Dpo4

From S. solfataricus (aliases:dna polymerase 4, pol Y1)
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This page presents all the information in Polbase for Dpo4.

Mutants:

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Structures/Sequence:

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References:

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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:
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

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