Skip to main content
Log in

Backbone and ILV side-chain methyl NMR resonance assignments of human Rev7/Rev3-RBM1 and Rev7/Rev3-RBM2 complexes

  • Article
  • Published:
Biomolecular NMR Assignments Aims and scope Submit manuscript

Abstract

Rev7 is a versatile HORMA (Hop1, Rev7, Mad2) family adaptor protein with multiple roles in mitotic regulation and DNA damage response, and an essential accessory subunit of the translesion synthesis (TLS) DNA polymerase Polζ employed in replication of damaged DNA. Within Polζ, the two copies of Rev7 interact with the two Rev7-bonding motifs (RBM1 and RBM2) of the catalytic subunit Rev3 by a mechanism characteristic of HORMA proteins whereby the “safety-belt” loop of Rev7 closes on the top of the ligand. Here we report the nearly complete backbone and Ile, Val, Leu side-chain methyl NMR resonance assignments of the 27 kDa human Rev7/Rev3-RBM1 and Rev7/Rev3-RBM2 complexes (BMRB deposition numbers 51651 and 51652) that will facilitate future NMR studies of Rev7 dynamics and interactions.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Figs. 1
Figs. 2
Figs. 3
Figs. 4

Similar content being viewed by others

References

  • Aravind L, Koonin EV (1998) The HORMA domain: a common structural denominator in mitotic checkpoints, chromosome synapsis and DNA repair. Trends Biochem Sci 23:284–286

    Article  Google Scholar 

  • Baranovskiy AG, Lada AG, Siebler HM, Zhang Y, Pavlov YI, Tahirov TH (2012) DNA polymerase δ and ζ switch by sharing accessory subunits of DNA polymerase δ. J Biol Chem 287:17281–17287

    Article  Google Scholar 

  • Berjanskii MV, Wishart DS (2008) Application of the random coil index to studying protein flexibility. J Biomol NMR 40:31–48

    Article  Google Scholar 

  • Corbett KD, Rosenberg SC (2015) The multifaceted roles of the HORMA domain in cellular signaling. J Cell Biol 211:745–755

    Article  Google Scholar 

  • Dai Y, Zhang F, Wang L, Shan S, Gong Z, Zhou Z (2019) Structural bases for shieldin complex subunity3-mediated recruitment of the checkpoint protein REV7 during DNA double-strand break repair. J Biol Chem 295:250–262

    Article  Google Scholar 

  • de Krijger I, Boersma V, Jacobs JJL (2021) REV7: Jack of many trades. Trends Cell Biol 31:686–701

    Article  Google Scholar 

  • Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293

    Article  Google Scholar 

  • Ghezraoui H, Oliveira C, Becker JR, Bilham K, Moralli D, Anzilotti C, Fischer R, Deobagkar-Lele M, Sanchiz-Calvo M, Fueyo-Marcos E, Bonham S, Kessler BM, Rottenberg S, Cornall RJ, Green CM, Chapman JR (2018) 53BP1 cooperation with the REV7–shieldin complex underpins DNA structure-specific NHEJ. Nature 560:122–127

    Article  ADS  Google Scholar 

  • Goto NK, Gardner KH, Mueller GA, Willis RC, Kay LE (1999) A robust and cost-effective method for the production of val, Leu, Ile (delta 1) methyl-protonated 15 N-, 13 C-, 2H-labeled proteins. J Biomol NMR 13:369–374

    Article  Google Scholar 

  • Guo C, Tugarinov V (2009) Identification of HN-methyl NOEs in large proteins using simultaneous amide-methyl TROSY-based detection. J Biomol NMR 43:21–30

    Article  Google Scholar 

  • Gupta R, Somyajit K, Narita T, Maskey E, Stanlie A, Kremer M, Typas D, Lammers M, Mailand N, Nussenzweig A, Lukas J, Choudhary C (2018) DNA Repair Network Analysis reveals Shieldin as a Key Regulator of NHEJ and PARP inhibitor sensitivity. Cell 173:972–988e923

    Article  Google Scholar 

  • Hanafusa T, Habu T, Tomida J, Ohashi E, Murakmo Y, Ohmori H (2010) Overlapping in short motif sequences for binding to human Rev7 and Mad2 proteins. Genes Cells 15:291–296

    Article  Google Scholar 

  • Hara K, Shimizu T, Unzai S, Akashi S, Sato M, Hashimoto H (2009) Purification, crystallization and initial X-ray diffraction study of human REV7 in complex with a REV3 fragment. Acta Cryst F 65:1302–1305

    Article  Google Scholar 

  • Hara K, Hashimoto H, Murakumo Y, Kobayashi S, Kogame T, Unzai S, Akashi S, Takeda S, Shimizu T, Sato M (2010) Crystal structure of human Rev7 in complex with a human Rev3 fragment and structural implication of the interaction between DNA polymerase ζ and REV1. J Bioll Chem 285:12299–12307

    Article  Google Scholar 

  • Hara K, Taharazako S, Ikeda M, Fujita H, Mikami Y, Kikuchi S, Hishiki A, Yokoyama H, Ishikawa Y, Kanno S, Tanaka K, Hashimoto H (2017) Dynamic feature of mitotic arrest deficient 2-like protein 2 (MAD2L2) and structural basis for its interaction with chromosome alignment-maintaining phosphoprotein (CAMP). J Biol Chem 292:17658–17667

    Article  Google Scholar 

  • Kikuchi S, Hara K, Shimizu T, Sato M, Hashimoto H (2012) Structural basis of recruitment of DNA polymerase ζ by interaction between REV1 and REV7 proteins. J Biol Chem 287:33847–33852

    Article  Google Scholar 

  • Korzhnev DM, Kay LE (2008) Probing invisible, low-populated states of protein molecules by relaxation dispersion NMR spectroscopy: an application to protein folding. Acc Chem Res 41:442–451

    Article  Google Scholar 

  • Lee YS, Gregory MT, Yang W (2014) Human Pol ζ purified with accessory subunits is active in translesion DNA synthesis and complements Pol η in cisplatin bypass. Proc Natl Acad Sci U S A 111:2954–2959

    Article  ADS  Google Scholar 

  • Lee W, Tonelli M, Markley JL (2015) NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31:1325–1327

    Article  Google Scholar 

  • Liang L, Feng J, Zuo P, Yang J, Lu Y, Yin Y (2020) Molecular basis for assembly of the shieldin comlex and its implications for NHEJ. Nat Comm 11:1–15

    Article  ADS  Google Scholar 

  • Listovsky T, Sale JE (2013) Sequestration of CDH1 by MAD2L2 prevents premature APC/C activation prior to anaphase onset. J Cell Biol 203:87–100

    Article  Google Scholar 

  • Maciejewski MW, Schuyler AD, Gryk MR, Moraru II, Romero PR, Ulrich EL, Eghbalnia HR, Livny M, Delaglio F, Hoch JC (2017) NMRbox: a resource for biomolecular NMR computation. Biophys J 112:1529–1534

    Article  Google Scholar 

  • Makarova AV, Burgers PM (2015) Eukaryotic DNA polymerase zeta. DNA Rep 29:47–55

    Article  Google Scholar 

  • Medendorp K, Vreede L, van Groningen J, Hetterschijt L, Brugmans L, Janssen P, van den Hurk W, de Bruijn D, van Kessel A (2010) The mitotic arrest deficient protein MAD2B interacts with the clathrin light chain A during mitosis. PLoS ONE 5:e15128

    Article  ADS  Google Scholar 

  • Muhandiram DR, Xu GY, Kay LE (1993) An enhanced-sensitivity pure absorption gradient 4D15 N,13 C-edited NOESY experiment. J Biomol NMR 3:463–470

    Article  Google Scholar 

  • Murakumo Y (2002) The property of DNA polymerase zeta: REV7 is a putative portein involved in translesion DNA synthesis and cell cycle control. Mutat Res 510:37–44

    Article  Google Scholar 

  • Murakumo Y, Roth T, Ishii H, Rasio D, Numata S, Croce CM, Fishel R (2000) A human REV7 homolog that interacts with the polymerase ζ catalytic subunit hREV3 and the spindle assembly checkpoint protein hMAD2. J Biol Chem 275:4391–4397

    Article  Google Scholar 

  • Noordermeer SM, Adam S, Setiaputra D, Barazas M, Pettitt SJ, Ling AK, Olivieri M, Álvarez-Quilón A, Moatti N, Zimmermann M, Annunziato S, Krastev DB, Song F, Brandsma I, Frankum J, Brough R, Sherker A, Landry S, Szilard RK, Munro MM, McEwan A, de Goullet T, Lin ZY, Hart T, Moffat J, Gingras AC, Martin A, van Attikum H, Jonkers J, Lord CJ, Rottenberg S, Durocher D (2018) The shieldin complex mediates 53BP1-dependent DNA repair. Nature 560:117–121

    Article  ADS  Google Scholar 

  • Pervushin K, Riek R, Wider G, Wuthrich K (1997) Attenuated T2 relaxation by mutual cancellation of dipole- dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc Natl Acad Sci U S A 94:12366–12371

    Article  ADS  Google Scholar 

  • Pfleger CM, Salic A, Lee E, Kirschner MW (2001) Inhibition of Cdh1–APC by the MAD2-related protein MAD2L2: a novel mechanism for regulating Cdh1. Genes Dev 15:1759–1764

    Article  Google Scholar 

  • Pustovalova Y, Bezsonova I, Korzhnev DM (2012) The C-terminal domain of human Rev1 contains independent binding sites for DNA polymerase η and Rev7 subunit of polymerase ζ. FEBS Lett 586:3051–3056

    Article  Google Scholar 

  • Rizzo AA, Korzhnev DM (2019) The Rev1-Polζ translesion synthesis mutasome: structure, interactions and inhibition. Enzymes 45:139–181

    Article  Google Scholar 

  • Rizzo AA, Vassel FM, Chatterjee N, D’Souza S, Li Y, Hao B, Hemann MT, Walker GC, Korzhnev DM (2018) Rev7 dimerization is important for assembly and function of the Rev1/Polζ translesion synthesis complex. Proc Natl Acad Sci U S A 115:E8191–E8200

    Article  Google Scholar 

  • Salzmann M, Wider G, Pervushin K, Senn H, Wüthrich K (1999) TROSY-type triple-resonance experiments for sequential NMR assignments of large proteins. J Am Chem Soc 121:844–848

    Article  Google Scholar 

  • Setiaputra D, Durocher D (2019) Shieldin - the protector of DNA ends. EMBO Rep 20:e47560

    Article  Google Scholar 

  • Shen Y, Bax A (2015) Protein structural information derived from NMR chemical shift with the neural network program TALOS-N. Methods Mol Biol 1260:17–32

    Article  Google Scholar 

  • Tomida J, Takata K, Lange SS, Schibler AC, Yousefzadeh MJ, Bhetawal S, Dent SYR, Wood RD (2015) Rev7 is essential for DNA damage tolerance via two Rev3L binding sites in mammalian DNA polymerase zeta. Nucleic Acids Res 43:1000–1011

    Article  Google Scholar 

  • Tugarinov V, Kay LE (2003) Ile, Leu, and val methyl assignments of the 723-residue malate synthase G using a new labeling strategy and novel NMR methods. J Am Chem Soc 125:13868–13878

    Article  Google Scholar 

  • Tugarinov V, Hwang PM, Ollerenshaw JE, Kay LE (2003) Cross-correlated relaxation enhanced 1H – 13 C NMR spectroscopy of Methyl Groups in very high Molecular Weight Proteins and protein complexes. J Am Chem Soc 125:10420–10428

    Article  Google Scholar 

  • Tugarinov V, Kay LE, Ibraghimov I, Orekhov VY (2005) High-resolution four-dimensional 1H-13 C NOE spectroscopy using methyl-TROSY, sparse data acquisition, and multidimensional decomposition. J Am Chem Soc 127:2767–2775

    Article  Google Scholar 

  • Vaisman A, Woodgate R (2017) Translesion DNA polymerases in eukaryotes: what makes them tick? Crit Rev Biochem Mol Biol 52:274–303

    Article  Google Scholar 

  • Wang X, Pernicone N, Pertz L, Hua D, Zhang T, Listovsky T, Xie W (2019) Rev7 has a dynamic adaptor region to accommodate small GTPase RAN/Shigella IpaB ligands and its activity is regulated by RanGTP/GDP switch. J Biol Chem 294:15733–15742

    Article  Google Scholar 

  • Waters LS, Minesinger BK, Wiltrout ME, D’Souza S, Woodruff RV, Walker GC (2009) Eukaryotic translesion polymerases and their roles and regulation in DNA damage tolerance. Microb Mol Biol Rev 73:134–154

    Article  Google Scholar 

  • Wojtaszek J, Lee CJ, D’Souza S, Minesinger B, Kim H, D’Andrea AD, Walker GC, Zhou P (2012) Structural basis of Rev1-mediated assembly of a quaternary vertebrate translesion polymerase complex consisting of Rev1, heterodimeric Pol ζ and Pol κ. J Biol Chem 287:33836–33846

    Article  Google Scholar 

  • Yang D, Kay LE (1999) Improved 1HN-detected triple resonance TROSY-based experiments. J Biomol NMR 13:3–10

    Article  Google Scholar 

  • Ying J, Delaglio F, Torchia DA, Bax A (2017) Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data. J Biomol NMR 68:101–118

    Article  Google Scholar 

  • Zambrello MA, Schuyler AD, Maciejewski MW, Delaglio F, Bezsonova I, Hoch JC (2018) Nonuniform sampling in multidimensional NMR for improving spectral sensitivity. Methods 138–139:62–68

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Institutes of Health R01CA233959 grant to D.M.K. and M. Kyle Hadden. The authors thank Dr. Lewis E. Kay for sharing library of custom pulse-sequences used in this work, Dr. Irina Semenova for assistance in generating the Rev7 triple-mutant constructs, and Mr. Sam Mahdi for discussion.

Author information

Authors and Affiliations

Authors

Contributions

D.H.G. and G.A.A. produced the proteins and performed assignments for the Rev7/Rev3-RBM1 and Rev7/Rev3-RBM2 complexes, respectively. D.M.K. performed NMR experiments. All authors contributed to the manuscript preparation.

Corresponding author

Correspondence to Dmitry M. Korzhnev.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Gianluca A. Arianna and Dane H. Geddes-Buehre: Shared first authorship.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Arianna, G.A., Geddes-Buehre, D.H. & Korzhnev, D.M. Backbone and ILV side-chain methyl NMR resonance assignments of human Rev7/Rev3-RBM1 and Rev7/Rev3-RBM2 complexes. Biomol NMR Assign 17, 107–114 (2023). https://doi.org/10.1007/s12104-023-10128-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12104-023-10128-4

Keywords

Navigation