: 10.1099/mic.0.000040] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 01/27/2015] [Indexed: 12/25/2022]
32
Benrezkallah D, Dauchez M, Krallafa A. Molecular dynamics of the salt dependence of a cold-adapted enzyme: endonuclease I. J Biomol Struct Dyn 2015;33:2511-21. [DOI: 10.1080/07391102.2014.1002007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
33
Moon AF, Gaudu P, Pedersen LC. Structural characterization of the virulence factor nuclease A from Streptococcus agalactiae. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014;70:2937-49. [PMID: 25372684 PMCID: PMC4220975 DOI: 10.1107/s1399004714019725] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/01/2014] [Indexed: 12/28/2022]
34
Németh E, Körtvélyesi T, Thulstrup PW, Christensen HEM, Kožíšek M, Nagata K, Czene A, Gyurcsik B. Fine tuning of the catalytic activity of colicin E7 nuclease domain by systematic N-terminal mutations. Protein Sci 2014;23:1113-22. [PMID: 24895333 DOI: 10.1002/pro.2497] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/20/2014] [Accepted: 05/29/2014] [Indexed: 11/11/2022]
35
Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 2014;156:935-49. [PMID: 24529477 PMCID: PMC4139937 DOI: 10.1016/j.cell.2014.02.001] [Citation(s) in RCA: 1351] [Impact Index Per Article: 122.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 02/02/2014] [Accepted: 02/02/2014] [Indexed: 12/26/2022]
36
Das A, Chakrabarti J, Ghosh M. Thermodynamics of interfacial changes in a protein–protein complex. ACTA ACUST UNITED AC 2014;10:437-45. [DOI: 10.1039/c3mb70249a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
37
Czene A, Tóth E, Németh E, Otten H, Poulsen JCN, Christensen HEM, Rulíšek L, Nagata K, Larsen S, Gyurcsik B. A new insight into the zinc-dependent DNA-cleavage by the colicin E7 nuclease: a crystallographic and computational study. Metallomics 2014;6:2090-9. [DOI: 10.1039/c4mt00195h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
38
Xu SY, Kuzin AP, Seetharaman J, Gutjahr A, Chan SH, Chen Y, Xiao R, Acton TB, Montelione GT, Tong L. Structure determination and biochemical characterization of a putative HNH endonuclease from Geobacter metallireducens GS-15. PLoS One 2013;8:e72114. [PMID: 24039739 PMCID: PMC3765158 DOI: 10.1371/journal.pone.0072114] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 07/12/2013] [Indexed: 01/07/2023]  Open
39
Lambert C, Sockett RE. Nucleases in Bdellovibrio bacteriovorus contribute towards efficient self-biofilm formation and eradication of preformed prey biofilms. FEMS Microbiol Lett 2013;340:109-16. [PMID: 23297829 PMCID: PMC3593177 DOI: 10.1111/1574-6968.12075] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/02/2013] [Indexed: 11/30/2022]  Open
40
Tsutakawa SE, Shin DS, Mol CD, Izumi T, Arvai AS, Mantha AK, Szczesny B, Ivanov IN, Hosfield DJ, Maiti B, Pique ME, Frankel KA, Hitomi K, Cunningham RP, Mitra S, Tainer JA. Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. J Biol Chem 2013;288:8445-8455. [PMID: 23355472 DOI: 10.1074/jbc.m112.422774] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]  Open
41
Czene A, Németh E, Zóka IG, Jakab-Simon NI, Körtvélyesi T, Nagata K, Christensen HEM, Gyurcsik B. The role of the N-terminal loop in the function of the colicin E7 nuclease domain. J Biol Inorg Chem 2013;18:309-21. [DOI: 10.1007/s00775-013-0975-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/31/2012] [Indexed: 01/10/2023]
42
Dickey TH, McKercher MA, Wuttke DS. Nonspecific recognition is achieved in Pot1pC through the use of multiple binding modes. Structure 2013;21:121-132. [PMID: 23201273 PMCID: PMC3545015 DOI: 10.1016/j.str.2012.10.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 10/26/2012] [Accepted: 10/26/2012] [Indexed: 01/07/2023]
43
Zhukhlistova NE, Balaev VV, Lyashenko AV, Lashkov AA. Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids. CRYSTALLOGR REP+ 2012. [DOI: 10.1134/s1063774512030236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
44
Functional specificity of extracellular nucleases of Shewanella oneidensis MR-1. Appl Environ Microbiol 2012;78:4400-11. [PMID: 22492434 DOI: 10.1128/aem.07895-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
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Lin JLJ, Nakagawa A, Lin CL, Hsiao YY, Yang WZ, Wang YT, Doudeva LG, Skeen-Gaar RR, Xue D, Yuan HS. Structural insights into apoptotic DNA degradation by CED-3 protease suppressor-6 (CPS-6) from Caenorhabditis elegans. J Biol Chem 2012;287:7110-20. [PMID: 22223640 PMCID: PMC3293555 DOI: 10.1074/jbc.m111.316075] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 12/30/2011] [Indexed: 11/06/2022]  Open
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Midon M, Gimadutdinow O, Meiss G, Friedhoff P, Pingoud A. Chemical Rescue of Active Site Mutants of S. pneumoniae Surface Endonuclease EndA and Other Nucleases of the HNH Family by Imidazole. Chembiochem 2012;13:713-21. [DOI: 10.1002/cbic.201100775] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Indexed: 11/08/2022]
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The binding process of a nonspecific enzyme with DNA. Biophys J 2011;101:1139-47. [PMID: 21889451 DOI: 10.1016/j.bpj.2011.07.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 06/20/2011] [Accepted: 07/05/2011] [Indexed: 11/22/2022]  Open
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Sharma A, Jenkins KR, Héroux A, Bowman GD. Crystal structure of the chromodomain helicase DNA-binding protein 1 (Chd1) DNA-binding domain in complex with DNA. J Biol Chem 2011;286:42099-42104. [PMID: 22033927 PMCID: PMC3234930 DOI: 10.1074/jbc.c111.294462] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/20/2011] [Indexed: 11/06/2022]  Open
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Bueren-Calabuig JA, Coderch C, Rico E, Jiménez-Ruiz A, Gago F. Mechanistic insight into the catalytic activity of ββα-metallonucleases from computer simulations: Vibrio vulnificus periplasmic nuclease as a test case. Chembiochem 2011;12:2615-22. [PMID: 22114054 DOI: 10.1002/cbic.201100485] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Indexed: 11/08/2022]
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Korczynska JE, Turkenburg JP, Taylor EJ. The structural characterization of a prophage-encoded extracellular DNase from Streptococcus pyogenes. Nucleic Acids Res 2011;40:928-38. [PMID: 21948797 PMCID: PMC3258162 DOI: 10.1093/nar/gkr789] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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