XPA: A key scaffold for human nucleotide excision repair
Tài liệu tham khảo
Scharer, 2013, Nucleotide excision repair in eukaryotes, Cold Spring Harb. Perspect. Biol., 5, 1, 10.1101/cshperspect.a012609
Gillet, 2006, Molecular mechanisms of mammalian global genome nucleotide excision repair, Chem. Rev., 106, 253, 10.1021/cr040483f
Truglio, 2006, Prokaryotic Nucleotide Excision Repair: the UvrABC System, Chem. Rev., 106, 233, 10.1021/cr040471u
DiGiovanna, 2012, Shining a light on xeroderma pigmentosum, J. Invest. Dermatol., 132, 785, 10.1038/jid.2011.426
Hoeijmakers, 2009, DNA damage, aging, and cancer, N. Engl. J. Med., 361, 1475, 10.1056/NEJMra0804615
Lehmann, 2011, Xeroderma pigmentosum, Orphanet. J. Rare Dis., 6
Lehmann, 2012, DNA repair, DNA replication and human disorders: a personal journey, DNA Repair (Amst), 11, 328, 10.1016/j.dnarep.2011.05.008
Bradford, 2011, Cancer and neurologic degeneration in xeroderma pigmentosum: long term follow-up characterises the role of DNA repair, J. Med. Genet., 48, 168, 10.1136/jmg.2010.083022
Cleaver, 2005, Cancer in xeroderma pigmentosum and related disorders of DNA repair, Nat. Rev. Cancer, 5, 564, 10.1038/nrc1652
Cleaver, 1997, The DNA damage-recognition problem in human and other eukaryotic cells: the XPA damage binding protein, Biochem. J, 12, 1, 10.1042/bj3280001
Rouillon, 2011, The evolution and mechanisms of nucleotide excision repair proteins, Res. Microbiol., 162, 19, 10.1016/j.resmic.2010.09.003
Shell, 2013, Xeroderma pigmentosum complementation group C protein (XPC) serves as a general sensor of damaged DNA, DNA Repair (Amst), 12, 947, 10.1016/j.dnarep.2013.08.013
Batty, 2000, Stable binding of human XPC complex to irradiated DNA confers strong discrimination for damaged sites, J. Mol. Biol., 300, 275, 10.1006/jmbi.2000.3857
Uchida, 2002, The carboxy-terminal domain of the XPC protein plays a crucial role in nucleotide excision repair through interactions with transcription factor IIH, DNA Repair (Amst), 1, 449, 10.1016/S1568-7864(02)00031-9
Min, 2007, Recognition of DNA damage by the Rad4 nucleotide excision repair protein, Nature, 449, 570, 10.1038/nature06155
Riedl, 2003, The comings and goings of nucleotide excision repair factors on damaged DNA, EMBO J., 22, 5293, 10.1093/emboj/cdg489
Yokoi, 2000, The xeroderma pigmentosum group C protein complex XPC-HR23B plays an important role in the recruitment of transcription factor IIH to damaged DNA, J. Biol. Chem., 275, 9870, 10.1074/jbc.275.13.9870
Fuss, 2011, XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase, DNA Repair (Amst)., 10, 697, 10.1016/j.dnarep.2011.04.028
Hermanson-Miller, 2002, Strand-specific binding of RPA and XPA to damaged duplex DNA, Biochemistry, 41, 2402, 10.1021/bi0112863
Krasikova, 2010, Localization of xeroderma pigmentosum group A protein and replication protein A on damaged DNA in nucleotide excision repair, Nucleic Acids Res., 38, 8083, 10.1093/nar/gkq649
O’Donovan, 1994, XPG endonuclease makes the 3′ incision in human DNA nucleotide excision repair, Nature, 371, 432, 10.1038/371432a0
Staresincic, 2009, Coordination of dual incision and repair synthesis in human nucleotide excision repair, EMBO J., 28, 1111, 10.1038/emboj.2009.49
Tsodikov, 2007, Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA, EMBO J., 26, 4768, 10.1038/sj.emboj.7601894
Shivji, 1999, Dual-incision assays for nucleotide excision repair using DNA with a lesion at a specific site, DNA Repair Protoc., 113, 373, 10.1385/1-59259-675-4:373
Feltes, 2015, Overview of xeroderma pigmentosum proteins architecture, mutations and post-translational modifications, Mutat. Res. Rev. Mutat. Res., 763, 306, 10.1016/j.mrrev.2014.12.002
Yang, 2006, Specific and efficient binding of xeroderma pigmentosum complementation group A to double-strand/single-strand DNA junctions with 3′- and/or 5'-ssDNA branches, Biochemistry, 45, 15921, 10.1021/bi061626q
Li, 2015, Tripartite DNA lesion recognition and verification by XPC, TFIIH, and XPA in nucleotide excision repair, Mol. Cell, 59, 1025, 10.1016/j.molcel.2015.08.012
Sugitani, 2014, Redefining the DNA-binding domain of human XPA, J. Am. Chem. Soc., 136, 10830, 10.1021/ja503020f
Hilton, 2014, A new structural insight into XPA-DNA interactions, Biosci. Rep., 34, 831, 10.1042/BSR20140158
States, 1998, Distribution of mutations in the human xeroderma pigmentosum group A gene and their relationships to the functional regions of the DNA damage recognition protein, Hum. Mutat., 12, 103, 10.1002/(SICI)1098-1004(1998)12:2<103::AID-HUMU5>3.0.CO;2-6
Ikegami, 1998, Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA, Nat. Struct. Biol., 5, 701, 10.1038/1400
Buchko, 1998, Structural features of the minimal DNA binding domain (M98–F219) of human nucleotide excision repair protein XPA, Nucleic Acids Res., 26, 2779, 10.1093/nar/26.11.2779
Kuraoka, 1996, Identification of a damaged-DNA binding domain of the XPA protein, Mutat. Res., 362, 87, 10.1016/0921-8777(95)00038-0
Bernardes de Jesus, 2008, Dissection of the molecular defects caused by pathogenic mutations in the DNA repair factor XPC, Mol. Cell. Biol., 28, 7225, 10.1128/MCB.00781-08
Li, 1994, Specific association between the human DNA repair proteins XPA and ERCC1, Proc. Natl. Acad. Sci. U. S. A., 91, 5012, 10.1073/pnas.91.11.5012
Nocentini, 1997, DNA damage recognition by XPA protein promotes efficient recruitment of transcription factor II H, J. Biol. Chem., 272, 22991, 10.1074/jbc.272.37.22991
Buchko, 1999, Interactions of human nucleotide excision repair protein XPA with DNA and RPA70 Delta C327: chemical shift mapping and 15N NMR relaxation studies, Biochemistry, 38, 15116, 10.1021/bi991755p
Mer, 2000, Structural basis for the recognition of DNA repair proteins UNG2, XPA, and RAD52 by replication factor RPA, Cell, 103, 449, 10.1016/S0092-8674(00)00136-7
Neher, 2003, Biochemical analysis of the damage recognition process in nucleotide excision repair, J. Biol. Chem., 278, 7476, 10.1074/jbc.M210603200
Wakasugi, 2009, Physical and functional interaction between DDB and XPA in nucleotide excision repair, Nucleic Acids Res., 37, 516, 10.1093/nar/gkn964
McNeil, 2012, DNA repair endonuclease ERCC1-XPF as a novel therapeutic target to overcome chemoresistance in cancer therapy, Nucleic Acids Res., 40, 9990, 10.1093/nar/gks818
Giglia-Mari, 2006, Dynamic interaction of TTDA with TFIIH is stabilized by nucleotide excision repair in living cells, PLoS Biol., 4, 0952, 10.1371/journal.pbio.0040156
Ziani, 2014, Sequential and ordered assembly of a large DNA repair complex on undamaged chromatin, J. Cell Biol., 206, 589, 10.1083/jcb.201403096
Buchko, 2001, DNA-XPA interactions: a (31)P NMR and molecular modeling study of dCCAATAACC association with the minimal DNA-binding domain (M98-F219) of the nucleotide excision repair protein XPA, Nucleic Acids Res., 29, 2635, 10.1093/nar/29.12.2635
Koch, 2015, Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA), Proc. Natl. Acad. Sci. U. S. A., 112, 8272, 10.1073/pnas.1508509112
Rademakers, 2003, Xeroderma pigmentosum group a protein loads as a separate factor onto DNA lesions, Mol. Cell. Biol., 23, 5755, 10.1128/MCB.23.16.5755-5767.2003
Yang, 2002, Dimerization of human XPA and formation of XPA2-RPA protein complex, Biochemistry, 13012, 10.1021/bi026064z
Shell, 2008, Other proteins interacting with XP proteins, Adv. Exp. Med. Biol., 637, 103, 10.1007/978-0-387-09599-8_11
Y.S. Krasikova et al. Influence of Centrin 2 on the Interaction of Nucleotide Excision Repair Factors with Damaged DNA, 77 (2012) 346–353.
Bunick, 2006, Biochemical and structural domain analysis of xeroderma pigmentosum complementation group C protein, Biochemistry, 45, 14965, 10.1021/bi061370o
Wittschieben, 2003, DDB complexities, DNA Repair (Amst), 2, 1065, 10.1016/S1568-7864(03)00113-7
Tang, 2002, Xeroderma pigmentosum complementation group E and UV-damaged DNA-binding protein, DNA Repair (Amst), 1, 601, 10.1016/S1568-7864(02)00052-6
Fujiwara, 1999, Characterization of DNA recognition by the human UV-damaged DNA-binding protein, J. Biol. Chem., 274, 20027, 10.1074/jbc.274.28.20027
Fei, 2011, Regulation of nucleotide excision repair by UV-DDB: prioritization of damage recognition to internucleosomal DNA, PLoS Biol., 9, e1001183, 10.1371/journal.pbio.1001183
Camenisch, 2007, Xeroderma pigmentosum complementation group A protein is driven to nucleotide excision repair sites by the electrostatic potential of distorted DNA, DNA Repair (Amst), 16, 1819, 10.1016/j.dnarep.2007.07.011
Di Lello, 2006, Structure of the Tfb1/p53 Complex: insights into the Interaction between the p62/Tfb1 Subunit of TFIIH and the activation domain of p53, Mol. Cell, 22, 731, 10.1016/j.molcel.2006.05.007
Vitorino, 2007, Solution structure and self-association properties of the p8 TFIIH subunit responsible for trichothiodystrophy, J. Mol. Biol., 268, 473, 10.1016/j.jmb.2007.02.020
Khoo, 2009, Stabilising the DNA-binding domain of p53 by rational design of its hydrophobic core, Protein Eng. Des. Sel., 22, 421, 10.1093/protein/gzp018
Hilario, 2013, Structure of the C-terminal half of human XPB helicase and the impact of the disease-causing mutation XP11BE, Acta Crystallogr. D Biol. Crystallogr., 69, 237, 10.1107/S0907444912045040
Natan, 2011, Interaction of the p53 DNA-binding domain with its N-terminal extension modulates the stability of the p53 tetramer, J. Mol. Biol., 409, 358, 10.1016/j.jmb.2011.03.047
Okuda, 2014, Extended string binding mode of the phosphorylated transactivation domain of tumor suppressor p53, J. Am. Chem. Soc., 136, 14143, 10.1021/ja506351f
Andersen, 1996, The crystal structure of human cyclin H, FEBS Lett., 397, 65, 10.1016/S0014-5793(96)01143-X
Gervais, 2001, Solution structure of the N-terminal domain of the human TFIIH MAT1 subunit: new insights into the RING finger family, J. Biol. Chem., 276, 7457, 10.1074/jbc.M007963200
Lolli, 2004, The crystal structure of human CDK7 and its protein recognition properties, Structure, 12, 2067, 10.1016/j.str.2004.08.013
Okuda, 2015, Structural insight into the mechanism of TFIIH recognition by the acidic string of the nucleotide excision repair factor XPC article structural insight into the mechanism of TFIIH recognition by the acidic string of the nucleotide excision repair factor X, Struct. Des., 23, 1, 10.1016/j.str.2015.07.009
Gervais, 2004, TFIIH contains a pH domain involved in DNA nucleotide excision repair, Nat. Struct. Mol. Biol., 11, 616, 10.1038/nsmb782
Kellenberger, 2005, Solution structure of the C-terminal domain of TFIIH P44 subunit reveals a novel type of C4C4 ring domain involved in protein-protein interactions, J. Biol. Chem., 280, 20785, 10.1074/jbc.M412999200
Schultz, 2000, Molecular structure of human TFIIH, Cell, 102, 599, 10.1016/S0092-8674(00)00082-9
Lafrance-Vanasse, 2013, Structural and functional evidence that Rad4 competes with Rad2 for binding to the Tfb1 subunit of TFIIH in NER, Nucleic Acids Res., 41, 2736, 10.1093/nar/gks1321
Coin, 2008, Nucleotide excision repair driven by the dissociation of CAK from TFIIH, Mol. Cell, 31, 9, 10.1016/j.molcel.2008.04.024
Park, 1995, The general transcription-repair factor TFIIH is recruited to hte excision repair complex by the XPA protein independent of the TFIIE transcription factor, J. Biol. Chem., 270, 4896, 10.1074/jbc.270.9.4896
Wold, 1997, Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism, Annu. Rev. Biochem., 66, 61, 10.1146/annurev.biochem.66.1.61
Fanning, 2006, A dynamic model for replication protein A (RPA) function in DNA processing pathways, Nucleic Acids Res., 34, 4126, 10.1093/nar/gkl550
Stauffer, 2004, Structural mechanisms of DNA replication, repair, and recombination, J. Biol. Chem., 279, 30915, 10.1074/jbc.R400015200
Sugitani, 2015, Characteristics and concepts of dynamic hub proteins in DNA processing machinery from studies of RPA, Prog. Biophys. Mol. Biol., 117, 206, 10.1016/j.pbiomolbio.2014.12.001
De Biasio, 2013, 91
Lee, 1995, Human xeroderma pigmentosum group A protein interacts with human replication protein a and inhibits DNA replication, J. Biol. Chem., 270, 21800, 10.1074/jbc.270.37.21800
Daughdrill, 2003, Chemical shift changes provide evidence for overlapping single-stranded DNA- and XPA-binding sites on the 70kDa subunit of human replication protein A, Nucleic Acids Res., 31, 4176, 10.1093/nar/gkg451
Li, 1995, An interaction between the DNA repair factor XPA and replication protein A appears essential for nucleotide excision repair, Mol. Cell. Biol., 15, 5396, 10.1128/MCB.15.10.5396
Saijo, 2011, Nucleotide excision repair by mutant xeroderma pigmentosum group A (XPA) proteins with deficiency in interaction with RPA, J. Biol. Chem., 286, 5476, 10.1074/jbc.M110.172916
Mailand, 2013, Regulation of PCNA-protein interactions for genome stability, Nat. Rev. Mol. Cell Biol., 14, 269, 10.1038/nrm3562
Gilljam, 2012, Nucleotide excision repair is associated with the replisome and its efficiency depends on a direct interaction between XPA and PCNA, PLoS One, 7, e49199, 10.1371/journal.pone.0049199
Wu, 2007, ATR-dependent checkpoint modulates XPA nuclear import in response to UV irradiation, Oncogene, 26, 757, 10.1038/sj.onc.1209828
Shell, 2009, Checkpoint kinase ATR promotes nucleotide excision repair of UV-induced DNA damage via physical interaction with xeroderma pigmentosum group A, J. Biol. Chem., 284, 24213, 10.1074/jbc.M109.000745
Farley, 2006, Menin localizes to chromatin through an ATR-CHK1 mediated pathway after UV-induced DNA damage, J. Surg. Res., 2133, 29, 10.1016/j.jss.2006.02.021
Vodenicharov, 2005, Mechanism of early biphasic activation of poly(ADP-ribose) polymerase-1 in response to ultraviolet B radiation, J. Cell Sci., 118, 589, 10.1242/jcs.01636
Robu, 2013, 1
Pines, 2012, PARP1 promotes nucleotide excision repair through DDB2 stabilization and recruitment of ALC1, J. Cell Biol., 199, 235, 10.1083/jcb.201112132
Luijsterburg, 2012, DDB2 promotes chromatin decondensation at UV-induced DNA damage, J. Cell Biol., 197, 267, 10.1083/jcb.201106074
King, 2012, Poly(ADP-ribose) contributes to an association between poly(ADP-ribose) polymerase-1 and xeroderma pigmentosum complementation group A in nucleotide excision repair, J. Biol. Chem., 287, 39824, 10.1074/jbc.M112.393504
Fischer, 2014, Poly(ADP-ribose)-mediated interplay of XPA and PARP1 leads to reciprocal regulation of protein function, FEBS J., 281, 3625, 10.1111/febs.12885
Jungmichel, 2013, Proteome-wide identification of poly(ADP-Ribosyl)ation targets in different genotoxic stress responses, Mol. Cell, 52, 272, 10.1016/j.molcel.2013.08.026
Nitta, 2000, A novel cytoplasmic GTPase XAB1 interacts with DNA repair protein XPA, Nucleic Acids Res., 28, 1, 10.1093/nar/28.21.4212
Lembo, 2003, MBD in, a novel MBD2-Interacting protein, relieves MBD2 repression potential and reactivates transcription from methylated promoters, Mol. Cell. Biol., 23, 1656, 10.1128/MCB.23.5.1656-1665.2003
Yonemasu, 2005, Disruption of mouse XAB2 gene involved in pre-mRNA splicing, transcription and transcription-coupled DNA repair results in preimplantation lethality, DNA Repair (Amst), 4, 479, 10.1016/j.dnarep.2004.12.004
Nakatsu, 2000, XAB2, a novel tetratricopeptide repeat protein involved in transcription-coupled DNA repair and transcription, J. Biol. Chem., 275, 34931, 10.1074/jbc.M004936200
Brosey, 2013, A new structural framework for integrating replication protein A into DNA processing machinery, Nucleic Acids Res., 41, 2313, 10.1093/nar/gks1332
Miętus, 2014, Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding, Nucleic Acids Res., 42, 10762, 10.1093/nar/gku729
Anttinen, 2008, Neurological symptoms and natural course of xeroderma pigmentosum, Brain, 131, 1979, 10.1093/brain/awn126
Tanaka, 1990, Analysis of a human DNA excision repair gene involved in group A xeroderma pigmentosum and containing a zinc-finger domain, Nature, 348, 73, 10.1038/348073a0
Miyamoto, 1992, Mutational analysis of the structure and function of the xeroderma pigmentosum group A complementing protein. Identification of essential domains for nuclear localization and DNA excision repair, J. Biol. Chem., 267, 12182, 10.1016/S0021-9258(19)49821-9
Morita, 1996, Implications of the zinc-finger motif found in the DNA-binding domain of the human XPA protein, Genes to Cells, 1, 437, 10.1046/j.1365-2443.1996.d01-252.x
Takahashi, 2010, XPA gene mutations resulting in subtle truncation of protein in xeroderma pigmentosum group A patients with mild skin symptoms, J. Invest. Dermatol., 130, 2481, 10.1038/jid.2010.137
Gao, 2013, Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal, Sci. Signal., 6, 10.1126/scisignal.2004088
Neher, 2010, Identification of novel small molecule inhibitors of the XPA protein using in silico based screening, ACS Chem. Biol., 5, 953, 10.1021/cb1000444
van Oers, 2014, Thirty years of baculovirus-insect cell protein expression: from dark horse to mainstream technology, J. Gen. Virol., 6
Sakuma, 2012, Lentiviral vectors: basic to translational, Biochem. J., 443, 603, 10.1042/BJ20120146
Giegé, 2013, A historical perspective on protein crystallization from 1840 to the present day, FEBS J., 280, 6456, 10.1111/febs.12580
Manjasetty, 2008, Automated technologies and novel techniques to accelerate protein crystallography for structural genomics, Proteomics, 8, 612, 10.1002/pmic.200700687
Juranić, 2014, High-precision x-ray FEL pulse arrival time measurements at SACLA by a THz streak camera with Xe clusters, Opt. Express, 22, 30004, 10.1364/OE.22.030004
Amr, 2014, Mutational spectrum of Xeroderma pigmentosum group A in Egyptian patients, Gene, 533, 52, 10.1016/j.gene.2013.09.125
Cleaver, 1997, The DNA damage-recognition problem in human and other eukaryotic cells: the XPA damage binding protein, Biochem. J, 12, 1, 10.1042/bj3280001
Ghafouri-Fard, 2015, A novel 5 nucleotide deletion in XPA gene is associated with severe neurological abnormalities, Gene, 1
Lehmann, 2014, A novel mutation in the XPA gene results in two truncated protein variants and leads to a severe XP/neurological symptoms phenotype, J. Eur. Acad. Dermatol. Venereol., 1
Maeda, 2000, Compound heterozygous group A xeroderma pigmentosum patient with a novel mutation and an inherited reciprocal translocation, Br. J. Dermatol., 143, 174, 10.1046/j.1365-2133.2000.03611.x
Messaoud, 2012, Severe phenotypes in two Tunisian families with novel XPA mutations: evidence for a correlation between mutation location and disease severity, Arch. Dermatol. Res., 304, 171, 10.1007/s00403-011-1190-4
Tanioka, 2005, A novel XPA gene mutation and its functional analysis in a Japanese patient with xeroderma pigmentosum group A, J. Invest. Dermatol., 125, 244, 10.1111/j.0022-202X.2005.23783.x
Pei, 2008, PROMALS3D: a tool for multiple protein sequence and structure alignments, Nucleic Acids Res., 36, 2295, 10.1093/nar/gkn072
Pettersen, 2004, UCSF Chimera – a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084
Porter, 2005, XP-A cells complemented with Arg228Gln and Val234Leu polymorphic XPA alleles repair BPDE-induced DNA damage better than cells complemented with the wild type allele, DNA Repair, 4, 341, 10.1016/j.dnarep.2004.10.007
Robert, 2014, Deciphering key features in protein structures with the new ENDscript server, Nucleic Acids Res., 42, W320, 10.1093/nar/gku316
Santiago, 2015, Xeroderma pigmentosum: low prevalence of germline XPA mutations in a Brazilian XP population, Int. J. Mol. Sci., 16, 8988, 10.3390/ijms16048988
Sato, 1996, Aberrant splicing and truncated-protein expression due to a newly identified XPA gene mutation, Mutat. Res., 362, 199, 10.1016/0921-8777(95)00052-6
Satokata, 1992, Molecular basis of group A xeroderma pigmentosum: a missense mutation and two deletions, Hum. Genet., 88, 603, 10.1007/BF02265282
Satokata, 1995, Two novel splicing mutations in the XPA gene in patients with group A xeroderma pigmentosum, Hum. Mol Genet., 4, 1993, 10.1093/hmg/4.10.1993
Sidwell, 2006, A novel mutation in the XPA gene associated with unusually mild clinical features in a patient who developed a spindle cell melanoma, Br. J. Dermatol., 155, 81, 10.1111/j.1365-2133.2006.07272.x
States, 1996, Splice site mutations in a xeroderma pigmentosum group A patient with delayed onset of neurological disease, Mutat. Res., 363, 171, 10.1016/0921-8777(96)00004-3
States, 1998, Distribution of mutations in the human xeroderma pigmentosum group A gene and their relationships to the functional regions of the DNA damage recognition protein, Hum. Mutat., 12, 103, 10.1002/(SICI)1098-1004(1998)12:2<103::AID-HUMU5>3.0.CO;2-6
Sun, 2015, Genotype-phenotype correlation of xeroderma pigmentosum in a Chinese Han population, Br. J. Dermatol., 172, 1096, 10.1111/bjd.13429
Takahashi, 2010, XPA gene mutations resulting in subtle truncation of protein in xeroderma pigmentosum group A patients with mild skin symptoms, J. Invest. Dermatol., 130, 2481, 10.1038/jid.2010.137
Wakasugi, 2009, Physical and functional interaction between DDB and XPA in nucleotide excision repair, Nucleic Acids Res., 37, 516, 10.1093/nar/gkn964