DNA building blocks: keeping control of manufacture

References

• Andersson J, Westman M, Hofer A, Sjöberg BM. 2000. Allosteric regulation of the class III anaerobic ribonucleotide reductase from bacteriophage T4. J Biol Chem 275:19443–19448.
   PubMed Web of Science ®Google Scholar
• Aravind L, Wolf YI, Koonin EV. 2000. The ATP-cone: an evolutionarily mobile, ATP-binding regulatory domain. J Mol Microbiol Biotechnol 2:191–194.
   PubMedGoogle Scholar
• Averett DR, Lubbers C, Elion GB, Spector T. 1983. Ribonucleotide reductase induced by herpes simplex type 1 virus. Characterization of a distinct enzyme. J Biol Chem 258:9831–9838.
   PubMedGoogle Scholar
• Aye Y, Stubbe J. 2011. Clofarabine 5′-di and -triphosphates inhibit human ribonucleotide reductase by altering the quaternary structure of its large subunit. Proc Natl Acad Sci USA 108:9815–9820.
   PubMedGoogle Scholar
• Bianchi V, Pontis E, Reichard P. 1986. Changes of deoxyribonucleoside triphosphate pools induced by hydroxyurea and their relation to DNA synthesis. J Biol Chem 261:16037–16042.
   PubMed Web of Science ®Google Scholar
• Birgander PL, Kasrayan A, Sjöberg BM. 2004. Mutant R1 proteins from Escherichia coli class Ia ribonucleotide reductase with altered responses to dATP inhibition. J Biol Chem 279:14496–14501.
   PubMedGoogle Scholar
• Bochner BR, Ames BN. 1982. Complete analysis of cellular nucleotides by two-dimensional thin layer chromatography. J Biol Chem 257:9759–9769.
   PubMed Web of Science ®Google Scholar
• Bourdon A, Minai L, Serre V, Jais JP, Sarzi E, Aubert S, Chrétien D, de Lonlay P, Paquis-Flucklinger V, Arakawa H, Nakamura Y, Munnich A, Rötig A. 2007. Mutation of RRM2B, encoding p53-controlled ribonucleotide reductase (p53R2), causes severe mitochondrial DNA depletion. Nat Genet 39:776–780.
   PubMed Web of Science ®Google Scholar
• Brown NC, Reichard P. 1969a. Ribonucleoside diphosphate reductase. Formation of active and inactive complexes of proteins B1 and B2. J Mol Biol 46:25–38.
   PubMed Web of Science ®Google Scholar
• Brown NC, Reichard P. 1969b. Role of effector binding in allosteric control of ribonucleoside diphosphate reductase. J Mol Biol 46:39–55.
   PubMed Web of Science ®Google Scholar
• Buckstein MH, He J, Rubin H. 2008. Characterization of nucleotide pools as a function of physiological state in Escherichia coli. J Bacteriol 190:718–726.
   PubMed Web of Science ®Google Scholar
• Caras IW, Martin DW Jr. 1988. Molecular cloning of the cDNA for a mutant mouse ribonucleotide reductase M1 that produces a dominant mutator phenotype in mammalian cells. Mol Cell Biol 8:2698–2704.
   PubMed Web of Science ®Google Scholar
• Chabes A, Domkin V, Larsson G, Liu A, Gräslund A, Wijmenga S, Thelander L. 2000. Yeast ribonucleotide reductase has a heterodimeric iron-radical-containing subunit. Proc Natl Acad Sci USA 97:2474–2479.
   PubMedGoogle Scholar
• Chabes A, Georgieva B, Domkin V, Zhao X, Rothstein R, Thelander L. 2003. Survival of DNA damage in yeast directly depends on increased dNTP levels allowed by relaxed feedback inhibition of ribonucleotide reductase. Cell 112:391–401.
   PubMed Web of Science ®Google Scholar
• Chimploy K, Mathews CK. 2001. Mouse ribonucleotide reductase control: influence of substrate binding upon interactions with allosteric effectors. J Biol Chem 276:7093–7100.
   PubMedGoogle Scholar
• Cory JG, Fleischer AE. 1982. The molecular weight of Ehrlich tumor cell ribonucleotide reductase and its subunits: effector-induced changes. Arch Biochem Biophys 217:546–551.
   PubMedGoogle Scholar
• Cotruvo JA, Stubbe J. 2011a. Class I ribonucleotide reductases: metallocofactor assembly and repair in vitro and in vivo. Annu Rev Biochem 80:733–767.
   PubMed Web of Science ®Google Scholar
• Cotruvo JA, Stubbe J. 2011b. Escherichia coli class Ib ribonucleotide reductase contains a dimanganese(III)-tyrosyl radical cofactor in vivo. Biochemistry 50:1672–1681.
   PubMedGoogle Scholar
• Cox N, Ogata H, Stolle P, Reijerse E, Auling G, Lubitz W. 2010. A tyrosyl-dimanganese coupled spin system is the native metalloradical cofactor of the R2F subunit of the ribonucleotide reductase of Corynebacterium ammoniagenes. J Am Chem Soc 132:11197–11213.
   PubMedGoogle Scholar
• Crona M, Furrer E, Torrents E, Edgell DR, Sjöberg BM. 2010. Subunit and small-molecule interaction of ribonucleotide reductases via surface plasmon resonance biosensor analyses. Protein Eng Des Sel 23:633–641.
   PubMedGoogle Scholar
• Crona M, Moffatt C, Friedrich NC, Hofer A, Sjöberg BM, Edgell DR. 2011a. Assembly of a fragmented ribonucleotide reductase by protein interaction domains derived from a mobile genetic element. Nucleic Acids Res 39:1381–1389.
   PubMedGoogle Scholar
• Crona M, Torrents E, Røhr AK, Hofer A, Furrer E, Tomter AB, Andersson KK, Sahlin M, Sjöberg BM. 2011b. NrdH-Redoxin Protein Mediates High Enzyme Activity in Manganese-reconstituted Ribonucleotide Reductase from Bacillus anthracis. J Biol Chem 286:33053–33060.
   PubMedGoogle Scholar
• Eriksson M, Uhlin U, Ramaswamy S, Ekberg M, Regnström K, Sjöberg BM, Eklund H. 1997. Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding. Structure 5:1077–1092.
   PubMedGoogle Scholar
• Eriksson S. 1983. Direct photoaffinity labeling of ribonucleotide reductase from Escherichia coli. Evidence for enhanced binding of the allosteric effector dTTP by the presence of substrates. J Biol Chem 258:5674–5678.
   PubMedGoogle Scholar
• Eriksson S, Gudas LJ, Clift SM, Caras IW, Ullman B, Martin DW Jr. 1981. Evidence for genetically independent allosteric regulatory domains of the protein M1 subunit of mouse ribonucleotide reductase. J Biol Chem 256:10193–10197.
   PubMedGoogle Scholar
• Fairman JW, Wijerathna SR, Ahmad MF, Xu H, Nakano R, Jha S, Prendergast J, Welin RM, Flodin S, Roos A, Nordlund P, Li Z, Walz T, Dealwis CG. 2011. Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization. Nat Struct Mol Biol 18:316–322.
   PubMed Web of Science ®Google Scholar
• Hall JD, Furman PA, St Clair MH, Knopf CW. 1985. Reduced in vivo mutagenesis by mutant herpes simplex DNA polymerase involves improved nucleotide selection. Proc Natl Acad Sci USA 82:3889–3893.
   PubMedGoogle Scholar
• Hendricks SP, Mathews CK. 1997. Regulation of T4 phage aerobic ribonucleotide reductase. Simultaneous assay of the four activities. J Biol Chem 272:2861–2865.
   PubMedGoogle Scholar
• Hofer A, Ekanem JT, Thelander L. 1998. Allosteric regulation of Trypanosoma brucei ribonucleotide reductase studied in vitro and in vivo. J Biol Chem 273:34098–34104.
   PubMedGoogle Scholar
• Hofer A, Schmidt PP, Gräslund A, Thelander L. 1997. Cloning and characterization of the R1 and R2 subunits of ribonucleotide reductase from Trypanosoma brucei. Proc Natl Acad Sci USA 94:6959–6964.
   PubMedGoogle Scholar
• Hofer A, Steverding D, Chabes A, Brun R, Thelander L. 2001. Trypanosoma brucei CTP synthetase: a target for the treatment of African sleeping sickness. Proc Natl Acad Sci USA 98:6412–6416.
   PubMed Web of Science ®Google Scholar
• Håkansson P, Hofer A, Thelander L. 2006. Regulation of mammalian ribonucleotide reduction and dNTP pools after DNA damage and in resting cells. J Biol Chem 281:7834–7841.
   PubMed Web of Science ®Google Scholar
• Högbom M, Stenmark P, Voevodskaya N, McClarty G, Gräslund A, Nordlund P. 2004. The radical site in chlamydial ribonucleotide reductase defines a new R2 subclass. Science 305:245–248.
   PubMedGoogle Scholar
• Ingemarson R, Thelander L. 1996. A kinetic study on the influence of nucleoside triphosphate effectors on subunit interaction in mouse ribonucleotide reductase. Biochemistry 35:8603–8609.
   PubMedGoogle Scholar
• Ji JP, Sargent RG, Mathews CK. 1991. T4 phage ribonucleotide reductase. Allosteric regulation in vivo by thymidine triphosphate. J Biol Chem 266:16289–16292.
   PubMedGoogle Scholar
• Kashlan OB, Cooperman BS. 2003. Comprehensive model for allosteric regulation of mammalian ribonucleotide reductase: refinements and consequences. Biochemistry 42:1696–1706.
   PubMedGoogle Scholar
• Kashlan OB, Scott CP, Lear JD, Cooperman BS. 2002. A comprehensive model for the allosteric regulation of mammalian ribonucleotide reductase. Functional consequences of ATP- and dATP-induced oligomerization of the large subunit. Biochemistry 41:462–474.
   PubMed Web of Science ®Google Scholar
• Kasrayan A, Birgander PL, Pappalardo L, Regnström K, Westman M, Slaby A, Gordon E, Sjöberg BM. 2004. Enhancement by effectors and substrate nucleotides of R1-R2 interactions in Escherichia coli class Ia ribonucleotide reductase. J Biol Chem 279:31050–31057.
   PubMedGoogle Scholar
• Kumar D, Abdulovic AL, Viberg J, Nilsson AK, Kunkel TA, Chabes A. 2011. Mechanisms of mutagenesis in vivo due to imbalanced dNTP pools. Nucleic Acids Res 39:1360–1371.
   PubMed Web of Science ®Google Scholar
• Larsson KM, Andersson J, Sjöberg BM, Nordlund P, Logan DT. 2001. Structural basis for allosteric substrate specificity regulation in anaerobic ribonucleotide reductases. Structure 9:739–750.
   PubMed Web of Science ®Google Scholar
• Larsson KM, Jordan A, Eliasson R, Reichard P, Logan DT, Nordlund P. 2004. Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase. Nat Struct Mol Biol 11:1142–1149.
   PubMedGoogle Scholar
• Larsson KM, Logan DT, Nordlund P. 2010. Structural basis for adenosylcobalamin activation in AdoCbl-dependent ribonucleotide reductases. ACS Chem Biol 5:933–942.
   PubMedGoogle Scholar
• Logan DT. (2008). Anaerobic riboncleotide reductases: recent progress in understanding. In: Anderssson, KK. (ed). Ribonucleotide reductase. Hauppauge, New York: Nova Science Publishers, pp. 185–208.
   Google Scholar
• Logan DT. 2011. Closing the circle on ribonucleotide reductases. Nat Struct Mol Biol 18:251–253.
   PubMedGoogle Scholar
• Logan DT, Andersson J, Sjöberg BM, Nordlund P. 1999. A glycyl radical site in the crystal structure of a class III ribonucleotide reductase. Science 283:1499–1504.
   PubMedGoogle Scholar
• Lundin D, Gribaldo S, Torrents E, Sjöberg BM, Poole AM. 2010. Ribonucleotide reduction – horizontal transfer of a required function spans all three domains. BMC Evol Biol 10:383.
   PubMed Web of Science ®Google Scholar
• Martin JE, Imlay JA. 2011. The alternative aerobic ribonucleotide reductase of Escherichia coli, NrdEF, is a manganese-dependent enzyme that enables cell replication during periods of iron starvation. Mol Microbiol 80:319–334.
   PubMedGoogle Scholar
• Mathews CK. 2006. DNA precursor metabolism and genomic stability. FASEB J 20:1300–1314.
   PubMed Web of Science ®Google Scholar
• Nakano K, Bálint E, Ashcroft M, Vousden KH. 2000. A ribonucleotide reductase gene is a transcriptional target of p53 and p73. Oncogene 19:4283–4289.
   PubMed Web of Science ®Google Scholar
• Nocentini G. 1996. Ribonucleotide reductase inhibitors: new strategies for cancer chemotherapy. Crit Rev Oncol Hematol 22:89–126.
   PubMed Web of Science ®Google Scholar
• Nordlund P, Reichard P. 2006. Ribonucleotide reductases. Annu Rev Biochem 75:681–706.
   PubMed Web of Science ®Google Scholar
• Ormö M, Sjöberg BM. 1990. An ultrafiltration assay for nucleotide binding to ribonucleotide reductase. Anal Biochem 189:138–141.
   PubMedGoogle Scholar
• Parker WB, Shaddix SC, Chang CH, White EL, Rose LM, Brockman RW, Shortnacy AT, Montgomery JA, Secrist JA 3rd, Bennett LL Jr. 1991. Effects of 2-chloro-9-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)adenine on K562 cellular metabolism and the inhibition of human ribonucleotide reductase and DNA polymerases by its 5′-triphosphate. Cancer Res 51:2386–2394.
   PubMed Web of Science ®Google Scholar
• Reichard P, Eliasson R, Ingemarson R, Thelander L. 2000. Cross-talk between the allosteric effector-binding sites in mouse ribonucleotide reductase. J Biol Chem 275:33021–33026.
   PubMedGoogle Scholar
• Riera J, Robb FT, Weiss R, Fontecave M. 1997. Ribonucleotide reductase in the archaeon Pyrococcus furiosus: a critical enzyme in the evolution of DNA genomes? Proc Natl Acad Sci USA 94:475–478.
   PubMed Web of Science ®Google Scholar
• Rofougaran R, Crona M, Vodnala M, Sjöberg BM, Hofer A. 2008. Oligomerization status directs overall activity regulation of the Escherichia coli class Ia ribonucleotide reductase. J Biol Chem 283:35310–35318.
   PubMedGoogle Scholar
• Rofougaran R, Vodnala M, Hofer A. 2006. Enzymatically active mammalian ribonucleotide reductase exists primarily as an alpha6beta2 octamer. J Biol Chem 281:27705–27711.
   PubMed Web of Science ®Google Scholar
• Roshick C, Iliffe-Lee ER, McClarty G. 2000. Cloning and characterization of ribonucleotide reductase from Chlamydia trachomatis. J Biol Chem 275:38111–38119.
   PubMed Web of Science ®Google Scholar
• Sintchak MD, Arjara G, Kellogg BA, Stubbe J, Drennan CL. 2002. The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer. Nat Struct Biol 9:293–300.
   PubMedGoogle Scholar
• Sjöberg BM, Torrents E. 2011. Shift in ribonucleotide reductase gene expression in Pseudomonas aeruginosa during infection. Infect Immun 79:2663–2669.
   PubMed Web of Science ®Google Scholar
• Skoog L, Nordenskjöld B. 1971. Effects of hydroxyurea and 1-beta-D-arabinofuranosyl-cytosine on deoxyribonucleotide pools in mouse embryo cells. Eur J Biochem 19:81–89.
   PubMedGoogle Scholar
• Tanaka H, Arakawa H, Yamaguchi T, Shiraishi K, Fukuda S, Matsui K, Takei Y, Nakamura Y. 2000. A ribonucleotide reductase gene involved in a p53-dependent cell-cycle checkpoint for DNA damage. Nature 404:42–49.
   PubMed Web of Science ®Google Scholar
• Thelander L, Eriksson S, Åkerman M. 1980. Ribonucleotide reductase from calf thymus. Separation of the enzyme into two nonidentical subunits, proteins M1 and M2. J Biol Chem 255:7426–7432.
   PubMed Web of Science ®Google Scholar
• Torrents E, Buist G, Liu A, Eliasson R, Kok J, Gibert I, Gräslund A, Reichard P. 2000. The anaerobic (class III) ribonucleotide reductase from Lactococcus lactis. Catalytic properties and allosteric regulation of the pure enzyme system. J Biol Chem 275:2463–2471.
   PubMedGoogle Scholar
• Torrents E, Eliasson R, Wolpher H, Gräslund A, Reichard P. 2001. The anaerobic ribonucleotide reductase from Lactococcus lactis. Interactions between the two proteins NrdD and NrdG. J Biol Chem 276:33488–33494.
   PubMedGoogle Scholar
• Torrents E, Poplawski A, Sjöberg BM. 2005. Two proteins mediate class II ribonucleotide reductase activity in Pseudomonas aeruginosa: expression and transcriptional analysis of the aerobic enzymes. J Biol Chem 280:16571–16578.
   PubMedGoogle Scholar
• Torrents E, Westman M, Sahlin M, Sjöberg BM. 2006. Ribonucleotide reductase modularity: Atypical duplication of the ATP-cone domain in Pseudomonas aeruginosa. J Biol Chem 281:25287–25296.
   PubMedGoogle Scholar
• Traut TW. 1994. Physiological concentrations of purines and pyrimidines. Mol Cell Biochem 140:1–22.
   PubMed Web of Science ®Google Scholar
• Uhlin U, Eklund H. 1994. Structure of ribonucleotide reductase protein R1. Nature 370:533–539.
   PubMed Web of Science ®Google Scholar
• Uppsten M, Färnegårdh M, Jordan A, Eliasson R, Eklund H, Uhlin U. 2003. Structure of the large subunit of class Ib ribonucleotide reductase from Salmonella typhimurium and its complexes with allosteric effectors. J Mol Biol 330:87–97.
   PubMedGoogle Scholar
• Wang J, Lohman GJ, Stubbe J. 2009. Mechanism of inactivation of human ribonucleotide reductase with p53R2 by gemcitabine 5′-diphosphate. Biochemistry 48:11612–11621.
   PubMed Web of Science ®Google Scholar
• Wang PJ, Chabes A, Casagrande R, Tian XC, Thelander L, Huffaker TC. 1997. Rnr4p, a novel ribonucleotide reductase small-subunit protein. Mol Cell Biol 17:6114–6121.
   PubMedGoogle Scholar
• Weinberg G, Ullman B, Martin DW Jr. 1981. Mutator phenotypes in mammalian cell mutants with distinct biochemical defects and abnormal deoxyribonucleoside triphosphate pools. Proc Natl Acad Sci USA 78:2447–2451.
   PubMed Web of Science ®Google Scholar
• von Döbeln U, Reichard P. 1976. Binding of substrates to Escherichia coli ribonucleotide reductase. J Biol Chem 251:3616–3622.
   PubMed Web of Science ®Google Scholar
• Xu H, Faber C, Uchiki T, Fairman JW, Racca J, Dealwis C. 2006. Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation. Proc Natl Acad Sci USA 103:4022–4027.
   PubMedGoogle Scholar