House cleaning, a part of good housekeeping

Molecular Microbiology

Volumn 59, Issue 1, 2006, Pages 5-19

  Galperin, Michael Y ^a   Moroz, Olga V ^b   Wilson, Keith S ^b   Murzin, Alexey G ^c  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b UNIVERSITY OF YORK   (United Kingdom)

^c MRC CENTRE FOR PROTEIN ENGINEERING   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYURIDINE TRIPHOSPHATE PYROPHOSPHATASE; DNA; DNA POLYMERASE; ENZYME; HYDROLASE; NUCLEOSIDE DIPHOSPHATASE; NUCLEOSIDE TRIPHOSPHATE; NUCLEOTIDE;

BINDING AFFINITY; BIOCHEMISTRY; CELL METABOLISM; DNA DAMAGE; DNA REPAIR; ENZYME ACTIVITY; GENETIC VARIABILITY; GENOMICS; HOSPITAL SERVICE; HUMAN; HYDROLYSIS; METABOLISM; METABOLITE; METHYLATION; MUTAGENESIS; NONHUMAN; OXIDATIVE STRESS; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; SHORT SURVEY; STRUCTURE ANALYSIS;

BINDING SITES; DNA DAMAGE; DNA REPAIR; HUMANS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEOSIDE-TRIPHOSPHATASE; NUCLEOSIDES; PHOSPHATES; PROTEIN CONFORMATION; PYROPHOSPHATASES; SUBSTRATE SPECIFICITY;

EID: 33645049083     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2005.04950.x     Document Type: Short Survey

References (94)

1. Akiyama M. Maki H. Sekiguchi M. Horiuchi T. 1989 A specific role of MutT protein: to prevent dG.dA mispairing in DNA replication Proc Natl Acad Sci USA 86 3949 3952
2. Andrianopoulos K. Wang L. Reeves PR. 1998 Identification of the fucose synthetase gene in the colanic acid gene cluster of Escherichia coli K-12 J Bacteriol 180 998 1001
3. Bacon DF. Treffers HP. 1961 Spontaneous and mutator-induced reversions of an Escherichia coli auxotroph. I. Prototrophic types and their growth characteristics J Bacteriol 81 786 793
4. Bergman AC. Nyman PO. Larsson G. 1998 Kinetic properties and stereospecificity of the monomeric dUTPase from herpes simplex virus type 1 FEBS Lett 441 327 330
5. m for free ADP-ribose Biochem J 299 679 682
6. Bessman MJ. Frick DN. O'Handley SF. 1996 The MutT proteins or 'Nudix' hydrolases, a family of versatile, widely distributed, 'housecleaning' enzymes J Biol Chem 271 25059 25062
7. Bhatnagar SK. Bessman MJ. 1988 Studies on the mutator gene, mutT of Escherichia coli. Molecular cloning of the gene, purification of the gene product, and identification of a novel nucleoside triphosphatase J Biol Chem 263 8953 8957
8. Bradshaw JS. Kuzminov A. 2003 RdgB acts to avoid chromosome fragmentation in Escherichia coli Mol Microbiol 48 1711 1725
9. Brodie AF. Lipmann F. 1955 Identification of a gluconolactonase J Biol Chem 212 677 685
10. Burgis NE. Brucker JJ. Cunningham RP. 2003 Repair system for noncanonical purines in Escherichia coli J Bacteriol 185 3101 3110
11. Butler YX. Abhayawardhane Y. Stewart GC. 1993 Amplification of the Bacillus subtilis maf gene results in arrested septum formation J Bacteriol 175 3139 3145
12. Cartwright JL. Gasmi L. Spiller DG. McLennan AG. 2000 The Saccharomyces cerevisiae PCD1 gene encodes a peroxisomal Nudix hydrolase active toward coenzyme A and its derivatives J Biol Chem 275 32925 32930
13. Chan S. Segelke B. Lekin T. Krupka H. Cho US. Kim MY. et al. 2004 Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism J Mol Biol 341 503 517
14. Chern CJ. MacDonald AB. Morris AJ. 1969 Purification and properties of a nucleoside triphosphate pyrophosphohydrolase from red cells of the rabbit J Biol Chem 244 5489 5495
15. Christie KR. Weng S. Balakrishnan R. Costanzo MC. Dolinski K. Dwight SS. et al. 2004 Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms Nucleic Acids Res 32 D311 D314
16. Chung JH. Back JH. Park YI. Han YS. 2001 Biochemical characterization of a novel hypoxanthine/xanthine dNTP pyrophosphatase from Methanococcus jannaschii Nucleic Acids Res 29 3099 3107
17. Collard F. Collet JF. Gerin I. Veiga-da-Cunha M. Van Schaftingen E. 1999 Identification of the cDNA encoding human 6-phosphogluconolactonase, the enzyme catalyzing the second step of the pentose phosphate pathway FEBS Lett 459 223 226
18. Cori O. Lipmann F. 1952 The primary oxidation product of enzymatic glucose-6-phosphate oxidation J Biol Chem 194 417 425
19. Cox EC. Yanofsky C. 1969 Mutator gene studies in Escherichia coli J Bacteriol 100 390 397
20. Dobrzanska M. Szurmak B. Wyslouch-Cieszynska A. Kraszewska E. 2002 Cloning and characterization of the first member of the Nudix family from Arabidopsis thaliana J Biol Chem 277 50482 50486
21. Dunn CA. O'Handley SF. Frick DN. Bessman MJ. 1999 Studies on the ADP-ribose pyrophosphatase subfamily of the Nudix hydrolases and tentative identification of trgB, a gene associated with tellurite resistance J Biol Chem 274 32318 32324
22. Ezraty B. Aussel L. Barras F. 2005 Methionine sulfoxide reductases in prokaryotes Biochim Biophys Acta 1703 221 229
23. Farrell CM. Grossman AD. Sauer RT. 2005 Cytoplasmic degradation of ssrA-tagged proteins Mol Microbiol 57 1750 1761
24. Frick DN. Townsend BD. Bessman MJ. 1995 A novel GDP-mannose mannosyl hydrolase shares homology with the MutT family of enzymes J Biol Chem 270 24086 24091
25. Fujikawa K. Kamiya H. Yakushiji H. Fujii Y. Nakabeppu Y. Kasai H. 1999 The oxidized forms of dATP are substrates for the human MutT homologue, the hMTH1 protein J Biol Chem 274 18201 18205
26. Gabelli SB. Bianchet MA. Azurmendi HF. Xia Z. Sarawat V. Mildvan AS. Amzel LM. 2004 Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus Structure (Camb) 12 927 935
27. Gadsden MH. McIntosh EM. Game JC. Wilson PJ. Haynes RH. 1993 dUTP pyrophosphatase is an essential enzyme in Saccharomyces cerevisiae EMBO J 12 4425 4431
28. Galperin MY. 2004 Bacterial signal transduction network in a genomic perspective Environ Microbiol 6 552 567
29. Galperin MY. Walker DR. Koonin EV. 1998 Analogous enzymes: independent inventions in enzyme evolution Genome Res 8 779 790
30. Gasmi L. Cartwright JL. McLennan AG. 1999 Cloning, expression and characterization of YSA1H, a human adenosine 5′-diphosphosugar pyrophosphatase possessing a MutT motif Biochem J 344 331 337
31. Greenberg GR. 1966 New dUTPase and dUDPase activites after infection of Escherichia coli by T2 bacteriophage Proc Natl Acad Sci USA 56 1226 1232
32. Hager PW. Calfee MW. Phibbs PV. 2000 The Pseudomonas aeruginosa devB/SOL homolog, pgl, is a member of the hex regulon and encodes 6- phosphogluconolactonase J Bacteriol 182 3934 3941
33. el-Hajj HH. Zhang H. Weiss B. 1988 Lethality of a dut (deoxyuridine triphosphatase) mutation in Escherichia coli J Bacteriol 170 1069 1075
34. Hamid S. Eckert KA. 2005 Effect of DNA polymerase loop variants on discrimination of O6-methyldeoxyguanosine modification present in the nucleotide versus template substrate Biochemistry 44 10378 10387
35. Harkiolaki M. Dodson EJ. Bernier-Villamor V. Turkenburg JP. Gonzalez-Pacanowska D. Wilson KS. 2004 The crystal structure of Trypanosoma cruzi dUTPase reveals a novel dUTP/dUDP binding fold Structure (Camb) 12 41 53
36. Hizi A. Kamath-Loeb AS. Rose KD. Loeb LA. 1997 Mutagenesis by human immunodeficiency virus reverse transcriptase: incorporation of O6-methyldeoxyguanosine triphosphate Mutat Res 374 41 50
37. Hwang KY. Chung JH. Kim SH. Han YS. Cho Y. 1999 Structure-based identification of a novel NTPase from Methanococcus jannaschii Nat Struct Biol 6 691 696
38. Imlay JA. 2002 How oxygen damages microbes: oxygen tolerance and obligate anaerobiosis Adv Microb Physiol 46 111 153
39. Imlay JA. 2003 Pathways of oxidative damage Annu Rev Microbiol 57 395 418
40. Johansson E. Fano M. Bynck JH. Neuhard J. Larsen S. Sigurskjold BW. et al. 2005 Structures of dCTP deaminase from Escherichia coli with bound substrate and product: reaction mechanism and determinants of mono- and bifunctionality for a family of enzymes J Biol Chem 280 3051 3059
41. Joseleau-Petit D. Vinella D. D'Ari R. 1999 Metabolic alarms and cell division in Escherichia coli J Bacteriol 181 9 14
42. Kamiya H. 2003 Mutagenic potentials of damaged nucleic acids produced by reactive oxygen/nitrogen species: approaches using synthetic oligonucleotides and nucleotides: survey and summary Nucleic Acids Res 31 517 531
43. Kamiya H. 2004 Mutagenicities of 8-hydroxyguanine and 2-hydroxyadenine produced by reactive oxygen species Biol Pharm Bull 27 475 479
44. Kamiya H. Yakushiji H. Dugue L. Tanimoto M. Pochet S. Nakabeppu Y. Harashima H. 2004 Probing the substrate recognition mechanism of the human MTH1 protein by nucleotide analogs J Mol Biol 336 843 850
45. Kim Y. Yakunin AF. Kuznetsova E. Xu X. Pennycooke M. Gu J. et al. 2004 Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum J Biol Chem 279 517 526
46. Kincaid K. Beckman J. Zivkovic A. Halcomb RL. Engels JW. Kuchta RD. 2005 Exploration of factors driving incorporation of unnatural dNTPs into DNA by Klenow fragment (DNA polymerase I) and DNA polymerase alpha Nucleic Acids Res 33 2620 2628
47. Klaus SM. Wegkamp A. Sybesma W. Hugenholtz J. Gregory JF., 3rd, and Hanson AD. 2005 A Nudix enzyme removes pyrophosphate from dihydroneopterin triphosphate in the folate synthesis pathway of bacteria and plants J Biol Chem 280 5274 5280
48. Koonin EV. 1993 A highly conserved sequence motif defining the family of MutT-related proteins from eubacteria, eukaryotes and viruses Nucleic Acids Res 21 4847
49. Kouzminova EA. Kuzminov A. 2004 Chromosomal fragmentation in dUTPase-deficient mutants of Escherichia coli and its recombinational repair Mol Microbiol 51 1279 1295
50. Kunkel TA. Bebenek K. 1988 Recent studies of the fidelity of DNA synthesis Biochim Biophys Acta 951 1 15
51. Kuznetsova E. Proudfoot M. Sanders SA. Reinking J. Savchenko A. Arrowsmith CH. et al. 2005 Enzyme genomics: application of general enzymatic screens to discover new enzymes FEMS Microbiol Rev 29 263 279
52. Larsson G. Nyman PO. Kvassman JO. 1996a Kinetic characterization of dUTPase from Escherichia coli J Biol Chem 271 24010 24016
53. Larsson G. Svensson LA. Nyman PO. 1996b Crystal structure of the Escherichia coli dUTPase in complex with a substrate analogue (dUDP) Nat Struct Biol 3 532 538
54. Lawhorn BG. Gerdes SY. Begley TP. 2004 A genetic screen for the identification of thiamin metabolic genes J Biol Chem 279 43555 43559
55. Liakopoulou A. Alivisatos SG. 1964 Distribution of nucleoside triphosphatases in human erythrocytes Biochim Biophys Acta 89 158 161
56. Lin S. McLennan AG. Ying K. Wang Z. Gu S. Jin H. et al. 2001 Cloning, expression, and characterization of a human inosine triphosphate pyrophosphatase encoded by the ITPA gene J Biol Chem 276 18695 18701
57. Loeb LA. Kunkel TA. 1982 Fidelity of DNA synthesis Annu Rev Biochem 51 429 457
58. Maki H. Sekiguchi M. 1992 MutT protein specifically hydrolyses a potent mutagenic substrate for DNA synthesis Nature 355 273 275
59. Marinaki AM. Ansari A. Duley JA. Arenas M. Sumi S. Lewis CM. et al. 2004 Adverse drug reactions to azathioprine therapy are associated with polymorphism in the gene encoding inosine triphosphate pyrophosphatase (ITPase) Pharmacogenetics 14 181 187
60. Michaels ML. Miller JH. 1992 The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8- oxoguanine) J Bacteriol 174 6321 6325
61. Miclet E. Stoven V. Michels PA. Opperdoes FR. Lallemand JY. Duffieux F. 2001 NMR spectroscopic analysis of the first two steps of the pentose-phosphate pathway elucidates the role of 6-phosphogluconolactonase J Biol Chem 276 34840 34846
62. Mildvan AS. Xia Z. Azurmendi HF. Saraswat V. Legler PM. Massiah MA. et al. 2005 Structures and mechanisms of Nudix hydrolases Arch Biochem Biophys 433 129 143
63. Minasov G. Teplova M. Stewart GC. Koonin EV. Anderson WF. Egli M. 2000 Functional implications from crystal structures of the conserved Bacillus subtilis protein Maf with and without dUTP Proc Natl Acad Sci USA 97 6328 6333
64. Mishima M. Sakai Y. Itoh N. Kamiya H. Furuichi M. Takahashi M. et al. 2004 Structure of human MTH1, a Nudix family hydrolase that selectively degrades oxidized purine nucleoside triphosphates J Biol Chem 279 33806 33815
65. Moroz OV. Harkiolaki M. Galperin MY. Vagin AA. Gonzalez-Pacanowska D. Wilson KS. 2004 The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue sheds light on the mechanism and suggests the 'basic module' for dimeric d(C/U)TPases J Mol Biol 342 1583 1597
66. Moroz OV. Murzin AG. Makarova KS. Koonin EV. Wilson KS. Galperin MY. 2005 Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential 'house-cleaning' functions J Mol Biol 347 243 255
67. Noskov VN. Staak K. Shcherbakova PV. Kozmin SG. Negishi K. Ono BC. et al. 1996 HAM1, the gene controlling 6-N-hydroxylaminopurine sensitivity and mutagenesis in the yeast Saccharomyces cerevisiae Yeast 12 17 29
68. Nunoshiba T. Ishida R. Sasaki M. Iwai S. Nakabeppu Y. Yamamoto K. 2004 A novel Nudix hydrolase for oxidized purine nucleoside triphosphates encoded by ORFYLR151c (PCD1 gene) in Saccharomyces cerevisiae Nucleic Acids Res 32 5339 5348
69. O'Handley SF. Frick DN. Dunn CA. Bessman MJ. 1998 Orf186 represents a new member of the Nudix hydrolases, active on adenosine (5′) triphospho (5′) adenosine, ADP-ribose, and NADH J Biol Chem 273 3192 3197
70. Ogawa T. Ueda Y. Yoshimura K. Shigeoka S. 2005 Comprehensive analysis of cytosolic Nudix hydrolases in Arabidopsis thaliana J Biol Chem 280 25277 25283
71. Perraud AL. Shen B. Dunn CA. Rippe K. Smith MK. Bessman MJ. et al. 2003 NUDT9, a member of the Nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphatase J Biol Chem 278 1794 1801
72. Persson R. Cedergren-Zeppezauer ES. Wilson KS. 2001 Homotrimeric dUTPases; structural solutions for specific recognition and hydrolysis of dUTP Curr Protein Pept Sci 2 287 300
73. Potterton E. McNicholas S. Krissinel E. Cowtan K. Noble M. 2002 The CCP4 molecular-graphics project Acta Cryst D58 1955 1957
74. Potterton L. McNicholas S. Krissinel E. Gruber J. Cowtan K. Emsley P. et al. 2004 Developments in the CCP4 molecular-graphics project Acta Cryst D60 2288 2294
75. Proudfoot M. Kuznetsova E. Brown G. Rao NN. Kitagawa M. Mori H. et al. 2004 General enzymatic screens identify three new nucleotidases in Escherichia coli. Biochemical characterization of SurE, YfbR, and YjjG J Biol Chem 279 54687 54694
76. Saraswat V. Massiah MA. Lopez G. Amzel LM. Mildvan AS. 2002 Interactions of the products, 8-oxo-dGMP, dGMP, and pyrophosphate with the MutT nucleoside triphosphate pyrophosphohydrolase Biochemistry 41 15566 15577
77. Sedgwick B. 2004 Repairing DNA-methylation damage Nat Rev Mol Cell Biol 5 148 157
78. Soga T. Ohashi Y. Ueno Y. Naraoka H. Tomita M. Nishioka T. 2003 Quantitative metabolome analysis using capillary electrophoresis mass spectrometry J Proteome Res 2 488 494
79. Stevenson G. Andrianopoulos K. Hobbs M. Reeves PR. 1996 Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid J Bacteriol 178 4885 4893
80. Stevenson G. Lan R. Reeves PR. 2000 The colanic acid gene cluster of Salmonella enterica has a complex history FEMS Microbiol Lett 191 11 16
81. Thomason LC. Court DL. Datta AR. Khanna R. Rosner JL. 2004 Identification of the Escherichia coli K-12 ybhE gene as pgl, encoding 6- phosphogluconolactonase J Bacteriol 186 8248 8253
82. Treffers HO. Spinelli V. Belser NO. 1954 A factor (or mutator gene) influencing mutation rates in Escherichia coli Proc Natl Acad Sci USA 40 1064 1071
83. Tsuzuki T. Egashira A. Igarashi H. Iwakuma T. Nakatsuru Y. Tominaga Y. et al. 2001 Spontaneous tumorigenesis in mice defective in the MTH1 gene encoding 8-oxo-dGTPase Proc Natl Acad Sci USA 98 11456 11461
84. Vincent F. Davies GJ. Brannigan JA. 2005 Structure and kinetics of a monomeric glucosamine 6-phosphate deaminase: missing link of the NagB superfamily? J Biol Chem 280 19649 19655
85. Wang Z. Jiao X. Carr-Schmid A. Kiledjian M. 2002 The hDcp2 protein is a mammalian mRNA decapping enzyme Proc Natl Acad Sci USA 99 12663 12668
86. Xu W. Gauss P. Shen J. Dunn CA. Bessman MJ. 2002 The gene e.1 (nudE.1) of T4 bacteriophage designates a new member of the Nudix hydrolase superfamily active on flavin adenine dinucleotide, adenosine 5′-triphospho-5′- adenosine, and ADP-ribose J Biol Chem 277 23181 23185
87. Xu W. Shen J. Dunn CA. Bessman MJ. 2003 A new subfamily of the Nudix hydrolase superfamily active on 5-methyl-UTP (ribo-TTP) and UTP J Biol Chem 278 37492 37496
88. Yakunin AF. Proudfoot M. Kuznetsova E. Savchenko A. Brown G. Arrowsmith CH. Edwards AM. 2004 The HD domain of the Escherichia coli tRNA nucleotidyltransferase has 2′,3′-cyclic phosphodiesterase, 2′-nucleotidase, and phosphatase activities J Biol Chem 279 36819 36827
89. Yang H. Slupska MM. Wei YF. Tai JH. Luther WM. Xia YR. et al. 2000 Cloning and characterization of a new member of the Nudix hydrolases from human and mouse J Biol Chem 275 8844 8853
90. Zhang J. Inouye M. 2002 MazG, a nucleoside triphosphate pyrophosphohydrolase, interacts with Era, an essential GTPase in Escherichia coli J Bacteriol 184 5323 5329
91. Zhang C. Kim SH. 2003 Overview of structural genomics: from structure to function Curr Opin Chem Biol 7 28 32
92. Zhang J. Zhang Y. Inouye M. 2003 Thermotoga maritima MazG protein has both nucleoside triphosphate pyrophosphohydrolase and pyrophosphatase activities J Biol Chem 278 21408 21414
93. Zimenkov D. Gulevich A. Skorokhodova A. Biriukova I. Kozlov Y. Mashko S. 2005 Escherichia coli ORF ybhE is pgl gene encoding 6-phosphogluconolactonase (EC 3.1.1.31) that has no homology with known 6PGLs from other organisms FEMS Microbiol Lett 244 275 280
94. Zimmerman SB. Kornberg A. 1961 Deoxycytidine di- and triphosphate cleavage by an enzyme formed in bacteriophage-infected Escherichia coli J Biol Chem 236 1480 1486