Dpo4
From
S. solfataricus
(aliases:dna polymerase 4, pol Y1)
Welcome to the Polymerase Page
This page presents all the information in Polbase for Dpo4.
Mutants:At the top of the page you'll find a map of all positions of known mutants. Text links to mutants and digestion products are listed in the Mutants section.
Structures/Sequence:If available, a representative structure is displayed at the upper right. All known structures are listed in the Structures section.
External links:Polbase polymerases are linked to UniProt and Genbank where possible. The UniProt search link directs you to a pre-constructed UniProt search containing relevant terms.
References:All references that refer to this Polymerase are listed with their topics and paper's title in the References table.
Results:All the results for this polymerase can be examined by following the "Results" link at the bottom of the page.
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Dpo4
is a family Y enzyme
from
S. solfataricus.
Dpo4 was identified in 2001 (She et al. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl Acad. Sci. USA, 2001; 98: 7835–7840) as a putative bypass polymerase (Sso2448) homologous to the Y family DinB SOS-induced polymerase IV of E. coli. This enzyme shares 53% sequence identity with the previously identified Dbh from closely related Sulfolobus acidocaldarius strain originally mistaken with Sulfolobus solfataricus P1 (Kulaeva et al. Identification of a DinB/UmuC homolog in the archeon Sulfolobus solfataricus. Mutat. Res., 1996; 357: 245–253). S. solfataricus P2 DinB has been termed DNA polymerase IV (Dpo4). It was first purified and characterized in 2001 (Boudsocq et al. Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic pol eta. Nucleic Acids Res., 2001; 29: 4607-16). In the same year, the first crystal structure of Dpo4 in ternary complexes with DNA and an incoming nucleotide, either correct or incorrect, has been published (Ling et al. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell, 2001; 107: 9-12).
Selected Properties for Dpo4: |
3'-5' exo activity | 5'-3' exo activity | Frameshift Rate | Substitution Rate | General Error Rate |
|---|---|---|---|---|---|
| No (1) | No (1) | 2.3e-03 errors/bp (1) | 6.5e-03 errors/bp (1) | 1.5e-04-3.2e-03 errors/bp (2) |
| Year | Authors | Title | Results by property |
|---|---|---|---|
| 2013 | Ganesh Shanmugam, Irina G Minko, Surajit Banerjee, Plamen P Christov, Ivan D Kozekov, Carmelo J Rizzo, R Stephen Lloyd, Martin Egli, Michael P Stone | Ring-opening of the γ-OH-PdG adduct p... | |
| 2013 | Shirly J Espinoza-Herrera, Vineet Gaur, Zucai Suo, Paul R Carey | Following DNA Chain Extension and Pro... | |
| 2013 | Alessia Stornetta, Todor Angelov, F Peter Guengerich, Shana J Sturla | Incorporation of Nucleoside Probes Op... | |
| 2012 | Prakasha Gowda A S, Gowdahalli Krishnegowda, Zucai Suo, Shantu G Amin, Thomas E Spratt | Low fidelity bypass of O2-... | |
| 2012 | Yong Wang, Xiakun Chu, Zucai Suo, Erkang Wang, Jin Wang | Multi-domain Protein Solves the Foldi... | |
| 2012 | Surajit Banerjee, Plamen P Christov, Albena Kozekova, Carmelo J Rizzo, Martin Egli, Michael P Stone | Replication bypass of the trans-4-Hyd... | |
| 2012 | Shanen M Sherrer, Brian A Maxwell, Lindsey R Pack, Kevin A Fiala, Jason D Fowler, Jun Zhang, Zucai Suo | Identification of an Unfolding Interm... | |
| 2012 | Shanen M Sherrer, DJ Taggart, Lindsey R Pack, Chanchal K Malik, Ashis K Basu, Zucai Suo | Quantitative analysis of the mutageni... | |
| 2011 | Kevin N Kirouac, Zucai Suo, Hong Ling | Structural mechanism of ribonucleotid... | |
| 2011 | Dejian Ma, Jason D Fowler, Zucai Suo | Backbone assignment of the little fin... | |
| 2011 | Surajit Banerjee, Kyle L Brown, Martin Egli, Michael P Stone | Bypass of Aflatoxin B(1) Adducts by t... | |
| 2010 | Shanen M Sherrer, David C Beyer, Cynthia X Xia, Jason D Fowler, Zucai Suo | Kinetic basis of sugar selection by a... | |
| 2010 | Adriana Irimia, Lioudmila V Loukachevitch, Robert Lawton Eoff, F Peter Guengerich, Martin Egli | Metal-ion dependence of the active-si... | |
| 2010 | Dejian Ma, Jason D Fowler, Chunhua Yuan, Zucai Suo | Backbone assignment of the catalytic ... | |
| 2010 | Olga Rechkoblit, Alexander Kolbanovskiy, Lucy Malinina, Nicholas E Geacintov, Suse Broyde, Dinshaw J Patel | Mechanism of error-free and semitarge... | |
| 2010 | Likui Zhang, Huiqiang Lou, Li Guo, Zhengyan Zhan, Zhenhong Duan, Xin Guo, Li Huang | Accurate DNA synthesis by Sulfolobus ... | |
| 2010 | Jimson H Y Wong, Jessica A Brown, Zucai Suo, Paul Blum, Takehiko Nohmi, Hong Ling | Structural insight into dynamic bypas... | |
| 2009 | Robert Lawton Eoff, Raymundo Sanchez-Ponce, F Peter Guengerich | Conformational changes during nucleot... | |
| 2009 | Haijiang Zhang, Robert Lawton Eoff, Ivan D Kozekov, Carmelo J Rizzo, Martin Egli, F Peter Guengerich | Versatility of Y-family Sulfolobus so... | |
| 2009 | Guangxin Xing, Kevin N Kirouac, Yoon Jung Shin, Stephen D Bell, Hong Ling | Structural insight into recruitment o... | |
| 2009 | Shanen M Sherrer, Jessica A Brown, Lindsey R Pack, Vijay P Jasti, Jason D Fowler, Ashis K Basu, Zucai Suo | Mechanistic studies of the bypass of ... | |
| 2009 | Sabine Schneider, Stephanie Schorr, Thomas Carell | Crystal structure analysis of DNA les... | |
| 2009 | Anna Valenti, Giuseppe Perugino, Takehiko Nohmi, Mosè Rossi, Maria Ciaramella | Inhibition of translesion DNA polymer... | |
| 2009 | Cuiling Xu, Brian A Maxwell, Jessica A Brown, Likui Zhang, Zucai Suo | Global conformational dynamics of a Y... | |
| 2009 | Olga Rechkoblit, Lucy Malinina, Yuan Cheng, Nicholas E Geacintov, Suse Broyde, Dinshaw J Patel | Impact of conformational heterogeneit... | |
| 2009 | Haijiang Zhang, Robert Lawton Eoff, Ivan D Kozekov, Carmelo J Rizzo, Martin Egli, F Peter Guengerich | Structure-function relationships in m... | |
| 2009 | Haijiang Zhang, Robert Lawton Eoff, Ivan D Kozekov, Carmelo J Rizzo, Martin Egli, F Peter Guengerich | Structure-function relationships in m... | |
| 2009 | Robert Lawton Eoff, Jennifer B Stafford, Jozsef Szekely, Carmelo J Rizzo, Martin Egli, F Peter Guengerich, Lawrence J Marnett | Structural and functional analysis of... | |
| 2009 | Robert Lawton Eoff, Jennifer B Stafford, Jozsef Szekely, Carmelo J Rizzo, Martin Egli, F Peter Guengerich, Lawrence J Marnett | Structural and functional analysis of... | |
| 2008 | Jimson H Y Wong, Kevin A Fiala, Zucai Suo, Hong Ling | Snapshots of a Y-family DNA polymeras... | |
| 2008 | Suse Broyde, Liming Wang, Olga Rechkoblit, Nicholas E Geacintov, Dinshaw J Patel | Lesion processing: high-fidelity vers... | |
| 2008 | Yazhen Wang, Sarah K Musser, Sam Saleh, Lawrence J Marnett, Martin Egli, Michael P Stone | Insertion of dNTPs opposite the 1,N2-... | |
| 2008 | Yazhen Wang, Tamar Schlick | Quantum mechanics/molecular mechanics... | |
| 2008 | Kevin A Fiala, Shanen M Sherrer, Jessica A Brown, Zucai Suo | Mechanistic consequences of temperatu... | |
| 2008 | Lindsey DeCarlo, A S Prakasha Gowda, Zucai Suo, Thomas E Spratt | Formation of purine-purine mispairs b... | |
| 2008 | Jeff W Beckman, Qixin Wang, F Peter Guengerich | Kinetic analysis of correct nucleotid... | KM,Kd,kcat,All properties |
| 2008 | Jessica A Brown, Sean A Newmister, Kevin A Fiala, Zucai Suo | Mechanism of double-base lesion bypas... | |
| 2008 | Patrick P Lestienne, François Boudsocq, Jacques E Bonnet | Initiation of DNA replication by a th... | |
| 2008 | Pingna Xu, Lida Oum, Nicholas E Geacintov, Suse Broyde | Nucleotide selectivity opposite a ben... | |
| 2007 | Kevin A Fiala, Zucai Suo | Sloppy bypass of an abasic lesion cat... | |
| 2007 | Sushil Chandani, Edward L Loechler | Molecular modeling benzo[a]pyrene N2-... | |
| 2007 | Robert Lawton Eoff, Karen C Angel, Martin Egli, F Peter Guengerich | Molecular basis of selectivity of nuc... | KM,kcat,All properties |
| 2007 | Flavia Barone, Scott D McCulloch, Peter Macpherson, Giovanni Maga, Masami Yamada, Takehiko Nohmi, Anna Minoprio, Filomena Mazzei, Thomas A Kunkel, Peter Karran, Margherita Bignami | Replication of 2-hydroxyadenine-conta... | |
| 2007 | Robert Lawton Eoff, Adriana Irimia, Martin Egli, F Peter Guengerich | Sulfolobus solfataricus DNA polymeras... | |
| 2007 | Kevin A Fiala, Cameron D Hypes, Zucai Suo | Mechanism of abasic lesion bypass cat... | |
| 2007 | Adriana Irimia, Robert Lawton Eoff, Pradeep S Pallan, F Peter Guengerich, Martin Egli | Structure and activity of Y-class DNA... | |
| 2007 | Rebecca A Perlow-Poehnelt, Ilya Likhterov, Liming Wang, David A Scicchitano, Nicholas E Geacintov, Suse Broyde | Increased flexibility enhances misinc... | Template lesions,All properties |
| 2007 | Adam P Silverman, Qingfei Jiang, Myron F Goodman, Eric T Kool | Steric and electrostatic effects in D... | |
| 2007 | Liming Wang, Xinyun Yu, Po Hu, Suse Broyde, Yongqing Zhang | A water-mediated and substrate-assist... | |
| 2007 | Robert Lawton Eoff, Adriana Irimia, Karen C Angel, Martin Egli, F Peter Guengerich | Hydrogen bonding of 7,8-dihydro-8-oxo... | |
| 2007 | Adriana Irimia, Robert Lawton Eoff, Pradeep S Pallan, F Peter Guengerich, Martin Egli | Structure and activity of Y-class DNA... | |
| 2007 | Kevin A Fiala, Jessica A Brown, Hong Ling, Ajay K Kshetry, Jun Zhang, John-Stephen Taylor, Wei Wen Yang, Zucai Suo | Mechanism of template-independent nuc... | |
| 2007 | Jacob Bauer, Guangxin Xing, Haruhiko Yagi, Jane M Sayer, Donald M Jerina, Hong Ling | A structural gap in Dpo4 supports mut... | |
| 2007 | Wei Wen Yang, Roger Woodgate | What a difference a decade makes: ins... | |
| 2006 | Alexander K Showalter, Brandon J Lamarche, Marina Bakhtina, Mei-I Su, Kuo-Hsiang Tang, Ming-Daw Tsai | Mechanistic comparison of high-fideli... | |
| 2006 | F Peter Guengerich | Interactions of carcinogen-bound DNA ... | |
| 2006 | Liming Wang, Suse Broyde | A new anti conformation for N-(deoxyg... | |
| 2006 | Hong Zang, Goutam Chowdhury, Karen C Angel, Thomas M Harris, F Peter Guengerich | Translesion synthesis across polycycl... | |
| 2006 | Hong Zang, Adriana Irimia, Jeong-Yun Choi, Karen C Angel, Lioudmila V Loukachevitch, Martin Egli, F Peter Guengerich | Efficient and high fidelity incorpora... | |
| 2006 | Shin Mizukami, Tae Woo Kim, Sandra A Helquist, Eric T Kool | Varying DNA base-pair size in subangs... | |
| 2006 | Ling Zhang, Olga Rechkoblit, Liming Wang, Dinshaw J Patel, Robert Shapiro, Suse Broyde | Mutagenic nucleotide incorporation an... | |
| 2006 | Olga Rechkoblit, Lucy Malinina, Yuan Cheng, Vitaly Kuryavyi, Suse Broyde, Nicholas E Geacintov, Dinshaw J Patel | Stepwise translocation of Dpo4 polyme... | |
| 2006 | Takehiko Nohmi | Environmental stress and lesion-bypas... | |
| 2006 | Chiu Hong Lee, Sushil Chandani, Edward L Loechler | Homology modeling of four Y-family, l... | |
| 2006 | James S Stover, Goutam Chowdhury, Hong Zang, F Peter Guengerich, Carmelo J Rizzo | Translesion synthesis past the C8- an... | |
| 2006 | John P McDonald, Ashley Hall, Didier Gasparutto, Jean Cadet, Jack Ballantyne, Roger Woodgate | Novel thermostable Y-family polymeras... | |
| 2006 | Yazhen Wang, Karunesh Arora, Tamar Schlick | Subtle but variable conformational re... | |
| 2006 | Adriana Irimia, Hong Zang, Lioudmila V Loukachevitch, Robert Lawton Eoff, F Peter Guengerich, Martin Egli | Calcium is a cofactor of polymerizati... | |
| 2005 | Satya Prakash, Robert E Johnson, Louise Prakash | Eukaryotic translesion synthesis DNA ... | |
| 2005 | Robert E Johnson, Louise Prakash, Satya Prakash | Distinct mechanisms of cis-syn thymin... | |
| 2005 | Hong Zang, Angela K Goodenough, Jeong-Yun Choi, Adriana Irimia, Lioudmila V Loukachevitch, Ivan D Kozekov, Karen C Angel, Carmelo J Rizzo, Martin Egli, F Peter Guengerich | DNA adduct bypass polymerization by S... | |
| 2005 | Liming Wang, Min Wu, S Frank Yan, Dinshaw J Patel, Nicholas E Geacintov, Suse Broyde | Accommodation of a 1S-(-)-benzo[c]phe... | |
| 2005 | Angela K Goodenough, Ivan D Kozekov, Hong Zang, Jeong-Yun Choi, F Peter Guengerich, Thomas M Harris, Carmelo J Rizzo | Site specific synthesis and polymeras... | |
| 2005 | Paula L Fischhaber, Errol C Friedberg | How are specialized (low-fidelity) eu... | |
| 2005 | Wei Wen Yang | Portraits of a Y-family DNA polymerase. | |
| 2005 | Paul J Rothwell, Gabriel Waksman | Structure and mechanism of DNA polyme... | |
| 2005 | Alexandra Vaisman, Hong Ling, Roger Woodgate, Wei Wen Yang | Fidelity of Dpo4: effect of metal ion... | |
| 2005 | Hong Zang, Angela K Goodenough, Jeong-Yun Choi, Adriana Irimia, Lioudmila V Loukachevitch, Ivan D Kozekov, Karen C Angel, Carmelo J Rizzo, Martin Egli, F Peter Guengerich | DNA adduct bypass polymerization by S... | |
| 2005 | Janina Cramer, Tobias Restle | Pre-steady-state kinetic characteriza... | |
| 2005 | Matthew Hogg, Susan S Wallace, Sylvie Doublié | Bumps in the road: how replicative DN... | |
| 2004 | Thomas A Kunkel | DNA replication fidelity. | |
| 2004 | Brian S Plosky, Roger Woodgate | Switching from high-fidelity replicas... | |
| 2004 | Brigette Tippin, Phuong Pham, Myron F Goodman | Error-prone replication for better or... | |
| 2004 | Rebecca A Perlow-Poehnelt, Ilya Likhterov, David A Scicchitano, Nicholas E Geacintov, Suse Broyde | The spacious active site of a Y-famil... | |
| 2004 | Catherine M Joyce, Stephen J Benkovic | DNA polymerase fidelity: kinetics, st... | |
| 2004 | Katarzyna Bebenek, Thomas A Kunkel | Functions of DNA polymerases. | |
| 2004 | Hong Ling, François Boudsocq, Roger Woodgate, Wei Wen Yang | Snapshots of replication through an a... | |
| 2004 | Hong Ling, Jane M Sayer, Brian S Plosky, Haruhiko Yagi, François Boudsocq, Roger Woodgate, Donald M Jerina, Wei Wen Yang | Crystal structure of a benzo[a]pyrene... | |
| 2004 | Oliver Fleck, Primo Schär | Translesion DNA synthesis: little fin... | |
| 2004 | Kevin A Fiala, Zucai Suo | Mechanism of DNA polymerization catal... | |
| 2004 | Kevin A Fiala, Zucai Suo | Pre-steady-state kinetic studies of t... | Cloned or native,Tagged,Tag Name,Full length or truncated,Vmax,Overall Error Rate,All properties |
| 2004 | François Boudsocq, Robert J Kokoska, Brian S Plosky, Alexandra Vaisman, Hong Ling, Thomas A Kunkel, Wei Wen Yang, Roger Woodgate | Investigating the role of the little ... | |
| 2004 | José Trincao, Robert E Johnson, William T Wolfle, Carlos R Escalante, Satya Prakash, Louise Prakash, Aneel K Aggarwal | Dpo4 is hindered in extending a G.T m... | |
| 2003 | Wei Wen Yang | Damage repair DNA polymerases Y. | |
| 2003 | Miguel García-Díaz, José F Ruiz, Raquel Juárez, Gloria Terrados, Luis Blanco | Are there mutator polymerases? | |
| 2003 | Hong Ling, François Boudsocq, Brian S Plosky, Roger Woodgate, Wei Wen Yang | Replication of a cis-syn thymine dime... | |
| 2003 | Suzanne Sommer, Olivier J Becherel, Geneviève Coste, Adriana Bailone, Robert P P Fuchs | Altered translesion synthesis in E. c... | |
| 2003 | Robert J Kokoska, Scott D McCulloch, Thomas A Kunkel | The efficiency and specificity of apu... | |
| 2003 | William A Beard, Samuel H Wilson | Structural insights into the origins ... | |
| 2002 | John-Stephen Taylor | New structural and mechanistic insigh... | |
| 2002 | Robert J Kokoska, Katarzyna Bebenek, François Boudsocq, Roger Woodgate, Thomas A Kunkel | Low fidelity DNA synthesis by a y fam... | 3-5' exo,5-3' exo,Frameshift Error Rate,Nucleotide Substitution Rate,All properties |
| 2002 | François Boudsocq, Hong Ling, Wei Wen Yang, Roger Woodgate | Structure-based interpretation of mis... | |
| 2001 | Petr Grúz, Francesca M Pisani, Masatomi Shimizu, Masami Yamada, I Hayashi, Kosuke Morikawa, Takehiko Nohmi | Synthetic activity of Sso DNA polymer... | |
| 2001 | Errol C Friedberg, Paula L Fischhaber, C Kisker | Error-prone DNA polymerases: novel st... | |
| 2001 | François Boudsocq, Shigenori Iwai, Fumio Hanaoka, Roger Woodgate | Sulfolobus solfataricus P2 DNA polyme... | Cloned or native,Tagged,Full length or truncated,Isoelectric Point,Molecular Weight,Template lesions,All properties |
| 2001 | Hong Ling, François Boudsocq, Roger Woodgate, Wei Wen Yang | Crystal structure of a Y-family DNA p... | Cloned or native,Full length or truncated,Amino Acids Contacting Template,Amino Acids Contacting NTP,Polymerase Catalytic Residue Amino Acids,All properties |
| 2001 | B L Zhou, Janice D Pata, Thomas A Steitz | Crystal structure of a DinB lesion by... | |
| 1998 | Francesca M Pisani, Mariarita De Felice, G Manco, Mosè Rossi | Domain organization and biochemical f... |
Protein sequence:
DNA sequence:
| Name | 3'-5' exo activity | 5'-3' exo activity | Frameshift Rate | Substitution Rate | General Error Rate |
|---|---|---|---|---|---|
| Dpo4 y12A | |||||
| Dpo4 N188W | |||||
| Dpo4 T239W | |||||
| Dpo4 x331AR332A | |||||
| Dpo4 R332E | |||||
| Dpo4 R332H | |||||
| Dpo4 R332L | |||||
| Dpo4 R332A |
Protein information: Uniprot P96022 search for Dpo4 at UniProt
Sequence information: NCBI nucleotides European nucleotide archive