Nucleic Acids Research, Vol 25, Issue 24 5110-5118, Copyright © 1997 by Oxford University Press
MJ Moser, WR Holley, A Chatterjee and IS Mian
Prior sequence analysis studies have suggested that bacterial ribonuclease
(RNase) Ds comprise a complete domain that is found also in Homo sapiens
polymyositis-scleroderma overlap syndrome 100 kDa autoantigen and Werner
syndrome protein. This RNase D 3'-->5' exoribonuclease domain was
predicted to have a structure and mechanism of action similar to the
3'-->5' exodeoxyibonuclease (proofreading) domain of DNA polymerases.
Here, hidden Markov model (HMM) and phylogenetic studies have been used to
identify and characterise other sequences that may possess this exonuclease
domain. Results indicate that it is also present in the RNase T family;
Borrelia burgdorferi P93 protein, an immunodominant antigen in Lyme
disease; bacteriophage T4 dexA and Escherichia coli exonuclease I,
processive 3'-->5' exodeoxyribonucleases that degrade single-stranded
DNA; Bacillus subtilis dinG, a probable helicase involved in DNA repair and
possibly replication, and peptide synthase 1; Saccharomyces cerevisiae
Pab1p- dependent poly(A) nuclease PAN2 subunit, required for shortening
mRNA poly(A) tails; Caenorhabditis elegans and Mus musculus CAF1,
transcription factor CCR4-associated factor 1; Xenopus laevis XPMC2,
prevention of mitotic catastrophe in fission yeast; Drosophila melanogaster
egalitarian, oocyte specification and axis determination, and exuperantia,
establishment of oocyte polarity; H.sapiens HEM45, expressed in tumour cell
lines and uterus and regulated by oestrogen; and 31 open reading frames
including one in Methanococcus jannaschii . Examination of a multiple
sequence alignment and two three-dimensional structures of proofreading
domains has allowed definition of the core sequence, structural and
functional elements of this exonuclease domain.
ARTICLES
The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains
Life Sciences Division (Mail Stop 29-100), Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. Dienstbier, F. Boehl, X. Li, and S. L. Bullock Egalitarian is a selective RNA-binding protein linking mRNA localization signals to the dynein motor Genes & Dev., July 1, 2009; 23(13): 1546 - 1558. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Horiuchi, K. Takeuchi, N. Noda, N. Muroya, T. Suzuki, T. Nakamura, J. Kawamura-Tsuzuku, K. Takahasi, T. Yamamoto, and F. Inagaki Structural Basis for the Antiproliferative Activity of the Tob-hCaf1 Complex J. Biol. Chem., May 8, 2009; 284(19): 13244 - 13255. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Lagunavicius, Z. Kiveryte, V. Zimbaite-Ruskuliene, T. Radzvilavicius, and A. Janulaitis Duality of polynucleotide substrates for Phi29 DNA polymerase: 3'->5' RNase activity of the enzyme RNA, March 1, 2008; 14(3): 503 - 513. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. D. Eckerle, X. Lu, S. M. Sperry, L. Choi, and M. R. Denison High Fidelity of Murine Hepatitis Virus Replication Is Decreased in nsp14 Exoribonuclease Mutants J. Virol., November 15, 2007; 81(22): 12135 - 12144. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. A. Stead, J. L. Costello, M. J. Livingstone, and P. Mitchell The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein Nucleic Acids Res., August 23, 2007; (2007) gkm614v2. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Ohn, Y.-C. Chiang, D. J. Lee, G. Yao, C. Zhang, and C. L. Denis CAF1 plays an important role in mRNA deadenylation separate from its contact to CCR4 Nucleic Acids Res., May 14, 2007; 35(9): 3002 - 3015. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Brucet, J. Querol-Audi, M. Serra, X. Ramirez-Espain, K. Bertlik, L. Ruiz, J. Lloberas, M. J. Macias, I. Fita, and A. Celada Structure of the Dimeric Exonuclease TREX1 in Complex with DNA Displays a Proline-rich Binding Site for WW Domains J. Biol. Chem., May 11, 2007; 282(19): 14547 - 14557. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Takahashi, K. Kontani, Y. Araki, and T. Katada Caf1 regulates translocation of ribonucleotide reductase by releasing nucleoplasmic Spd1-Suc22 assembly Nucleic Acids Res., February 28, 2007; 35(4): 1187 - 1197. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. M. Hisama, V. A. Bohr, and J. Oshima WRN's Tenth Anniversary Sci. Aging Knowl. Environ., June 28, 2006; 2006(10): pe18 - pe18. [Abstract] [Full Text]
|
|
|
|
 |
|
 E. Minskaia, T. Hertzig, A. E. Gorbalenya, V. Campanacci, C. Cambillau, B. Canard, and J. Ziebuhr Discovery of an RNA virus 3'->5' exoribonuclease that is critically involved in coronavirus RNA synthesis PNAS, March 28, 2006; 103(13): 5108 - 5113. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. W. Perrino, S. Harvey, S. McMillin, and T. Hollis The Human TREX2 3' -> 5'-Exonuclease Structure Suggests a Mechanism for Efficient Nonprocessive DNA Catalysis J. Biol. Chem., April 15, 2005; 280(15): 15212 - 15218. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-G. Ren, L. A. Kirsebom, and A. Virtanen Coordination of Divalent Metal Ions in the Active Site of Poly(A)-specific Ribonuclease J. Biol. Chem., November 19, 2004; 279(47): 48702 - 48706. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Choudhary, J. A. Sommers, and R. M. Brosh Jr. Biochemical and Kinetic Characterization of the DNA Helicase and Exonuclease Activities of Werner Syndrome Protein J. Biol. Chem., August 13, 2004; 279(33): 34603 - 34613. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Berthet, A.-M. Morera, M.-J. Asensio, M.-A. Chauvin, A.-P. Morel, F. Dijoud, J.-P. Magaud, P. Durand, and J.-P. Rouault CCR4-Associated Factor CAF1 Is an Essential Factor for Spermatogenesis Mol. Cell. Biol., July 1, 2004; 24(13): 5808 - 5820. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Mangus, M. C. Evans, N. S. Agrin, M. Smith, P. Gongidi, and A. Jacobson Positive and Negative Regulation of Poly(A) Nuclease Mol. Cell. Biol., June 15, 2004; 24(12): 5521 - 5533. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Viswanathan, T. Ohn, Y.-C. Chiang, J. Chen, and C. L. Denis Mouse CAF1 Can Function As a Processive Deadenylase/3'-5'-Exonuclease in Vitro but in Yeast the Deadenylase Function of CAF1 Is Not Required for mRNA Poly(A) Removal J. Biol. Chem., June 4, 2004; 279(23): 23988 - 23995. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S.-J. Lee, J.-S. Yook, S. M. Han, and H.-S. Koo A Werner syndrome protein homolog affects C. elegans development, growth rate, life span and sensitivity to DNA damage by acting at a DNA damage checkpoint Development, June 1, 2004; 131(11): 2565 - 2575. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Li, S. Navarro, N. Kasahara, and L. Comai Identification and Biochemical Characterization of a Werner's Syndrome Protein Complex with Ku70/80 and Poly(ADP-ribose) Polymerase-1 J. Biol. Chem., April 2, 2004; 279(14): 13659 - 13667. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Le Chatelier, O. J. Becherel, E. d'Alencon, D. Canceill, S. D. Ehrlich, R. P. P. Fuchs, and L. Janniere Involvement of DnaE, the Second Replicative DNA Polymerase from Bacillus subtilis, in DNA Mutagenesis J. Biol. Chem., January 16, 2004; 279(3): 1757 - 1767. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Mitchell, E. Petfalski, R. Houalla, A. Podtelejnikov, M. Mann, and D. Tollervey Rrp47p Is an Exosome-Associated Protein Required for the 3' Processing of Stable RNAs Mol. Cell. Biol., October 1, 2003; 23(19): 6982 - 6992. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. PHILLIPS and J. S. BUTLER Contribution of domain structure to the RNA 3' end processing and degradation functions of the nuclear exosome subunit Rrp6p RNA, September 1, 2003; 9(9): 1098 - 1107. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Espert, G. Degols, C. Gongora, D. Blondel, B. R. Williams, R. H. Silverman, and N. Mechti ISG20, a New Interferon-induced RNase Specific for Single-stranded RNA, Defines an Alternative Antiviral Pathway against RNA Genomic Viruses J. Biol. Chem., April 25, 2003; 278(18): 16151 - 16158. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M.-T. Liu, H.-P. Hu, T.-Y. Hsu, and J.-Y. Chen Site-directed mutagenesis in a conserved motif of Epstein-Barr virus DNase that is homologous to the catalytic centre of type II restriction endonucleases J. Gen. Virol., March 1, 2003; 84(3): 677 - 686. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. W. Faber, C. Voisine, D. C. King, E. A. Bates, and A. C. Hart Glutamine/proline-rich PQE-1 proteins protect Caenorhabditis elegans neurons from huntingtin polyglutamine neurotoxicity PNAS, December 24, 2002; 99(26): 17131 - 17136. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. A. Eppens, A. W. Faber, M. Rondaij, R. S. Jahangir, S. van Hemert, J. C. Vos, J. Venema, and H. A. Raue Deletions in the S1 domain of Rrp5p cause processing at a novel site in ITS1 of yeast pre-rRNA that depends on Rex4p Nucleic Acids Res., October 1, 2002; 30(19): 4222 - 4231. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. J. Decker and R. Parker mRNA decay enzymes: Decappers conserved between yeast and mammals PNAS, October 1, 2002; 99(20): 12512 - 12514. [Full Text] [PDF]
|
|
|
|
|
|
B. Li and L. Comai Displacement of DNA-PKcs from DNA ends by the Werner syndrome protein Nucleic Acids Res., September 1, 2002; 30(17): 3653 - 3661. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. M. Brosh Jr., J. Waheed, and J. A. Sommers Biochemical Characterization of the DNA Substrate Specificity of Werner Syndrome Helicase J. Biol. Chem., June 21, 2002; 277(26): 23236 - 23245. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Hammet, B. L. Pike, and J. Heierhorst Posttranscriptional Regulation of the RAD5 DNA Repair Gene by the Dun1 Kinase and the Pan2-Pan3 Poly(A)-Nuclease Complex Contributes to Survival of Replication Blocks J. Biol. Chem., June 14, 2002; 277(25): 22469 - 22474. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Fry The Werner Syndrome Helicase-Nuclease--One Protein, Many Mysteries Sci. Aging Knowl. Environ., April 3, 2002; 2002(13): re2 - 2. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-G. Ren, J. Martinez, and A. Virtanen Identification of the Active Site of Poly(A)-specific Ribonuclease by Site-directed Mutagenesis and Fe2+-mediated Cleavage J. Biol. Chem., February 15, 2002; 277(8): 5982 - 5987. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. A. Perez-Amador, P. Lidder, M. A. Johnson, J. Landgraf, E. Wisman, and P. J. Green New Molecular Phenotypes in the dst Mutants of Arabidopsis Revealed by DNA Microarray Analysis PLANT CELL, December 1, 2001; 13(12): 2703 - 2717. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Z. Ozsoy, J. J. Sekelsky, and S. W. Matson Biochemical characterization of the small isoform of Drosophila melanogaster RECQ5 helicase Nucleic Acids Res., July 15, 2001; 29(14): 2986 - 2993. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M.-C. Daugeron, F. Mauxion, and B. Seraphin The yeast POP2 gene encodes a nuclease involved in mRNA deadenylation Nucleic Acids Res., June 15, 2001; 29(12): 2448 - 2455. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. L. Denis, Y.-C. Chiang, Y. Cui, and J. Chen Genetic Evidence Supports a Role for the Yeast CCR4-NOT Complex in Transcriptional Elongation Genetics, June 1, 2001; 158(2): 627 - 634. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zuo and M. P. Deutscher Exoribonuclease superfamilies: structural analysis and phylogenetic distribution Nucleic Acids Res., March 1, 2001; 29(5): 1017 - 1026. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. S. Goldberg, Z. Jin, H. Ichikawa, A. Naito, M. Ohki, W. S. El-Deiry, and H. Tsuda Global Effects of Anchorage on Gene Expression during Mammary Carcinoma Cell Growth Reveal Role of Tumor Necrosis Factor-related Apoptosis-inducing Ligand in Anoikis Cancer Res., February 1, 2001; 61(4): 1334 - 1337. [Abstract] [Full Text]
|
|
|
|
|
|
L. Aravind, K. S. Makarova, and E. V. Koonin SURVEY AND SUMMARY: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories Nucleic Acids Res., September 15, 2000; 28(18): 3417 - 3432. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-C. Shen and L. A. Loeb Werner syndrome exonuclease catalyzes structure-dependent degradation of DNA Nucleic Acids Res., September 1, 2000; 28(17): 3260 - 3268. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Xia, Y. Peng, I. S. Mian, and N. F. Lue Identification of Functionally Important Domains in the N-Terminal Region of Telomerase Reverse Transcriptase Mol. Cell. Biol., July 15, 2000; 20(14): 5196 - 5207. [Abstract] [Full Text]
|
|
|
|
|
|
S. Huang, S. Beresten, B. Li, J. Oshima, N. A. Ellis, and J. Campisi Characterization of the human and mouse WRN 3'->5' exonuclease Nucleic Acids Res., June 15, 2000; 28(12): 2396 - 2405. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. S. Jacobs Anderson and R. Parker Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae Nucleic Acids Res., April 1, 2000; 28(7): 1604 - 1617. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. T. D. Burkard and J. S. Butler A Nuclear 3'-5' Exonuclease Involved in mRNA Degradation Interacts with Poly(A) Polymerase and the hnRNA Protein Npl3p Mol. Cell. Biol., January 15, 2000; 20(2): 604 - 616. [Abstract] [Full Text]
|
|
|
|
 |
|
 C Pare and B Suter Subcellular localization of Bic-D::GFP is linked to an asymmetric oocyte nucleus J. Cell Sci., January 6, 2000; 113(12): 2119 - 2127. [Abstract] [PDF]
|
|
|
|
|
|
M. Viswanathan and S. T. Lovett Exonuclease X of Escherichia coli. A NOVEL 3'-5' DNase AND DnaQ SUPERFAMILY MEMBER INVOLVED IN DNA REPAIR J. Biol. Chem., October 15, 1999; 274(42): 30094 - 30100. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Mazur and F. W. Perrino Identification and Expression of the TREX1 and TREX2 cDNA Sequences Encoding Mammalian 3'right-arrow5' Exonucleases J. Biol. Chem., July 9, 1999; 274(28): 19655 - 19660. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. M. Brosh Jr., D. K. Orren, J. O. Nehlin, P. H. Ravn, M. K. Kenny, A. Machwe, and V. A. Bohr Functional and Physical Interaction between WRN Helicase and Human Replication Protein A J. Biol. Chem., June 25, 1999; 274(26): 18341 - 18350. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Zhao, L. Hyman, and C. Moore Formation of mRNA 3' Ends in Eukaryotes: Mechanism, Regulation, and Interrelationships with Other Steps in mRNA Synthesis Microbiol. Mol. Biol. Rev., June 1, 1999; 63(2): 405 - 445. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Viswanathan, A. Lanjuin, and S. T. Lovett Identification of RNase T as a High-Copy Suppressor of the UV Sensitivity Associated With Single-Strand DNA Exonuclease Deficiency in Escherichia coli Genetics, March 1, 1999; 151(3): 929 - 934. [Abstract] [Full Text]
|
|
|
|
|
|
M. Viswanathan, K. W. Dower, and S. T. Lovett Identification of a Potent DNase Activity Associated with RNase T of Escherichia coli J. Biol. Chem., December 25, 1998; 273(52): 35126 - 35131. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. E. Brown and A. B. Sachs Poly(A) Tail Length Control in Saccharomyces cerevisiae Occurs by Message-Specific Deadenylation Mol. Cell. Biol., November 1, 1998; 18(11): 6548 - 6559. [Abstract] [Full Text]
|
|
|
|
|
|
J.-P. Rouault, D. Prevot, C. Berthet, A.-M. Birot, M. Billaud, J.-P. Magaud, and L. Corbo Interaction of BTG1 and p53-regulated BTG2 Gene Products with mCaf1, the Murine Homolog of a Component of the Yeast CCR4 Transcriptional Regulatory Complex J. Biol. Chem., August 28, 1998; 273(35): 22563 - 22569. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Martinez, Y.-G. Ren, A.-C. Thuresson, U. Hellman, J. Astrom, and A. Virtanen A 54-kDa Fragment of the Poly(A)-specific Ribonuclease Is an Oligomeric, Processive, and Cap-interacting Poly(A)-specific 3' Exonuclease J. Biol. Chem., July 28, 2000; 275(31): 24222 - 24230. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. H. Nguyen, J. P. Erzberger, J. Root, and D. M. Wilson III The Human Homolog of Escherichia coli Orn Degrades Small Single-stranded RNA and DNA Oligomers J. Biol. Chem., August 18, 2000; 275(34): 25900 - 25906. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. M. Montano, B. M. Wittmann, and N. R. Bianco Identification and Characterization of a Novel Factor That Regulates Quinone Reductase Gene Transcriptional Activity J. Biol. Chem., October 27, 2000; 275(44): 34306 - 34313. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Li and L. Comai Requirements for the Nucleolytic Processing of DNA Ends by the Werner Syndrome Protein-Ku70/80 Complex J. Biol. Chem., March 23, 2001; 276(13): 9896 - 9902. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Mazur and F. W. Perrino Structure and Expression of the TREX1 and TREX2 3'right-arrow5' Exonuclease Genes J. Biol. Chem., April 27, 2001; 276(18): 14718 - 14727. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Aphasizhev and L. Simpson Isolation and Characterization of a U-specific 3'-5'-Exonuclease from Mitochondria of Leishmania tarentolae J. Biol. Chem., June 8, 2001; 276(24): 21280 - 21284. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Mazur and F. W. Perrino Excision of 3' Termini by the Trex1 and TREX2 3'right-arrow5' Exonucleases. CHARACTERIZATION OF THE RECOMBINANT PROTEINS J. Biol. Chem., May 11, 2001; 276(20): 17022 - 17029. [Abstract] [Full Text] [PDF]
|
|