P. H. Patel and L. A. Loeb, Getting a grip on how DNA polymerases function, Nature Structural Biology, vol.8, issue.8, pp.656-659, 2001.
DOI : 10.1038/90344

D. K. Braithwaite and J. Ito, Compilation, alignment, and phylogenetic relationships of DNA polymerases, Nucleic Acids Research, vol.21, issue.4, pp.787-802, 1993.
DOI : 10.1093/nar/21.4.787

S. Wu, W. A. Beard, L. G. Pedersen, and S. H. Wilson, Structural Comparison of DNA Polymerase Architecture Suggests a Nucleotide Gateway to the Polymerase Active Site, Chemical Reviews, vol.114, issue.5, pp.2759-2774, 2014.
DOI : 10.1021/cr3005179

I. K. Cann, K. Komori, H. Toh, S. Kanai, and Y. Ishino, A heterodimeric DNA polymerase: Evidence that members of Euryarchaeota possess a distinct DNA polymerase, Proc. Natl Acad. Sci. USA 95, pp.14250-14255, 1998.
DOI : 10.1073/pnas.95.24.14250

L. Greenough, Z. Kelman, and A. Gardner, The roles of family B and D DNA polymerases in Thermococcus species 9°N Okazaki fragment maturation

G. Henneke, D. Flament, U. Hübscher, J. Querellou, and J. Raffin, The Hyperthermophilic Euryarchaeota Pyrococcus abyssi Likely Requires the Two DNA Polymerases D and B for DNA Replication, Journal of Molecular Biology, vol.350, issue.1, pp.53-64, 2005.
DOI : 10.1016/j.jmb.2005.04.042

L. Cubonová, Archaeal DNA Polymerase D but Not DNA Polymerase B Is Required for Genome Replication in Thermococcus kodakarensis, Journal of Bacteriology, vol.195, issue.10, pp.2322-2328, 2013.
DOI : 10.1128/JB.02037-12

K. Yamasaki, Y. Urushibata, T. Yamasaki, F. Arisaka, and I. Matsui, Solution structure of the N-terminal domain of the archaeal D-family DNA polymerase small subunit reveals evolutionary relationship to eukaryotic B-family polymerases, FEBS Letters, vol.25, issue.15, pp.3370-3375, 2010.
DOI : 10.1016/j.febslet.2010.06.026

L. Aravind and E. Koonin, Phosphoesterase domains associated with DNA polymerases of diverse origins, Nucleic Acids Research, vol.26, issue.16, pp.3746-3752, 1998.
DOI : 10.1093/nar/26.16.3746

T. H. Tahirov, K. S. Makarova, I. B. Rogozin, Y. I. Pavlov, and E. Koonin, Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol ?? and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors, Biology Direct, vol.4, issue.1, p.11, 2009.
DOI : 10.1186/1745-6150-4-11

Y. Shen, X. Tang, H. Yokoyama, E. Matsui, and I. Matsui, A 21-amino acid peptide from the cysteine cluster II of the family D DNA polymerase from Pyrococcus horikoshii stimulates its nuclease activity which is Mre11-like and prefers manganese ion as the cofactor, Nucleic Acids Research, vol.32, issue.1, pp.158-168, 2004.
DOI : 10.1093/nar/gkh153

J. P. Griffith, X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex, Cell, vol.82, issue.3, pp.507-522, 1995.
DOI : 10.1016/0092-8674(95)90439-5

N. Sträter, T. Klabunde, P. Tucker, H. Witzel, and B. Krebs, Crystal structure of a purple acid phosphatase containing a dinuclear Fe(III)-Zn(II) active site, Science, vol.268, issue.5216, pp.1489-1492, 1995.
DOI : 10.1126/science.7770774

T. T. Paull and M. Gellert, The 3??? to 5??? Exonuclease Activity of Mre11 Facilitates Repair of DNA Double-Strand Breaks, Molecular Cell, vol.1, issue.7, pp.969-979, 1998.
DOI : 10.1016/S1097-2765(00)80097-0

K. P. Hopfner, Structural Biochemistry and Interaction Architecture of the DNA Double-Strand Break Repair Mre11 Nuclease and Rad50-ATPase, Cell, vol.105, issue.4, pp.473-485, 2001.
DOI : 10.1016/S0092-8674(01)00335-X

D. A. Bressan, H. A. Olivares, B. E. Nelms, and J. H. Petrini, Alteration of N-terminal phosphoesterase signature motifs inactivates Saccharomyces cerevisiae Mre11, Genetics, vol.150, pp.591-600, 1998.

A. Palud, in replicating abasic sites: possible role in DNA damage tolerance?, Molecular Microbiology, vol.246, issue.3, pp.746-761, 2008.
DOI : 10.1111/j.1365-2958.2008.06446.x

URL : https://hal.archives-ouvertes.fr/hal-00617129

F. Rusnak and P. Mertz, Calcineurin: form and function, Physiol. Rev, vol.80, pp.1483-1521, 2000.

M. De-jager, C. Wyman, D. C. Van-gent, and R. Kanaar, DNA end-binding specificity of human Rad50/Mre11 is influenced by ATP, Nucleic Acids Research, vol.30, issue.20, pp.4425-4431, 2002.
DOI : 10.1093/nar/gkf574

M. Jokela, A. Eskelinen, H. Pospiech, J. Rouvinen, and J. Syväoja, Characterization of the 3' exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D, Nucleic Acids Research, vol.32, issue.8, pp.2430-2440, 2004.
DOI : 10.1093/nar/gkh558

L. Holm and P. Rosenström, Dali server: conservation mapping in 3D, Nucleic Acids Research, vol.38, issue.Web Server, pp.545-549, 2010.
DOI : 10.1093/nar/gkq366

A. G. Baranovskiy, X-ray structure of the complex of regulatory subunits of human DNA polymerase delta, Cell Cycle, vol.7, issue.19, pp.3026-3036, 2008.
DOI : 10.4161/cc.7.19.6720

Y. Suwa, Crystal Structure of the Human Pol ?? B Subunit in Complex with the C-terminal Domain of the Catalytic Subunit, Journal of Biological Chemistry, vol.290, issue.23, pp.14328-14337, 2015.
DOI : 10.1074/jbc.M115.649954

M. Delarue, Crystal structure of a prokaryotic aspartyl tRNA-synthetase

Y. Shamoo, A. M. Friedman, M. R. Parsons, W. H. Konigsberg, and T. A. Steitz, Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA, Nature, vol.376, issue.6538, pp.362-366, 1995.
DOI : 10.1038/376362a0

V. Arcus, OB-fold domains: a snapshot of the evolution of sequence, structure and function, Current Opinion in Structural Biology, vol.12, issue.6, pp.794-801, 2002.
DOI : 10.1016/S0959-440X(02)00392-5

K. S. Makarova, M. Krupovic, and E. Koonin, Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery, Frontiers in Microbiology, vol.7, issue.744, p.354, 2014.
DOI : 10.1371/journal.pone.0036972

Y. Shen, Invariant Asp-1122 and Asp-1124 Are Essential Residues for Polymerization Catalysis of Family D DNA Polymerase fromPyrococcus horikoshii, Journal of Biological Chemistry, vol.276, issue.29, pp.27376-27383, 2001.
DOI : 10.1074/jbc.M011762200

M. Okuda, A Novel Zinc Finger Structure in the Large Subunit of Human General Transcription Factor TFIIE, Journal of Biological Chemistry, vol.279, issue.49, pp.51395-51403, 2004.
DOI : 10.1074/jbc.M404722200

L. A. Kelley, S. Mezulis, C. M. Yates, M. N. Wass, and M. J. Sternberg, The Phyre2 web portal for protein modeling, prediction and analysis, Nature Protocols, vol.1, issue.6, pp.845-858, 2015.
DOI : 10.1093/bioinformatics/btl677

G. Ruprich-robert and P. Thuriaux, Non-canonical DNA transcription enzymes and the conservation of two-barrel RNA polymerases, Nucleic Acids Research, vol.38, issue.14, pp.4559-4569, 2010.
DOI : 10.1093/nar/gkq201

L. M. Iyer, E. V. Koonin, and L. Aravind, Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases, BMC Structural Biology, vol.3, issue.1, p.1, 2003.
DOI : 10.1186/1472-6807-3-1

F. Werner and D. Grohmann, Evolution of multisubunit RNA polymerases in the three domains of life, Nature Reviews Microbiology, vol.282, issue.2, pp.85-98, 2011.
DOI : 10.1038/nrmicro2507

E. Lehmann, F. Brueckner, and P. Cramer, Molecular basis of RNA-dependent RNA polymerase II activity, Nature, vol.315, issue.7168, pp.445-449, 2007.
DOI : 10.1038/nature06290

S. Sainsbury, J. Niesser, and P. Cramer, Structure and function of the initially transcribing RNA polymerase II???TFIIB complex, Nature, vol.39, issue.7432, pp.437-440, 2013.
DOI : 10.1038/nature11715

E. V. Makeyev and D. H. Bamford, Cellular RNA-Dependent RNA Polymerase Involved in Posttranscriptional Gene Silencing Has Two Distinct Activity Modes, Molecular Cell, vol.10, issue.6, pp.1417-1427, 2002.
DOI : 10.1016/S1097-2765(02)00780-3

P. S. Salgado, The Structure of an RNAi Polymerase Links RNA Silencing and Transcription, PLoS Biology, vol.15, issue.12, p.434, 2006.
DOI : 10.1371/journal.pbio.0040434.sg001

B. Castrec, S. Laurent, G. Henneke, D. Flament, and J. Raffin, The Glycine-Rich Motif of Pyrococcus abyssi DNA Polymerase D Is Critical for Protein Stability, Journal of Molecular Biology, vol.396, issue.4, pp.840-848, 2010.
DOI : 10.1016/j.jmb.2010.01.006

URL : https://hal.archives-ouvertes.fr/hal-00609913

I. K. Cann and Y. Ishino, Archaeal DNA replication: identifying the pieces to solve a puzzle, Genetics, vol.152, pp.1249-1267, 1999.

B. Castrec, Binding to PCNA in Euryarchaeal DNA Replication Requires Two PIP Motifs for DNA Polymerase D and One PIP Motif for DNA Polymerase B, Journal of Molecular Biology, vol.394, issue.2, pp.209-218, 2009.
DOI : 10.1016/j.jmb.2009.09.044

URL : https://hal.archives-ouvertes.fr/hal-00609928

D. L. Ollis, P. Brick, R. Hamlin, N. G. Xuong, and T. A. Steitz, Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP, Nature, vol.55, issue.6005, pp.762-766, 1985.
DOI : 10.1038/313762a0

L. S. Beese, V. Derbyshire, and T. A. Steitz, Structure of DNA polymerase I Klenow fragment bound to duplex DNA, Science, vol.260, issue.5106, pp.352-355, 1993.
DOI : 10.1126/science.8469987

M. Delarue, O. Poch, N. Tordo, D. Moras, and P. Argos, An attempt to unify the structure of polymerases, "Protein Engineering, Design and Selection", vol.3, issue.6, pp.461-467, 1990.
DOI : 10.1093/protein/3.6.461

M. H. Lamers, R. E. Georgescu, S. Lee, M. Donnell, and J. Kuriyan, Crystal Structure of the Catalytic ?? Subunit of E. coli Replicative DNA Polymerase III, Cell, vol.126, issue.5, pp.881-892, 2006.
DOI : 10.1016/j.cell.2006.07.028

S. Bailey, R. A. Wing, and T. A. Steitz, The Structure of T. aquaticus DNA Polymerase III Is Distinct from Eukaryotic Replicative DNA Polymerases, Cell, vol.126, issue.5, pp.893-904, 2006.
DOI : 10.1016/j.cell.2006.07.027

R. J. Evans, Structure of PolC reveals unique DNA binding and fidelity determinants, Proc. Natl Acad. Sci. USA 105, pp.20695-20700, 2008.
DOI : 10.1073/pnas.0809989106

S. Hamdan, P. D. Carr, S. E. Brown, D. L. Ollis, and N. Dixon, Structural Basis for Proofreading during Replication of the Escherichia coli Chromosome, Structure, vol.10, issue.4, pp.535-546, 2002.
DOI : 10.1016/S0969-2126(02)00738-4

C. A. Brautigam and T. A. Steitz, Structural principles for the inhibition of the 3???-5??? exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates, Journal of Molecular Biology, vol.277, issue.2, pp.363-377, 1998.
DOI : 10.1006/jmbi.1997.1586

E. Koonin, Conserved sequence pattern in a wide variety of phosphoesterases, Protein Science, vol.285, issue.2, pp.356-358, 1994.
DOI : 10.1002/pro.5560030218

G. Schenk, Binuclear Metallohydrolases: Complex Mechanistic Strategies for a Simple Chemical Reaction, Accounts of Chemical Research, vol.45, issue.9, pp.1593-1603, 2012.
DOI : 10.1021/ar300067g

T. Killelea, C. Ralec, A. Bossé, and G. Henneke, PCR performance of a thermostable heterodimeric archaeal DNA polymerase, Frontiers in Microbiology, vol.13, p.195, 2014.
DOI : 10.1002/(SICI)1098-2825(1999)13:3133::AID-JCLA83.0.CO;2-0

URL : https://hal.archives-ouvertes.fr/hal-01111507

P. D. Adams, The Phenix software for automated determination of macromolecular structures, Methods, vol.55, issue.1, pp.94-106, 2011.
DOI : 10.1016/j.ymeth.2011.07.005

P. Emsley and K. Cowtan, : model-building tools for molecular graphics, Acta Crystallographica Section D Biological Crystallography, vol.60, issue.12, pp.2126-2132, 2004.
DOI : 10.1107/S0907444904019158

I. W. Davis, MolProbity: all-atom contacts and structure validation for proteins and nucleic acids, Nucleic Acids Research, vol.35, issue.Web Server, pp.375-383, 2007.
DOI : 10.1093/nar/gkm216

J. Painter and E. A. Merritt, Optimal description of a protein structure in terms of multiple groups undergoing TLS motion, Acta Crystallographica Section D Biological Crystallography, vol.62, issue.4, pp.439-450, 2006.
DOI : 10.1107/S0907444906005270/sx5049sup1.pdf

E. Krissinel and K. Henrick, Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions, Acta Crystallographica Section D Biological Crystallography, vol.60, issue.12, pp.2256-2268, 2004.
DOI : 10.1107/S0907444904026460

B. Lee and F. M. Richards, The interpretation of protein structures: Estimation of static accessibility, Journal of Molecular Biology, vol.55, issue.3, pp.379-400, 1971.
DOI : 10.1016/0022-2836(71)90324-X

N. A. Baker, D. Sept, S. Joseph, M. J. Holst, and J. A. Mccammon, Electrostatics of nanosystems: Application to microtubules and the ribosome, Proc. Natl Acad. Sci. USA 98, pp.10037-10041, 2001.
DOI : 10.1073/pnas.181342398

E. F. Pettersen, UCSF Chimera?A visualization system for exploratory research and analysis, Journal of Computational Chemistry, vol.373, issue.13, pp.1605-1612, 2004.
DOI : 10.1002/jcc.20084

M. Landau, ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures, Nucleic Acids Research, vol.33, issue.Web Server, pp.299-302, 2005.
DOI : 10.1093/nar/gki370

Y. B. Park, J. Chae, Y. C. Kim, and Y. Cho, Crystal Structure of Human Mre11: Understanding Tumorigenic Mutations, Structure, vol.19, issue.11, pp.1591-1602, 2011.
DOI : 10.1016/j.str.2011.09.010

C. B. Schiller, Structure of Mre11???Nbs1 complex yields insights into ataxia-telangiectasia???like disease mutations and DNA damage signaling, Nature Structural & Molecular Biology, vol.9, issue.7, pp.693-700, 2012.
DOI : 10.1093/nar/gkh430

C. Möckel, K. Lammens, A. Schele, and K. Hopfner, ATP driven structural changes of the bacterial Mre11:Rad50 catalytic head complex, Nucleic Acids Research, vol.40, issue.2, pp.914-927, 2012.
DOI : 10.1093/nar/gkr749

S. Klinge, R. Núñez-ramírez, O. Llorca, and L. Pellegrini, 3D architecture of DNA Pol ?? reveals the functional core of multi-subunit replicative polymerases, The EMBO Journal, vol.426, issue.13, pp.1978-1987, 2009.
DOI : 10.1038/nri2281