Role Of The Unstructured N-Terminal Domain Of The Human Apurinic/Apyrimidinic Endonuclease 1 (hape1) In The Modulation Of Its Interaction With Nucleic Acids And Nucleophosmin (npm1) (496 views)
Biochem J (ISSN: 0264-6021, 1470-8728electronic, 0264-6021linking), 2013; 452(3): 545-557.
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Paper type: Journal Article,
Impact factor: 4.779, 5-year impact factor: 4.95
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84878400065&partnerID=40&md5=ac301c35524b260c492ada6cd017035a
Keywords: Apurinic Apyrimidinic Endonuclease 1 (ape1), Nucleophosmin (npm1), Phylogenesis, Protein-Dna Interaction, Protein-Protein Interaction, Dna (apurinic Or Apyrimidinic Site) Lyase, Acetylation, Article, Binding Affinity, Dna Protein Complex, Dna Sequence, Dna Strand, Human, Human Cell, In Vitro Study, Nonhuman, Priority Journal, Protein Binding, Protein Conformation, Protein Cross Linking, Protein Protein Interaction, Protein Secondary Structure, Protein Stability, Signal Transduction, Stereospecificity, Ubiquitination, Amino Acid Sequence, Animals, Dna Damage, Dna-(apurinic Or Apyrimidinic Site) Lyase, Hela Cells, Molecular Sequence Data, Nuclear Proteins, Nucleic Acids, Sequence Homology, Zebrafish, Eukaryota,
Affiliations:
*** IBB - CNR ***
Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
Department of Pharmacy, CIRPEB (Centro Interuniversitario di Ricerca Sui Peptidi Bioattivi), University of Naples 'Federico II', 80134 Naples, Italy
Institute of Biostructures and Bioimaging CNR, 80134 Naples, Italy
References:
Fung, H., Demple, B., A vital role for Ape1/Ref1 protein in repairing spontaneous DNA damage in human cells (2005) Molecular Cell, 17 (3), pp. 463-470. , DOI 10. 1016/j. molcel. 2004. 12. 029, PII S109727650501039
Bhakat, K. K., Izumi, T., Yang, S. -H., Hazra, T. K., Mitra, S., Role of acetylated human AP-endonuclease (APE1/Ref-1) in regulation of the parathyroid hormone gene (2003) EMBO Journal, 22 (23), pp. 6299-6309. , DOI 10. 1093/emboj/cdg595
Vascotto, C., Cesaratto, L., Zeef, L. A., Deganuto, M., D'Ambrosio, C., Scaloni, A., Romanello, M., Delneri, D., Genome-wide analysis and proteomic studies reveal APE1/Ref-1 multifunctional role in mammalian cells (2009) Proteomics, 9, pp. 1058-1074
Tell, G., Damante, G., Caldwell, D., Kelley, M. R., The intracellular localization of APE1/Ref-1: More than a passive phenomenon? (2005) Antioxidants and Redox Signaling, 7 (3-4), pp. 367-384. , DOI 10. 1089/ars. 2005. 7. 367
Xanthoudakis, S., Miao, G. G., Curran, T., The redox and DNA-repair activities of Ref-1 are encoded by nonoverlapping domains (1994) Proceedings of the National Academy of Sciences of the United States of America, 91 (1), pp. 23-27. , DOI 10. 1073/pnas. 91. 1. 23
Erzberger, J. P., Barsky, D., Scharer, O. D., Colvin, M. E., Wilson III, D. M., Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases (1998) Nucleic Acids Research, 26 (11), pp. 2771-2778. , DOI 10. 1093/nar/26. 11. 2771
Fan, J., Matsumoto, Y., Wilson III, D. M., Nucleotide sequence and DNA secondary structure, as well as replication protein A, modulate the single-stranded abasic endonuclease activity of APE1 (2006) Journal of Biological Chemistry, 281 (7), pp. 3889-3898. , http: //www. jbc. org/cgi/reprint/281/7/3889, DOI 10. 1074/jbc. M511004200
Marenstein, D. R., Wilson III, D. M., Teebor, G. W., Human AP endonuclease (APE1) demonstrates endonucleolytic activity against AP sites in single-stranded DNA (2004) DNA Repair, 3 (5), pp. 527-533. , DOI 10. 1016/j. dnarep. 2004. 01. 010, PII S1568786404000291
Sengupta, S., Mantha, A. K., Mitra, S., Bhakat, K. K., Human AP endonuclease (APE1/Ref-1) and its acetylation regulate YB-1-p300 recruitment and RNA polymerase II loading in the drug-induced activation of multidrug resistance gene MDR1 (2011) Oncogene, 30, pp. 482-493
Tell, G., Wilson III, D. M., Lee, C. H., Intrusion of a DNA repair protein in the RNome world: Is this the beginning of a new era? (2010) Mol. Cell. Biol., 30, pp. 366-371
Beloglazova, N. G., Kirpota, O. O., Starostin, K. V., Ishchenko, A. A., Yamkovoy, V. I., Zharkov, D. O., Douglas, K. T., Nevinsky, G. A., Thermodynamic, kinetic and structural basis for recognition and repair of abasic sites in DNA by apurinic/apyrimidinic endocuclease from human placenta (2004) Nucleic Acids Research, 32 (17), pp. 5134-5146. , DOI 10. 1093/nar/gkh846
Vascotto, C., Fantini, D., Romanello, M., Cesaratto, L., Deganuto, M., Leonardi, A., Radicella, J. P., Scaloni, A., APE1/Ref-1 interacts with NPM1 within nucleoli and plays a role in the rRNA quality control process (2009) Mol. Cell. Biol., 29, pp. 1834-1854
Barnes, T., Kim, W. C., Mantha, A. K., Kim, S. E., Izumi, T., Mitra, S., Lee, C. H., Identification of apurinic/apyrimidinic endonuclease 1 (APE1) as the endoribonuclease that cleaves c-myc mRNA (2009) Nucleic Acids Res., 37, pp. 3946-3958
Gorman, M. A., Morera, S., Rothwell, D. G., De La, F. E., Mol, C. D., Tainer, J. A., Hickson, I. D., Freemont, P. S., The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites (1997) EMBO Journal, 16 (21), pp. 6548-6558. , DOI 10. 1093/emboj/16. 21. 6548
Beernink, P. T., Segelke, B. W., Hadi, M. Z., Erzberger, J. P., Wilson III, D. M., Rupp, B., Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: Implications for the catalytic mechanism (2001) Journal of Molecular Biology, 307 (4), pp. 1023-1034. , DOI 10. 1006/jmbi. 2001. 4529
Strauss, P. R., Holt, C. M., Domain mapping of human apurinic/apyrimidinic endonuclease: Structural and functional evidence for a disordered amino terminus and a tight globular carboxyl domain (1998) Journal of Biological Chemistry, 273 (23), pp. 14435-14441. , DOI 10. 1074/jbc. 273. 23. 14435
Fantini, D., Vascotto, C., Marasco, D., D'Ambrosio, C., Romanello, M., Vitagliano, L., Pedone, C., Quadrifoglio, F., Critical lysine residues within the overlooked N-terminal domain of human APE1 regulate its biological functions (2010) Nucleic Acids Res., 38, pp. 8239-8256
Fan, Z., Beresford, P. J., Zhang, D., Xu, Z., Novina, C. D., Yoshida, A., Pommier, Y., Lieberman, J., Cleaving the oxidative repair protein Ape I enhances cell death mediated by granzyme A (2003) Nature Immunology, 4 (2), pp. 145-153. , DOI 10. 1038/ni885
Busso, C. S., Iwakuma, T., Izumi, T., Ubiquitination of mammalian AP endonuclease (APE1) regulated by the p53-MDM2 signaling pathway (2009) Oncogene, 28, pp. 1616-1625
Meisenberg, C., Tait, P. S., Dianova, I. I., Wright, K., Edelmann, M. J., Ternette, N., Tasaki, T., Dianov, G. L., Ubiquitin ligase UBR3 regulates cellular levels of the essential DNA repair protein APE1 and is required for genome stability (2011) Nucleic Acids Res., 40, pp. 701-711
Lirussi, L., Antoniali, G., Vascotto, C., D'Ambrosio, C., Poletto, M., Romanello, M., Marasco, D., Bhakat, K. K., Nucleolar accumulation of APE1 depends on charged lysine residues that undergo acetylation upon genotoxic stress and modulate its BER activity in cells (2012) Mol. Biol. Cell, 23, pp. 4079-4096
Hedge, M. L., Izumi, T., Mitra, S., Oxidized base damage and single-strand break repairin mammalian genomes: Role of disordered regions and posttranslational modifications in early enzymes (2012) Prog. Mol. Biol. Transl. Sci., 110, pp. 123-153
Tell, G., Fantini, D., Quadrifoglio, F., Understanding different functions of mammalian AP endonuclease (APE1) as a promising tool for cancer treatment (2010) Cell. Mol. Life Sci., 67, pp. 3589-3608
Sch gger, H., Tricine-SDS-PAGE (2006) Nat. Protoc., 1, pp. 16-22
Nguyen, L. H., Barsky, D., Erzberger, J. P., Wilson III, D. M., Mapping the protein-DNA interface and the metal-binding site of the major human apurinic/apyrimidinic endonuclease (2000) J. Mol. Biol., 298, pp. 447-459
Berquist, B. R., McNeill, D. R., Wilson III, D. M., Characterization of abasic endonuclease activity of human Ape1 on alternative substrates, as well as effects of ATP and sequence context on AP site incision (2008) J. Mol. Biol., 379, pp. 17-27
Mol, C. D., Izumi, T., Mitra, S., Talner, J. A., DNA-bound structures and mutants reveal abasic DNA binding by APE1 DNA repair and coordination (2000) Nature, 403 (6768), pp. 451-456. , DOI 10. 1038/35000249
Katsamba, P. S., Park, S., Laird-Offringa, I. A., Kinetic studies of RNA-protein interactions using surface plasmon resonance (2002) Methods, 26 (2), pp. 95-104. , DOI 10. 1016/S1046-2023 (02) 00012-9, PII S1046202302000129
Law, M. J., Rice, A. J., Lin, P., Laird-Offringa, I. A., The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA (2006) RNA, 12 (7), pp. 1168-1178. , http: //www. rnajournal. org/cgi/reprint/12/7/1168, DOI 10. 1261/rna. 75206
Izumi, T., Henner, W. D., Mitra, S., Negative regulation of the major human AP-endonuclease, a multifunctional protein (1996) Biochemistry, 35 (47), pp. 14679-14683. , DOI 10. 1021/bi961995u
Kim, W. C., Berquist, B. R., Chohan, M., Uy, C., Wilson III, D. M., Lee, C. H., Characterization of the endoribonuclease active site of human apurinic/apyrimidinic endonuclease 1 (2011) J. Mol. Biol., 411, pp. 960-971
Vuzman, D., Levy, Y., Intrinsically disordered regions as affinity tuners in protein-DNA interactions (2012) Mol. Biosyst., 8, pp. 47-57
Masuda, Y., Bennett, R. A. O., Demple, B., Dynamics of the interaction of human apurinic endonuclease (Ape1) with its substrate and product (1998) Journal of Biological Chemistry, 273 (46), pp. 30352-30359. , DOI 10. 1074/jbc. 273. 46. 30352
Yung, B. Y., Chan, P. K., Identification and characterization of a hexameric form of nucleolar phosphoprotein B23 (1987) Biochim. Biophys. Acta, 925, pp. 74-82
Vascotto, C., Bisetto, E., Li, M., Zeef, L. A., D'Ambrosio, C., Domenis, R., Comelli, M., Altieri, F., Knock-in reconstitution studies reveal an unexpected role of Cys 65 in regulating APE1/Ref-1 subcellular trafficking and function (2011) Mol. Biol. Cell, 22, pp. 3887-3901
Jackson, E. B., Theriot, C. A., Chattopadhyay, R., Mitra, S., Izumi, T., Analysis of nuclear transport signals in the human apurinic/apyrimidinic endonuclease (APE1/Ref1) (2005) Nucleic Acids Research, 33 (10), pp. 3303-3312. , DOI 10. 1093/nar/gki641
Weibrecht, I., Leuchowius, K. J., Clausson, C. M., Conze, T., Jarvius, M., Howell, W. M., Kamali-Moghaddam, M., S derberg, O., Proximity ligation assays: A recent addition to the proteomics toolbox (2010) Expert Rev. Proteomics, 7, pp. 401-409
Yoshida, A., Urasaki, Y., Waltham, M., Bergman, A. -C., Pourquier, P., Rothwell, D. G., Inuzuka, M., Pommier, Y., Human apurinic/apyrimidinic endonuclease (Ape1) and its N-terminal truncated form (AN34) are involved in DNA fragmentation during apoptosis (2003) Journal of Biological Chemistry, 278 (39), pp. 37768-37776. , DOI 10. 1074/jbc. M304914200
Guo, Y., Chen, J., Zhao, T., Fan, Z., Granzyme K degrades the redox/DNA repair enzyme Ape1 to trigger oxidative stress of target cells leading to cytotoxicity (2008) Mol. Immunol., 45, pp. 2225-2235
Vidal, A. E., Boiteux, S., Hickson, I. D., Radicella, J. P., XRCC1 coordinates the initial and late stages of DNA abasic site repair through protein-protein interactions (2001) EMBO Journal, 20 (22), pp. 6530-6539. , DOI 10. 1093/emboj/20. 22. 6530
Yu, E., Gaucher, S. P., Hadi, M. Z., Probing conformational changes in Ape1 during the progression of base excision repair (2010) Biochemistry, 49, pp. 3786-3796
Wong, H. -K., Muftuoglu, M., Beck, G., Imam, S. Z., Bohr, V. A., Wilson III, D. M., Cockayne syndrome B protein stimulates apurinic endonuclease 1 activity and protects against agents that introduce base excision repair intermediates (2007) Nucleic Acids Research, 35 (12), pp. 4103-4113. , DOI 10. 1093/nar/gkm404
Georgiadis, M. M., Luo, M., Gaur, R. K., Delaplane, S., Li, X., Kelley, M. R., Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease (2008) Mutat. Res., 643, pp. 54-63
Yamamori, T., DeRicco, J., Naqvi, A., Hoffman, T. A., Mattagajasingh, I., Kasuno, K., Jung, S. B., Irani, K., SIRT1 deacetylates APE1 and regulates cellular base excision repair (2010) Nucleic Acids Res., 38, pp. 832-845
Bhakat, K.K., Izumi, T., Yang, S.-H., Hazra, T.K., Mitra, S., Role of acetylated human AP-endonuclease (APE1/Ref-1) in regulation of the parathyroid hormone gene (2003) EMBO Journal, 22 (23), pp. 6299-6309. , DOI 10.1093/emboj/cdg595
Erzberger, J.P., Barsky, D., Scharer, O.D., Colvin, M.E., Wilson III, D.M., Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases (1998) Nucleic Acids Research, 26 (11), pp. 2771-2778. , DOI 10.1093/nar/26.11.2771
Marenstein, D.R., Wilson III, D.M., Teebor, G.W., Human AP endonuclease (APE1) demonstrates endonucleolytic activity against AP sites in single-stranded DNA (2004) DNA Repair, 3 (5), pp. 527-533. , DOI 10.1016/j.dnarep.2004.01.010, PII S1568786404000291
Beloglazova, N.G., Kirpota, O.O., Starostin, K.V., Ishchenko, A.A., Yamkovoy, V.I., Zharkov, D.O., Douglas, K.T., Nevinsky, G.A., Thermodynamic, kinetic and structural basis for recognition and repair of abasic sites in DNA by apurinic/apyrimidinic endocuclease from human placenta (2004) Nucleic Acids Research, 32 (17), pp. 5134-5146. , DOI 10.1093/nar/gkh846
Gorman, M.A., Morera, S., Rothwell, D.G., De La, F.E., Mol, C.D., Tainer, J.A., Hickson, I.D., Freemont, P.S., The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites (1997) EMBO Journal, 16 (21), pp. 6548-6558. , DOI 10.1093/emboj/16.21.6548
Beernink, P.T., Segelke, B.W., Hadi, M.Z., Erzberger, J.P., Wilson III, D.M., Rupp, B., Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: Implications for the catalytic mechanism (2001) Journal of Molecular Biology, 307 (4), pp. 1023-1034. , DOI 10.1006/jmbi.2001.4529
Strauss, P.R., Holt, C.M., Domain mapping of human apurinic/apyrimidinic endonuclease: Structural and functional evidence for a disordered amino terminus and a tight globular carboxyl domain (1998) Journal of Biological Chemistry, 273 (23), pp. 14435-14441. , DOI 10.1074/jbc.273.23.14435
Busso, C.S., Iwakuma, T., Izumi, T., Ubiquitination of mammalian AP endonuclease (APE1) regulated by the p53-MDM2 signaling pathway (2009) Oncogene, 28, pp. 1616-1625
Hedge, M.L., Izumi, T., Mitra, S., Oxidized base damage and single-strand break repairin mammalian genomes: Role of disordered regions and posttranslational modifications in early enzymes (2012) Prog. Mol. Biol. Transl. Sci., 110, pp. 123-153
Schägger, H., Tricine-SDS-PAGE (2006) Nat. Protoc., 1, pp. 16-22
Nguyen, L.H., Barsky, D., Erzberger, J.P., Wilson III, D.M., Mapping the protein-DNA interface and the metal-binding site of the major human apurinic/apyrimidinic endonuclease (2000) J. Mol. Biol., 298, pp. 447-459
Berquist, B.R., McNeill, D.R., Wilson III, D.M., Characterization of abasic endonuclease activity of human Ape1 on alternative substrates, as well as effects of ATP and sequence context on AP site incision (2008) J. Mol. Biol., 379, pp. 17-27
Mol, C.D., Izumi, T., Mitra, S., Talner, J.A., DNA-bound structures and mutants reveal abasic DNA binding by APE1 DNA repair and coordination (2000) Nature, 403 (6768), pp. 451-456. , DOI 10.1038/35000249
Wilson III, D.M., Takeshita, M., Demple, B., Abasic site binding by the human apurinic endonuclease, Ape, and determination of the DNA contact sites (1997) Nucleic Acids Research, 25 (5), pp. 933-939. , DOI 10.1093/nar/25.5.933
Katsamba, P.S., Park, S., Laird-Offringa, I.A., Kinetic studies of RNA-protein interactions using surface plasmon resonance (2002) Methods, 26 (2), pp. 95-104. , DOI 10.1016/S1046-2023(02)00012-9, PII S1046202302000129
Law, M.J., Rice, A.J., Lin, P., Laird-Offringa, I.A., The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA (2006) RNA, 12 (7), pp. 1168-1178. , http://www.rnajournal.org/cgi/reprint/12/7/1168, DOI 10.1261/rna.75206
Kim, W.C., Berquist, B.R., Chohan, M., Uy, C., Wilson III, D.M., Lee, C.H., Characterization of the endoribonuclease active site of human apurinic/apyrimidinic endonuclease 1 (2011) J. Mol. Biol., 411, pp. 960-971
Yung, B.Y., Chan, P.K., Identification and characterization of a hexameric form of nucleolar phosphoprotein B23 (1987) Biochim. Biophys. Acta, 925, pp. 74-82
Jackson, E.B., Theriot, C.A., Chattopadhyay, R., Mitra, S., Izumi, T., Analysis of nuclear transport signals in the human apurinic/apyrimidinic endonuclease (APE1/Ref1) (2005) Nucleic Acids Research, 33 (10), pp. 3303-3312. , DOI 10.1093/nar/gki641
Vidal, A.E., Boiteux, S., Hickson, I.D., Radicella, J.P., XRCC1 coordinates the initial and late stages of DNA abasic site repair through protein-protein interactions (2001) EMBO Journal, 20 (22), pp. 6530-6539. , DOI 10.1093/emboj/20.22.6530
Wong, H.-K., Muftuoglu, M., Beck, G., Imam, S.Z., Bohr, V.A., Wilson III, D.M., Cockayne syndrome B protein stimulates apurinic endonuclease 1 activity and protects against agents that introduce base excision repair intermediates (2007) Nucleic Acids Research, 35 (12), pp. 4103-4113. , DOI 10.1093/nar/gkm404
Georgiadis, M.M., Luo, M., Gaur, R.K., Delaplane, S., Li, X., Kelley, M.R., Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease (2008) Mutat. Res., 643, pp. 54-63
Biochem J (ISSN: 0264-6021, 1470-8728electronic, 0264-6021linking), 2013; 452(3): 545-557.
Export to BibTeX Export to EndNote
Paper type: Journal Article,
Impact factor: 4.779, 5-year impact factor: 4.95
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84878400065&partnerID=40&md5=ac301c35524b260c492ada6cd017035a
Keywords: Apurinic Apyrimidinic Endonuclease 1 (ape1), Nucleophosmin (npm1), Phylogenesis, Protein-Dna Interaction, Protein-Protein Interaction, Dna (apurinic Or Apyrimidinic Site) Lyase, Acetylation, Article, Binding Affinity, Dna Protein Complex, Dna Sequence, Dna Strand, Human, Human Cell, In Vitro Study, Nonhuman, Priority Journal, Protein Binding, Protein Conformation, Protein Cross Linking, Protein Protein Interaction, Protein Secondary Structure, Protein Stability, Signal Transduction, Stereospecificity, Ubiquitination, Amino Acid Sequence, Animals, Dna Damage, Dna-(apurinic Or Apyrimidinic Site) Lyase, Hela Cells, Molecular Sequence Data, Nuclear Proteins, Nucleic Acids, Sequence Homology, Zebrafish, Eukaryota,
Affiliations:
*** IBB - CNR ***
Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
Department of Pharmacy, CIRPEB (Centro Interuniversitario di Ricerca Sui Peptidi Bioattivi), University of Naples 'Federico II', 80134 Naples, Italy
Institute of Biostructures and Bioimaging CNR, 80134 Naples, Italy
References:
Fung, H., Demple, B., A vital role for Ape1/Ref1 protein in repairing spontaneous DNA damage in human cells (2005) Molecular Cell, 17 (3), pp. 463-470. , DOI 10. 1016/j. molcel. 2004. 12. 029, PII S109727650501039
Bhakat, K. K., Izumi, T., Yang, S. -H., Hazra, T. K., Mitra, S., Role of acetylated human AP-endonuclease (APE1/Ref-1) in regulation of the parathyroid hormone gene (2003) EMBO Journal, 22 (23), pp. 6299-6309. , DOI 10. 1093/emboj/cdg595
Vascotto, C., Cesaratto, L., Zeef, L. A., Deganuto, M., D'Ambrosio, C., Scaloni, A., Romanello, M., Delneri, D., Genome-wide analysis and proteomic studies reveal APE1/Ref-1 multifunctional role in mammalian cells (2009) Proteomics, 9, pp. 1058-1074
Tell, G., Damante, G., Caldwell, D., Kelley, M. R., The intracellular localization of APE1/Ref-1: More than a passive phenomenon? (2005) Antioxidants and Redox Signaling, 7 (3-4), pp. 367-384. , DOI 10. 1089/ars. 2005. 7. 367
Xanthoudakis, S., Miao, G. G., Curran, T., The redox and DNA-repair activities of Ref-1 are encoded by nonoverlapping domains (1994) Proceedings of the National Academy of Sciences of the United States of America, 91 (1), pp. 23-27. , DOI 10. 1073/pnas. 91. 1. 23
Erzberger, J. P., Barsky, D., Scharer, O. D., Colvin, M. E., Wilson III, D. M., Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases (1998) Nucleic Acids Research, 26 (11), pp. 2771-2778. , DOI 10. 1093/nar/26. 11. 2771
Fan, J., Matsumoto, Y., Wilson III, D. M., Nucleotide sequence and DNA secondary structure, as well as replication protein A, modulate the single-stranded abasic endonuclease activity of APE1 (2006) Journal of Biological Chemistry, 281 (7), pp. 3889-3898. , http: //www. jbc. org/cgi/reprint/281/7/3889, DOI 10. 1074/jbc. M511004200
Marenstein, D. R., Wilson III, D. M., Teebor, G. W., Human AP endonuclease (APE1) demonstrates endonucleolytic activity against AP sites in single-stranded DNA (2004) DNA Repair, 3 (5), pp. 527-533. , DOI 10. 1016/j. dnarep. 2004. 01. 010, PII S1568786404000291
Sengupta, S., Mantha, A. K., Mitra, S., Bhakat, K. K., Human AP endonuclease (APE1/Ref-1) and its acetylation regulate YB-1-p300 recruitment and RNA polymerase II loading in the drug-induced activation of multidrug resistance gene MDR1 (2011) Oncogene, 30, pp. 482-493
Tell, G., Wilson III, D. M., Lee, C. H., Intrusion of a DNA repair protein in the RNome world: Is this the beginning of a new era? (2010) Mol. Cell. Biol., 30, pp. 366-371
Beloglazova, N. G., Kirpota, O. O., Starostin, K. V., Ishchenko, A. A., Yamkovoy, V. I., Zharkov, D. O., Douglas, K. T., Nevinsky, G. A., Thermodynamic, kinetic and structural basis for recognition and repair of abasic sites in DNA by apurinic/apyrimidinic endocuclease from human placenta (2004) Nucleic Acids Research, 32 (17), pp. 5134-5146. , DOI 10. 1093/nar/gkh846
Vascotto, C., Fantini, D., Romanello, M., Cesaratto, L., Deganuto, M., Leonardi, A., Radicella, J. P., Scaloni, A., APE1/Ref-1 interacts with NPM1 within nucleoli and plays a role in the rRNA quality control process (2009) Mol. Cell. Biol., 29, pp. 1834-1854
Barnes, T., Kim, W. C., Mantha, A. K., Kim, S. E., Izumi, T., Mitra, S., Lee, C. H., Identification of apurinic/apyrimidinic endonuclease 1 (APE1) as the endoribonuclease that cleaves c-myc mRNA (2009) Nucleic Acids Res., 37, pp. 3946-3958
Gorman, M. A., Morera, S., Rothwell, D. G., De La, F. E., Mol, C. D., Tainer, J. A., Hickson, I. D., Freemont, P. S., The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites (1997) EMBO Journal, 16 (21), pp. 6548-6558. , DOI 10. 1093/emboj/16. 21. 6548
Beernink, P. T., Segelke, B. W., Hadi, M. Z., Erzberger, J. P., Wilson III, D. M., Rupp, B., Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: Implications for the catalytic mechanism (2001) Journal of Molecular Biology, 307 (4), pp. 1023-1034. , DOI 10. 1006/jmbi. 2001. 4529
Strauss, P. R., Holt, C. M., Domain mapping of human apurinic/apyrimidinic endonuclease: Structural and functional evidence for a disordered amino terminus and a tight globular carboxyl domain (1998) Journal of Biological Chemistry, 273 (23), pp. 14435-14441. , DOI 10. 1074/jbc. 273. 23. 14435
Fantini, D., Vascotto, C., Marasco, D., D'Ambrosio, C., Romanello, M., Vitagliano, L., Pedone, C., Quadrifoglio, F., Critical lysine residues within the overlooked N-terminal domain of human APE1 regulate its biological functions (2010) Nucleic Acids Res., 38, pp. 8239-8256
Fan, Z., Beresford, P. J., Zhang, D., Xu, Z., Novina, C. D., Yoshida, A., Pommier, Y., Lieberman, J., Cleaving the oxidative repair protein Ape I enhances cell death mediated by granzyme A (2003) Nature Immunology, 4 (2), pp. 145-153. , DOI 10. 1038/ni885
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Hedge, M.L., Izumi, T., Mitra, S., Oxidized base damage and single-strand break repairin mammalian genomes: Role of disordered regions and posttranslational modifications in early enzymes (2012) Prog. Mol. Biol. Transl. Sci., 110, pp. 123-153
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Nguyen, L.H., Barsky, D., Erzberger, J.P., Wilson III, D.M., Mapping the protein-DNA interface and the metal-binding site of the major human apurinic/apyrimidinic endonuclease (2000) J. Mol. Biol., 298, pp. 447-459
Berquist, B.R., McNeill, D.R., Wilson III, D.M., Characterization of abasic endonuclease activity of human Ape1 on alternative substrates, as well as effects of ATP and sequence context on AP site incision (2008) J. Mol. Biol., 379, pp. 17-27
Mol, C.D., Izumi, T., Mitra, S., Talner, J.A., DNA-bound structures and mutants reveal abasic DNA binding by APE1 DNA repair and coordination (2000) Nature, 403 (6768), pp. 451-456. , DOI 10.1038/35000249
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Law, M.J., Rice, A.J., Lin, P., Laird-Offringa, I.A., The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA (2006) RNA, 12 (7), pp. 1168-1178. , http://www.rnajournal.org/cgi/reprint/12/7/1168, DOI 10.1261/rna.75206
Kim, W.C., Berquist, B.R., Chohan, M., Uy, C., Wilson III, D.M., Lee, C.H., Characterization of the endoribonuclease active site of human apurinic/apyrimidinic endonuclease 1 (2011) J. Mol. Biol., 411, pp. 960-971
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Jackson, E.B., Theriot, C.A., Chattopadhyay, R., Mitra, S., Izumi, T., Analysis of nuclear transport signals in the human apurinic/apyrimidinic endonuclease (APE1/Ref1) (2005) Nucleic Acids Research, 33 (10), pp. 3303-3312. , DOI 10.1093/nar/gki641
Vidal, A.E., Boiteux, S., Hickson, I.D., Radicella, J.P., XRCC1 coordinates the initial and late stages of DNA abasic site repair through protein-protein interactions (2001) EMBO Journal, 20 (22), pp. 6530-6539. , DOI 10.1093/emboj/20.22.6530
Wong, H.-K., Muftuoglu, M., Beck, G., Imam, S.Z., Bohr, V.A., Wilson III, D.M., Cockayne syndrome B protein stimulates apurinic endonuclease 1 activity and protects against agents that introduce base excision repair intermediates (2007) Nucleic Acids Research, 35 (12), pp. 4103-4113. , DOI 10.1093/nar/gkm404
Georgiadis, M.M., Luo, M., Gaur, R.K., Delaplane, S., Li, X., Kelley, M.R., Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease (2008) Mutat. Res., 643, pp. 54-63
Role Of The Unstructured N-Terminal Domain Of The Human Apurinic/Apyrimidinic Endonuclease 1 (hape1) In The Modulation Of Its Interaction With Nucleic Acids And Nucleophosmin (npm1)
The hAPE1 (human apurinic/apyrimidinic endonuclease 1) is an essential enzyme, being the main abasic endonuclease in higher eukaryotes. However, there is strong evidence to show that hAPE1 can directly bind specific gene promoters, thus modulating their transcriptional activity, even in the absence of specific DNA damage. Recent findings, moreover, suggest a role for hAPE1 in RNA processing, which is modulated by the interaction with NPM1 (nucleophosmin). Independent domains account for many activities of hAPE1; however, whereas the endonuclease and the redox-active portions of the protein arewell characterized, a better understanding of the role of the unstructured N-terminal region is needed. In the present study, we characterized the requirements for the interaction of hAPE1 with NPM1 and undamaged nucleic acids. We show that DNA/RNA secondary structure has an impact on hAPE1 binding in the absence of damage. Biochemical studies, using the isolated N-terminal region of the protein, reveal that the hAPE1 N-terminal domain represents an evolutionary gain of function, since its composition affects the protein's stability and ability to interact with both nucleic acids and NPM1. Although required, however, this region is not sufficient itself to stably interact with DNA or NPM1. The Authors Journal compilation 2013 Biochemical Society
The hAPE1 (human apurinic/apyrimidinic endonuclease 1) is an essential enzyme, being the main abasic endonuclease in higher eukaryotes. However, there is strong evidence to show that hAPE1 can directly bind specific gene promoters, thus modulating their transcriptional activity, even in the absence of specific DNA damage. Recent findings, moreover, suggest a role for hAPE1 in RNA processing, which is modulated by the interaction with NPM1 (nucleophosmin). Independent domains account for many activities of hAPE1; however, whereas the endonuclease and the redox-active portions of the protein arewell characterized, a better understanding of the role of the unstructured N-terminal region is needed. In the present study, we characterized the requirements for the interaction of hAPE1 with NPM1 and undamaged nucleic acids. We show that DNA/RNA secondary structure has an impact on hAPE1 binding in the absence of damage. Biochemical studies, using the isolated N-terminal region of the protein, reveal that the hAPE1 N-terminal domain represents an evolutionary gain of function, since its composition affects the protein's stability and ability to interact with both nucleic acids and NPM1. Although required, however, this region is not sufficient itself to stably interact with DNA or NPM1. The Authors Journal compilation 2013 Biochemical Society
Role Of The Unstructured N-Terminal Domain Of The Human Apurinic/Apyrimidinic Endonuclease 1 (hape1) In The Modulation Of Its Interaction With Nucleic Acids And Nucleophosmin (npm1)
Role Of The Unstructured N-Terminal Domain Of The Human Apurinic/Apyrimidinic Endonuclease 1 (hape1) In The Modulation Of Its Interaction With Nucleic Acids And Nucleophosmin (npm1)
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Vitagliano L, Ruggiero A, Pedone C, Berisio R
* Conformational states and association mechanism of Yersinia pestis Caf1 subunits (324 views)
Biochem Biophys Res Commun (ISSN: 0006-291x, 1090-2104, 1090-2104electronic), 2008 Sep 8; 372(4): 804-810.
Impact Factor: 2.648
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Ruvo M, Marasco D, Viparelli F, Tornatore L, Sandomenico A, Doti N, Pedone C, Benedetti E, Monti SM
* Peptide antagonists of protein-protein interactions identified by screening protein fragments derived by enzyme degradation (349 views)
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2008 Sep; 14(8): N/D-N/D.
Impact Factor: 1.654
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Viparelli F, Doti N, Sandomenico A, Marasco D, Dathan NA, Miele C, Beguinot F, Monti SM, Ruvo M
* Expression and purification of the D4 region of PLD1 and characterization of its interaction with PED-PEA15 (446 views)
Protein Expr Purif (ISSN: 1046-5928), 2008 Jun; 59(2): 302-308.
Impact Factor: 1.621
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Tornatore L, Marasco D, Dathan N, Vitale RM, Benedetti E, Papa S, Franzoso G, Ruvo M, Monti SM
* Gadd45 beta forms a homodimeric complex that binds tightly to MKK7 (483 views)
J Mol Biol (ISSN: 0022-2836, 0022-2283, 1089-8638), 2008 Apr 18; 378(1): 97-111.
Impact Factor: 5.673
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Vitagliano L, Ruggiero A, Pedone C, Berisio R
* A Molecular Dynamics Study of Pilus Subunits: Insights into Pilus Biogenesis (493 views)
J Mol Biol (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 2007 Apr 6; 367(4): 935-941.
Impact Factor: 4.472
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* Protein with negative surface charge distribution, Bnr1, shows characteristics of a DNA-mimic protein and may be involved in the adaptation of Burkholderia cenocepacia (5 views)
Microbiologyopen (ISSN: 2045-8827linking), 2022 Feb; 11(1): e1264-N/D.
Impact Factor: 3.48
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Vincenzi M, Mercurio FA, Leone M
* Protein Interaction Domains: structural features and drug discovery applications (part 2) (80 views)
Curr Med Chem (ISSN: 0929-8673linking, 1875-533xelectronic), 2021; 28(5): 854-892.
Impact Factor: 4.184
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Tornatore L, Capece D, Sandomenico A, Verzella D, Vecchiotti D, Zazzeroni F, Ruvo M, Franzoso G
* The Screening of Combinatorial Peptide Libraries for Targeting Key Molecules or Protein-Protein Interactions in the NF-κB Pathway (9 views)
Methods Mol Biol (ISSN: 1064-3745linking, 1940-6029electronic), 2021; 2366: 343-356.
Impact Factor: 1.17
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Mercurio FA, Di Natale C, Pirone L, Vincenzi M, Marasco D, De Luca S, Pedone EM, Leone M
* Exploring the ability of cyclic peptides to target SAM domains: a computational and experimental study (266 views)
Chembiochem (ISSN: 1439-4227linking, 1439-7633), 2020 Mar 2; 21(5): 702-711.
Impact Factor: 2.641
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Vincenzi M, Mercurio FA, Leone M
* Sam Domains in Multiple Diseases (237 views)
Curr Med Chem (ISSN: 0929-8673linking, 1875-533xelectronic), 2020; 27(3): 450-476.
Impact Factor: 3.469
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Rega C, Russo R, Foca A, Sandomenico A, Iaccarino E, Raimondo D, Milanetti E, Tornatore L, Franzoso G, Pedone PV, Ruvo M, Chambery A
* Probing the interaction interface of the GADD45beta/MKK7 and MKK7/DTP3 complexes by chemical cross-linking mass spectrometry (276 views)
Int J Biol Macromol (ISSN: 1879-0003electronic, 0141-8130linking), 2018 Jul 15; 114: 114-123.
Impact Factor: 1.427
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Pirone L, Ripoll-rozada J, Leone M, Ronca R, Lombardo F, Fiorentino G, Andersen JF, Pereira PJB, Arcà B, Pedone E
* Functional analyses yield detailedinsight into the mechanism of thrombin inhibition by the antihemostatic salivary protein cE5 from Anopheles gambiae (367 views) (PDF 190 views)
Jbc Papers (ISSN: 0021-9258linking, 1083-351x), 2017 Jul 28; 292(30): 12632-12642.
Impact Factor: 4.125
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Sacchi S, Cappelletti P, Pirone L, Smaldone G, Pedone E, Pollegioni L
* Elucidating the role of the pLG72 R30K substitution in schizophrenia susceptibility (358 views)
Febs Lett (ISSN: 1873-3468, 0014-5793, 0014-5793print), 2017 Feb; 591(4): 646-655.
Impact Factor: 2.999
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Lanza V, Travaglia A, Malgieri G, Fattorusso R, GrassoG, Di Natale G, Zito V, Arena G, Milardi D, Rizzarelli E
* Ubiquitin Associates with the N-Terminal Domain of Nerve Growth Factor: The Role of Copper(II) Ions (279 views) (PDF 172 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2016 Dec 05; 22(49): 17767-17775.
Impact Factor: 5.317
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Pirone L, Smaldone G, Esposito C, Balasco N, Petoukhov MV, Spilotros A, Svergun DI, Di Gaetano S, Vitagliano L, Pedone E
* Proteins involved in sleep homeostasis: Biophysical characterization of INC and its partners (323 views) (PDF 192 views)
Biochimie (ISSN: 0300-9084, 1638-6183, 0300-9084linking), 2016 Sep 24; 131: 106-114.
Impact Factor: 3.112
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Birolo L, Sacchi S, Smaldone G, Molla G, Leo G, Caldinelli L, Pirone L, Eliometri P, Di Gaetano S, Orefice I, Pedone E, Pucci P, Pollegioni L
* Regulating levels of the neuromodulator d-serine in human brain: structural insight into pLG72 and d-amino acid oxidase interaction (261 views) (PDF 207 views)
Febs J (ISSN: 1742-464x), 2016 Sep; 283(18): 3353-3370.
Impact Factor: 3.902
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Ruvo M, Doti N, Lorenzo V, Vitagliano L, Mascanzoni F
* The Interacting Domains of PREP1 and p160 are Endowed with a Remarkable Structural Stability (280 views)
Mol Biotechnol (ISSN: 1073-6085, 1559-0305electronic, 1073-6085linking), 2016 May; 58(5): 328-339.
Impact Factor: 1.634
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Bottini A, Wu B, Barile E, De SK, Leone M, Pellecchia M
* High-Throughput Screening (HTS) by NMR Guided Identification of Novel Agents Targeting the Protein Docking Domain of YopH (422 views)
Chemmedchem (ISSN: 1860-7179, 1860-7187, 1860-7179linking), 2015 Nov 23; 11(8): 919-927.
Impact Factor: 2.98
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Correale S, de Paola I, Morgillo CM, Federico A, Zaccaro L, Pallante P, Galeone A, Fusco A, Pedone E, Luque FJ, Catalanotti B
* Structural Model of the hUbA1-UbcH10 Quaternary Complex: In Silico and Experimental Analysis of the Protein-Protein Interactions between E1, E2 and Ubiquitin (437 views)
Plosone (ISSN: 1932-6203, 1932-6203electronic, 1932-6203linking), 2014 Nov 6; 9(11): e112082-e112082.
Impact Factor: 3.234
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Balasco N, Pirone L, Smaldone G, Di Gaetano S, Esposito L, Pedone E, Vitagliano L
* Molecular recognition of Cullin3 by KCTDs: Insights from experimental and computational investigations (371 views)
Bba-Gen Subjects (ISSN: 0925-4439, 0006-3002, 1570-9639), 2014 Jul; 1844(7): 1289-1298.
Impact Factor: 4.882
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Diana D, Smaldone G, De Antonellis P, Pirone L, Carotenuto M, Alonzi A, Di Gaetano S, Zollo M, Pedone E, Fattorusso R
* Mapping Functional Interaction Sites of Human Prune C-Terminal Domain by NMR Spectroscopy in Human Cell Lysates (389 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2013 Sep 9; 19(37): 12217-12220.
Impact Factor: 5.696
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Farina B, Doti N, Pirone L, Malgieri G, Pedone E, Ruvo M, Fattorusso R
* Molecular basis of the PED/PEA15 interaction with the C-terminal fragment of phospholipase D1 revealed by NMR spectroscopy (471 views)
Bba-Gen Subjects (ISSN: 1570-9639, 0006-3002, 0925-4439), 2013 Sep; 1834(8): 1572-1580.
Impact Factor: 3.191
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Attanasio F, Convertino M, Magno A, Caflisch A, Corazza A, Haridas H, Esposito G, Cataldo S, Pignataro B, Milardi D, Rizzarelli E
* Carnosine Inhibits Abeta(42) Aggregation By Perturbing The H-Bond Network In And Around The Central Hydrophobic Cluster (763 views)
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2013 Mar 18; 14(5): 583-592.
Impact Factor: 3.06
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Grasso G, Spoto G
* Plasmonics for the study of metal ion-protein interactions (471 views)
Anal Bioanal Chem (ISSN: 1618-2642), 2013 Feb; 405(6): 1833-1843.
Impact Factor: 3.578
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Mercurio FA, Marasco D, Pirone L, Scognamiglio PL, Pedone E, Pellecchia M, Leone M
* Heterotypic Sam-Sam Association Between Odin-Sam1 And Arap3-Sam: Binding Affinity And Structural Insights (402 views)
Chembiochem (ISSN: 1439-4227, 1439-9422, 1439-7633), 2013 Jan 2; 14(1): 100-106.
Impact Factor: 2.92
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Viparelli F, Doti N, Sandomenico A, Marasco D, Dathan NA, Miele C, Beguinot F, Monti SM, Ruvo M
* GSM48878: CD8 IL2-D2 (393 views)
Gene Expression Omnibus, 2011 Dec 2; 59(2): 302-308.
Impact Factor: 2.082
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Ruvo M, Sandomenico A, Tudisco L, De Falco S
* Branched peptides for the modulation of protein-protein interactions: More arms are better than one? (532 views)
Curr Med Chem (ISSN: 0929-8673, 1875-533x, 1875-533xelectronic), 2011 Jun; 18(16): 2429-2437.
Impact Factor: 4.859
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Correale S, Pirone L, Di Marcotullio L, De Smaele E, Greco A, Mazzà D, Moretti M, Alterio V, Vitagliano L, Di Gaetano S, Gulino A, Pedone E
* Molecular organization of the cullin E3 ligase adaptor KCTD11 (568 views)
Biochimie (ISSN: 0300-9084, 1638-6183, 1638-6183electronic), 2011 Apr; 93(4): 715-724.
Impact Factor: 3.022
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Farina B, Pirone L, Russo L, Viparelli F, Doti N, Pedone C, Pedone E, Fattorusso R
* NMR backbone dynamics studies of human PED/PEA-15 outline protein functional sites (720 views)
Febs J (ISSN: 1742-4658, 1742-464x, 1742-4658electronic), 2010 Oct; 277(20): 4229-4240.
Impact Factor: 3.129
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Sandomenico A, Monti SM, Sabatella M, De Capua A, Tornatore L, Doti N, Viparelli F, Dathan NA, Pedone C, Ruvo M, Marasco D
* Protein-protein interactions: a simple strategy to identify binding sites and peptide antagonists (605 views)
Chem Biol Drug Des (ISSN: 1747-0285, 1747-0277), 2009 May; 73(5): 483-493.
Impact Factor: 2.473
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Vitagliano L, Ruggiero A, Pedone C, Berisio R
* Molecular dynamics studies of the P pilus rod subunit PapA (572 views)
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2009 Mar; 15(3): 192-199.
Impact Factor: 1.807
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Merlino A, Varriale S, Coscia MR, Mazzarella L, Oreste U
* Structure and dimerization of the teleost transmembrane immunoglobulin region (395 views)
Journal Of Molecular Graphics & Modelling (ISSN: 1093-3263), 2008 Oct; 27(3): 401-407.
Impact Factor: 2.347
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Vitagliano L, Ruggiero A, Pedone C, Berisio R
* Conformational states and association mechanism of Yersinia pestis Caf1 subunits (324 views)
Biochem Biophys Res Commun (ISSN: 0006-291x, 1090-2104, 1090-2104electronic), 2008 Sep 8; 372(4): 804-810.
Impact Factor: 2.648
View Export to BibTeX Export to EndNote
Ruvo M, Marasco D, Viparelli F, Tornatore L, Sandomenico A, Doti N, Pedone C, Benedetti E, Monti SM
* Peptide antagonists of protein-protein interactions identified by screening protein fragments derived by enzyme degradation (349 views)
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2008 Sep; 14(8): N/D-N/D.
Impact Factor: 1.654
View Export to BibTeX Export to EndNote
Viparelli F, Doti N, Sandomenico A, Marasco D, Dathan NA, Miele C, Beguinot F, Monti SM, Ruvo M
* Expression and purification of the D4 region of PLD1 and characterization of its interaction with PED-PEA15 (446 views)
Protein Expr Purif (ISSN: 1046-5928), 2008 Jun; 59(2): 302-308.
Impact Factor: 1.621
View Export to BibTeX Export to EndNote
Tornatore L, Marasco D, Dathan N, Vitale RM, Benedetti E, Papa S, Franzoso G, Ruvo M, Monti SM
* Gadd45 beta forms a homodimeric complex that binds tightly to MKK7 (483 views)
J Mol Biol (ISSN: 0022-2836, 0022-2283, 1089-8638), 2008 Apr 18; 378(1): 97-111.
Impact Factor: 5.673
View Export to BibTeX Export to EndNote
Vitagliano L, Ruggiero A, Pedone C, Berisio R
* A Molecular Dynamics Study of Pilus Subunits: Insights into Pilus Biogenesis (493 views)
J Mol Biol (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 2007 Apr 6; 367(4): 935-941.
Impact Factor: 4.472
View Export to BibTeX Export to EndNote
32 Records (29 excluding Abstracts).
Total impact factor: 102.788 (92.227 excluding Abstracts).
Total 5 year impact factor: 115.636 (105.419 excluding Abstracts).
Total impact factor: 102.788 (92.227 excluding Abstracts).
Total 5 year impact factor: 115.636 (105.419 excluding Abstracts).
496 views. Last view on Thursday 11 May 2023, 6:52:45
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