Structural basis for role of ring finger protein RNF168 RING domain

References

• Pickart CM, Eddins MJ. Ubiquitin: structures, functions, mechanisms. Biochim Biophys Acta 2004; 1695:55 - 72; http://dx.doi.org/10.1016/j.bbamcr.2004.09.019; PMID: 15571809
   PubMed Web of Science ®Google Scholar
• Haglund K, Dikic I. Ubiquitylation and cell signaling. EMBO J 2005; 24:3353 - 9; http://dx.doi.org/10.1038/sj.emboj.7600808; PMID: 16148945
   PubMed Web of Science ®Google Scholar
• Thrower JS, Hoffman L, Rechsteiner M, Pickart CM. Recognition of the polyubiquitin proteolytic signal. EMBO J 2000; 19:94 - 102; http://dx.doi.org/10.1093/emboj/19.1.94; PMID: 10619848
   PubMed Web of Science ®Google Scholar
• Ulrich HD, Walden H. Ubiquitin signalling in DNA replication and repair. Nat Rev Mol Cell Biol 2010; 11:479 - 89; http://dx.doi.org/10.1038/nrm2921; PMID: 20551964
   PubMed Web of Science ®Google Scholar
• Huang TT, D’Andrea AD. Regulation of DNA repair by ubiquitylation. Nat Rev Mol Cell Biol 2006; 7:323 - 34; http://dx.doi.org/10.1038/nrm1908; PMID: 16633336
   PubMed Web of Science ®Google Scholar
• Negrini S, Gorgoulis VG, Halazonetis TD. Genomic instability--an evolving hallmark of cancer. Nat Rev Mol Cell Biol 2010; 11:220 - 8; http://dx.doi.org/10.1038/nrm2858; PMID: 20177397
   PubMed Web of Science ®Google Scholar
• Jackson SP, Bartek J. The DNA-damage response in human biology and disease. Nature 2009; 461:1071 - 8; http://dx.doi.org/10.1038/nature08467; PMID: 19847258
   PubMed Web of Science ®Google Scholar
• Ciccia A, Elledge SJ. The DNA damage response: making it safe to play with knives. Mol Cell 2010; 40:179 - 204; http://dx.doi.org/10.1016/j.molcel.2010.09.019; PMID: 20965415
   PubMed Web of Science ®Google Scholar
• Huen MS, Chen J. Assembly of checkpoint and repair machineries at DNA damage sites. Trends Biochem Sci 2010; 35:101 - 8; http://dx.doi.org/10.1016/j.tibs.2009.09.001; PMID: 19875294
   PubMed Web of Science ®Google Scholar
• Polo SE, Jackson SP. Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications. Genes Dev 2011; 25:409 - 33; http://dx.doi.org/10.1101/gad.2021311; PMID: 21363960
   PubMed Web of Science ®Google Scholar
• Huen MSY, Grant R, Manke I, Minn K, Yu XC, Yaffe MB, et al. RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly. Cell 2007; 131:901 - 14; http://dx.doi.org/10.1016/j.cell.2007.09.041; PMID: 18001825
   PubMed Web of Science ®Google Scholar
• Mailand N, Bekker-Jensen S, Faustrup H, Melander F, Bartek J, Lukas C, et al. RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins. Cell 2007; 131:887 - 900; http://dx.doi.org/10.1016/j.cell.2007.09.040; PMID: 18001824
   PubMed Web of Science ®Google Scholar
• Kolas NK, Chapman JR, Nakada S, Ylanko J, Chahwan R, Sweeney FD, et al. Orchestration of the DNA-damage response by the RNF8 ubiquitin ligase. Science 2007; 318:1637 - 40; http://dx.doi.org/10.1126/science.1150034; PMID: 18006705
   PubMed Web of Science ®Google Scholar
• Wang B, Elledge SJ. Ubc13/Rnf8 ubiquitin ligases control foci formation of the Rap80/Abraxas/Brca1/Brcc36 complex in response to DNA damage. Proc Natl Acad Sci USA 2007; 104:20759 - 63; http://dx.doi.org/10.1073/pnas.0710061104; PMID: 18077395
   PubMed Web of Science ®Google Scholar
• Doil C, Mailand N, Bekker-Jensen S, Menard P, Larsen DH, Pepperkok R, et al. RNF168 binds and amplifies ubiquitin conjugates on damaged chromosomes to allow accumulation of repair proteins. Cell 2009; 136:435 - 46; http://dx.doi.org/10.1016/j.cell.2008.12.041; PMID: 19203579
   PubMed Web of Science ®Google Scholar
• Stewart GS, Panier S, Townsend K, Al-Hakim AK, Kolas NK, Miller ES, et al. The RIDDLE syndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNA damage. Cell 2009; 136:420 - 34; http://dx.doi.org/10.1016/j.cell.2008.12.042; PMID: 19203578
   PubMed Web of Science ®Google Scholar
• Sy SM, Jiang J, Dong SS, Lok GT, Wu J, Cai H, et al. Critical roles of ring finger protein RNF8 in replication stress responses. J Biol Chem 2011; 286:22355 - 61; http://dx.doi.org/10.1074/jbc.M111.232041; PMID: 21558560
   PubMed Web of Science ®Google Scholar
• Feng L, Chen J. The E3 ligase RNF8 regulates KU80 removal and NHEJ repair. Nat Struct Mol Biol 2012; 19:201 - 6; http://dx.doi.org/10.1038/nsmb.2211; PMID: 22266820
   PubMed Web of Science ®Google Scholar
• Poulsen M, Lukas C, Lukas J, Bekker-Jensen S, Mailand N. Human RNF169 is a negative regulator of the ubiquitin-dependent response to DNA double-strand breaks. J Cell Biol 2012; 197:189 - 99; http://dx.doi.org/10.1083/jcb.201109100; PMID: 22492721
   PubMed Web of Science ®Google Scholar
• Gudjonsson T, Altmeyer M, Savic V, Toledo L, Dinant C, Grøfte M, et al. TRIP12 and UBR5 suppress spreading of chromatin ubiquitylation at damaged chromosomes. Cell 2012; 150:697 - 709; http://dx.doi.org/10.1016/j.cell.2012.06.039; PMID: 22884692
   PubMed Web of Science ®Google Scholar
• Chen J, Feng W, Jiang J, Deng Y, Huen MS. Ring finger protein RNF169 antagonizes the ubiquitin-dependent signaling cascade at sites of DNA damage. J Biol Chem 2012; 287:27715 - 22; http://dx.doi.org/10.1074/jbc.M112.373530; PMID: 22733822
   PubMed Web of Science ®Google Scholar
• Panier S, Ichijima Y, Fradet-Turcotte A, Leung CC, Kaustov L, Arrowsmith CH, et al. Tandem protein interaction modules organize the ubiquitin-dependent response to DNA double-strand breaks. Mol Cell 2012; 47:383 - 95; http://dx.doi.org/10.1016/j.molcel.2012.05.045; PMID: 22742833
   PubMed Web of Science ®Google Scholar
• Nakada S, Tai I, Panier S, Al-Hakim A, Iemura S, Juang YC, et al. Non-canonical inhibition of DNA damage-dependent ubiquitination by OTUB1. Nature 2010; 466:941 - 6; http://dx.doi.org/10.1038/nature09297; PMID: 20725033
   PubMed Web of Science ®Google Scholar
• Borden KL, Freemont PS. The RING finger domain: a recent example of a sequence-structure family. Curr Opin Struct Biol 1996; 6:395 - 401; http://dx.doi.org/10.1016/S0959-440X(96)80060-1; PMID: 8804826
   PubMed Web of Science ®Google Scholar
• Chasapis CT, Spyroulias GA. RING finger E(3) ubiquitin ligases: structure and drug discovery. Curr Pharm Des 2009; 15:3716 - 31; http://dx.doi.org/10.2174/138161209789271825; PMID: 19925422
   PubMed Web of Science ®Google Scholar
• Yin Q, Lin SC, Lamothe B, Lu M, Lo YC, Hura G, et al. E2 interaction and dimerization in the crystal structure of TRAF6. Nat Struct Mol Biol 2009; 16:658 - 66; http://dx.doi.org/10.1038/nsmb.1605; PMID: 19465916
   PubMed Web of Science ®Google Scholar
• Zhang M, Windheim M, Roe SM, Peggie M, Cohen P, Prodromou C, et al. Chaperoned ubiquitylation--crystal structures of the CHIP U box E3 ubiquitin ligase and a CHIP-Ubc13-Uev1a complex. Mol Cell 2005; 20:525 - 38; http://dx.doi.org/10.1016/j.molcel.2005.09.023; PMID: 16307917
   PubMed Web of Science ®Google Scholar
• Campbell SJ, Edwards RA, Leung CC, Neculai D, Hodge CD, Dhe-Paganon S, et al. Molecular insights into the function of RING finger (RNF)-containing proteins hRNF8 and hRNF168 in Ubc13/Mms2-dependent ubiquitylation. J Biol Chem 2012; 287:23900 - 10; http://dx.doi.org/10.1074/jbc.M112.359653; PMID: 22589545
   PubMed Web of Science ®Google Scholar
• Stewart GS, Panier S, Townsend K, Al-Hakim AK, Kolas NK, Miller ES, et al. The RIDDLE syndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNA damage. Cell 2009; 136:420 - 34; http://dx.doi.org/10.1016/j.cell.2008.12.042; PMID: 19203578
   PubMed Web of Science ®Google Scholar
• Lok GT, Sy SM, Dong SS, Ching YP, Tsao SW, Thomson TM, et al. Differential regulation of RNF8-mediated Lys48- and Lys63-based poly-ubiquitylation. Nucleic Acids Res 2012; 40:196 - 205; http://dx.doi.org/10.1093/nar/gkr655; PMID: 21911360
   PubMed Web of Science ®Google Scholar
• Plans V, Scheper J, Soler M, Loukili N, Okano Y, Thomson TM. The RING finger protein RNF8 recruits UBC13 for lysine 63-based self polyubiquitylation. J Cell Biochem 2006; 97:572 - 82; http://dx.doi.org/10.1002/jcb.20587; PMID: 16215985
   PubMed Web of Science ®Google Scholar
• Huen MS, Huang J, Yuan J, Yamamoto M, Akira S, Ashley C, et al. Noncanonical E2 variant-independent function of UBC13 in promoting checkpoint protein assembly. Mol Cell Biol 2008; 28:6104 - 12; http://dx.doi.org/10.1128/MCB.00987-08; PMID: 18678647
   PubMed Web of Science ®Google Scholar
• Stewart GS, Stankovic T, Byrd PJ, Wechsler T, Miller ES, Huissoon A, et al. RIDDLE immunodeficiency syndrome is linked to defects in 53BP1-mediated DNA damage signaling. Proc Natl Acad Sci USA 2007; 104:16910 - 5; http://dx.doi.org/10.1073/pnas.0708408104; PMID: 17940005
   PubMed Web of Science ®Google Scholar
• Bekker-Jensen S, Rendtlew Danielsen J, Fugger K, Gromova I, Nerstedt A, Lukas C, et al. HERC2 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Nat Cell Biol 2010; 12:80-6; sup pp 1-12.
   Google Scholar
• Mattiroli F, Vissers JH, van Dijk WJ, Ikpa P, Citterio E, Vermeulen W, et al. RNF168 ubiquitinates K13-15 on H2A/H2AX to drive DNA damage signaling. Cell 2012; 150:1182 - 95; http://dx.doi.org/10.1016/j.cell.2012.08.005; PMID: 22980979
   PubMed Web of Science ®Google Scholar
• Otwinowski Z, Minor W. Processing of X-Ray Diffraction Data Collected in Oscillation Mode. Methods Enzymol 1997; 276:307 - 26; http://dx.doi.org/10.1016/S0076-6879(97)76066-X
   PubMed Web of Science ®Google Scholar
• Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 2002; 58:1948 - 54; http://dx.doi.org/10.1107/S0907444902016657; PMID: 12393927
   PubMed Web of Science ®Google Scholar
• Vagin AA, Steiner RA, Lebedev AA, Potterton L, McNicholas S, Long F, et al. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr D Biol Crystallogr 2004; 60:2184 - 95; http://dx.doi.org/10.1107/S0907444904023510; PMID: 15572771
   PubMed Web of Science ®Google Scholar
• Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004; 60:2126 - 32; http://dx.doi.org/10.1107/S0907444904019158; PMID: 15572765
   PubMed Web of Science ®Google Scholar
• Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993; 26:283 - 91; http://dx.doi.org/10.1107/S0021889892009944
   Web of Science ®Google Scholar