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PDBsum entry 1b8h
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protein Protein-protein interface(s) links
Transferase PDB id
1b8h

 

 

 

 

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Contents
Protein chains
228 a.a. *
11 a.a. *
* Residue conservation analysis
PDB id:
1b8h
Name: Transferase
Title: Sliding clamp, DNA polymerase
Structure: DNA polymerase processivity component. Chain: a, b, c. Synonym: gp45, DNA polymerase sliding clamp, DNA polymerase accessory protein 45. Engineered: yes. DNA polymerase fragment. Chain: d. Fragment: residues 893-903. Synonym: gp43.
Source: Enterobacteria phage rb69. Organism_taxid: 12353. Gene: gene 45. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21(de3). Synthetic: yes. Other_details: sequence from bacteriophage rb69, gene 43
Biol. unit: Tetramer (from PQS)
Resolution:
3.00Å     R-factor:   0.265     R-free:   0.313
Authors: Y.Shamoo,T.A.Steitz
Key ref:
Y.Shamoo and T.A.Steitz (1999). Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex. Cell, 99, 155-166. PubMed id: 10535734 DOI: 10.1016/S0092-8674(00)81647-5
Date:
01-Feb-99     Release date:   09-Feb-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O80164  (DPA5_BPR69) -  Sliding clamp from Escherichia phage RB69
Seq:
Struc: 		228 a.a.
228 a.a.
Protein chain
Pfam   ArchSchema ?
Q38087  (DPOL_BPR69) -  DNA-directed DNA polymerase from Escherichia phage RB69
Seq:
Struc: 		 
Seq:
Struc: 		903 a.a.
11 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain D: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
DNA(n)
 + 2'-deoxyribonucleoside 5'-triphosphate
 = DNA(n+1)
 + diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1016/S0092-8674(00)81647-5 Cell 99:155-166 (1999)
PubMed id: 10535734  
 
 
Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex.
Y.Shamoo, T.A.Steitz.
 
  ABSTRACT  
 
We have solved the crystal structures of the bacteriophage RB69 sliding clamp, its complex with a peptide essential for DNA polymerase interactions, and the DNA polymerase complexed with primer-template DNA. The editing complex structure shows a partially melted duplex DNA exiting from the exonuclease domain at an unexpected angle and significant changes in the protein structure. The clamp complex shows the C-terminal 11 residues of polymerase bound in a hydrophobic pocket, and it allows docking of the editing and clamp structures together. The peptide binds to the sliding clamp at a position identical to that of a replication inhibitor peptide bound to PCNA, suggesting that the replication inhibitor protein p21CIP1 functions by competing with eukaryotic polymerases for the same binding pocket on the clamp.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Peptide Interactions with the Sliding ClampThe interaction of pol-CT with RB69 sliding clamp is close fitting and consists mainly of hydrophobic interactions. Accessible surface of RB69 sliding clamp is shown in blue, while pol-CT is displayed as a stick model. To illustrate the pol-CT-binding pocket, all the sliding clamp surfaces within 4.5 Å of the pol-CT model are colored in yellow. The figure was made using GRASP ([37]). 		Figure 4.
Figure 4. Residues of the T4 and RB69 Pol-CTs that Are Similar to the ClampResidues in the RB69 pol-CT that are colored in blue are different in the T4 pol-CT. Residues that are the same in T4 and RB69 are shown in red. Residues that differ point away from the pol-CT-binding pocket (Table 1).
 
  The above figures are reprinted by permission from Cell Press: Cell (1999, 99, 155-166) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21062827 C.J.Hansen, L.Wu, J.D.Fox, B.Arezi, and H.H.Hogrefe (2011).
Engineered split in Pfu DNA polymerase fingers domain improves incorporation of nucleotide gamma-phosphate derivative.
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21245343 K.Mayanagi, S.Kiyonari, H.Nishida, M.Saito, D.Kohda, Y.Ishino, T.Shirai, and K.Morikawa (2011).
Architecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex.
  Proc Natl Acad Sci U S A, 108, 1845-1849.  
21117129 S.K.Jozwiakowski, and B.A.Connolly (2011).
A modified family-B archaeal DNA polymerase with reverse transcriptase activity.
  Chembiochem, 12, 35-37.  
21185718 Y.W.Yin (2011).
Structural insight on processivity, human disease and antiviral drug toxicity.
  Curr Opin Struct Biol, 21, 83-91.  
20163964 E.Johansson, and S.A.Macneill (2010).
The eukaryotic replicative DNA polymerases take shape.
  Trends Biochem Sci, 35, 339-347.  
  21029432 E.P.Geiduschek, and G.A.Kassavetis (2010).
Transcription of the T4 late genes.
  Virol J, 7, 288.  
20123134 J.D.Pata (2010).
Structural diversity of the Y-family DNA polymerases.
  Biochim Biophys Acta, 1804, 1124-1135.  
20166748 M.Hogg, J.Rudnicki, J.Midkiff, L.Reha-Krantz, S.Doublié, and S.S.Wallace (2010).
Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69.
  Biochemistry, 49, 2317-2325.
PDB code: 3lds
  21129204 T.C.Mueser, J.M.Hinerman, J.M.Devos, R.A.Boyer, and K.J.Williams (2010).
Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives.
  Virol J, 7, 359.  
20334433 X.Meng, Y.Zhou, E.Y.Lee, M.Y.Lee, and D.N.Frick (2010).
The p12 subunit of human polymerase delta modulates the rate and fidelity of DNA synthesis.
  Biochemistry, 49, 3545-3554.  
19576301 Z.Zhuang, and Y.Ai (2010).
Processivity factor of DNA polymerase and its expanding role in normal and translesion DNA synthesis.
  Biochim Biophys Acta, 1804, 1081-1093.  
19661923 B.Ibarra, Y.R.Chemla, S.Plyasunov, S.B.Smith, J.M.Lázaro, M.Salas, and C.Bustamante (2009).
Proofreading dynamics of a processive DNA polymerase.
  EMBO J, 28, 2794-2802.  
19622750 E.P.Tchesnokov, A.Obikhod, R.F.Schinazi, and M.Götte (2009).
Engineering of a chimeric RB69 DNA polymerase sensitive to drugs targeting the cytomegalovirus enzyme.
  J Biol Chem, 284, 26439-26446.  
19881914 F.J.López de Saro (2009).
Regulation of interactions with sliding clamps during DNA replication and repair.
  Curr Genomics, 10, 206-215.  
19119875 G.A.Cisneros, L.Perera, R.M.Schaaper, L.C.Pedersen, R.E.London, L.G.Pedersen, and T.A.Darden (2009).
Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues.
  J Am Chem Soc, 131, 1550-1556.  
19783818 H.J.Russell, T.T.Richardson, K.Emptage, and B.A.Connolly (2009).
The 3'-5' proofreading exonuclease of archaeal family-B DNA polymerase hinders the copying of template strand deaminated bases.
  Nucleic Acids Res, 37, 7603-7611.  
19934045 H.Nishida, K.Mayanagi, S.Kiyonari, Y.Sato, T.Oyama, Y.Ishino, and K.Morikawa (2009).
Structural determinant for switching between the polymerase and exonuclease modes in the PCNA-replicative DNA polymerase complex.
  Proc Natl Acad Sci U S A, 106, 20693-20698.  
19522539 H.Zhang, J.Beckman, J.Wang, and W.Konigsberg (2009).
RB69 DNA polymerase mutants with expanded nascent base-pair-binding pockets are highly efficient but have reduced base selectivity.
  Biochemistry, 48, 6940-6950.  
19033368 I.Rodríguez, J.M.Lázaro, M.Salas, and M.de Vega (2009).
Involvement of the TPR2 subdomain movement in the activities of phi29 DNA polymerase.
  Nucleic Acids Res, 37, 193-203.  
19411253 K.Datta, N.P.Johnson, V.J.Licata, and P.H.von Hippel (2009).
Local Conformations and Competitive Binding Affinities of Single- and Double-stranded Primer-Template DNA at the Polymerization and Editing Active Sites of DNA Polymerases.
  J Biol Chem, 284, 17180-17193.  
19801550 K.Murayama, S.Nakayama, M.Kato-Murayama, R.Akasaka, N.Ohbayashi, Y.Kamewari-Hayami, T.Terada, M.Shirouzu, T.Tsurumi, and S.Yokoyama (2009).
Crystal structure of epstein-barr virus DNA polymerase processivity factor BMRF1.
  J Biol Chem, 284, 35896-35905.
PDB code: 2z0l
19213612 L.B.Bloom (2009).
Loading clamps for DNA replication and repair.
  DNA Repair (Amst), 8, 570-578.  
19228037 M.Wang, H.R.Lee, and W.Konigsberg (2009).
Effect of A and B metal ion site occupancy on conformational changes in an RB69 DNA polymerase ternary complex.
  Biochemistry, 48, 2075-2086.  
19282446 S.D.McCulloch, R.J.Kokoska, P.Garg, P.M.Burgers, and T.A.Kunkel (2009).
The efficiency and fidelity of 8-oxo-guanine bypass by DNA polymerases delta and eta.
  Nucleic Acids Res, 37, 2830-2840.  
19298182 S.M.Hamdan, and C.C.Richardson (2009).
Motors, switches, and contacts in the replisome.
  Annu Rev Biochem, 78, 205-243.  
19863063 S.Puthenveetil, D.S.Liu, K.A.White, S.Thompson, and A.Y.Ting (2009).
Yeast display evolution of a kinetically efficient 13-amino acid substrate for lipoic acid ligase.
  J Am Chem Soc, 131, 16430-16438.  
19388052 W.Strzalka, T.Oyama, K.Tori, and K.Morikawa (2009).
Crystal structures of the Arabidopsis thaliana proliferating cell nuclear antigen 1 and 2 proteins complexed with the human p21 C-terminal segment.
  Protein Sci, 18, 1072-1080.
PDB codes: 2zvv 2zvw
18495197 A.Garcia-Maruniak, J.E.Maruniak, W.Farmerie, and D.G.Boucias (2008).
Sequence analysis of a non-classified, non-occluded DNA virus that causes salivary gland hypertrophy of Musca domestica, MdSGHV.
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18178550 G.Komazin-Meredith, W.L.Santos, D.J.Filman, J.M.Hogle, G.L.Verdine, and D.M.Coen (2008).
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19099556 J.Hubscher, L.Luthy, B.Berger-Bachi, and P.Stutzmann Meier (2008).
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17959669 K.F.Bryant, and D.M.Coen (2008).
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  J Virol, 82, 77-85.  
18448432 P.Kukreti, K.Singh, A.Ketkar, and M.J.Modak (2008).
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  J Biol Chem, 283, 17979-17990.  
18191219 R.E.Georgescu, S.S.Kim, O.Yurieva, J.Kuriyan, X.P.Kong, and M.O'Donnell (2008).
Structure of a sliding clamp on DNA.
  Cell, 132, 43-54.
PDB code: 3bep
18455735 S.Nechaev, and E.P.Geiduschek (2008).
Dissection of the bacteriophage T4 late promoter complex.
  J Mol Biol, 379, 402-413.  
  19023449 X.Chen, T.P.Patel, V.I.Simirskii, and M.K.Duncan (2008).
PCNA interacts with Prox1 and represses its transcriptional activity.
  Mol Vis, 14, 2076-2086.  
17321543 A.Jacewicz, K.Makiela, A.Kierzek, J.W.Drake, and A.Bebenek (2007).
The roles of Tyr391 and Tyr619 in RB69 DNA polymerase replication fidelity.
  J Mol Biol, 368, 18-29.  
17702757 E.Fidalgo da Silva, and L.J.Reha-Krantz (2007).
DNA polymerase proofreading: active site switching catalyzed by the bacteriophage T4 DNA polymerase.
  Nucleic Acids Res, 35, 5452-5463.  
17766250 H.Zhang, W.Cao, E.Zakharova, W.Konigsberg, and E.M.De La Cruz (2007).
Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/template complexes upon binding and incorporation of matched deoxynucleoside triphosphates.
  Nucleic Acids Res, 35, 6052-6062.  
17693399 J.M.Devos, S.J.Tomanicek, C.E.Jones, N.G.Nossal, and T.C.Mueser (2007).
Crystal structure of bacteriophage T4 5' nuclease in complex with a branched DNA reveals how flap endonuclease-1 family nucleases bind their substrates.
  J Biol Chem, 282, 31713-31724.
PDB code: 2ihn
18496613 M.Garcia-Diaz, and K.Bebenek (2007).
Multiple functions of DNA polymerases.
  CRC Crit Rev Plant Sci, 26, 105-122.  
17098747 M.Hogg, P.Aller, W.Konigsberg, S.S.Wallace, and S.Doublié (2007).
Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family.
  J Biol Chem, 282, 1432-1444.
PDB code: 2dtu
17605817 N.Schormann, A.Grigorian, A.Samal, R.Krishnan, L.DeLucas, and D.Chattopadhyay (2007).
Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly.
  BMC Struct Biol, 7, 45.
PDB codes: 2owq 2owr
16945955 A.S.Doré, M.L.Kilkenny, S.A.Jones, A.W.Oliver, S.M.Roe, S.D.Bell, and L.H.Pearl (2006).
Structure of an archaeal PCNA1-PCNA2-FEN1 complex: elucidating PCNA subunit and client enzyme specificity.
  Nucleic Acids Res, 34, 4515-4526.
PDB code: 2izo
16371349 B.A.Appleton, J.Brooks, A.Loregian, D.J.Filman, D.M.Coen, and J.M.Hogle (2006).
Crystal structure of the cytomegalovirus DNA polymerase subunit UL44 in complex with the C terminus from the catalytic subunit. Differences in structure and function relative to unliganded UL44.
  J Biol Chem, 281, 5224-5232.
PDB code: 1yyp
16955075 C.Indiani, and M.O'Donnell (2006).
The replication clamp-loading machine at work in the three domains of life.
  Nat Rev Mol Cell Biol, 7, 751-761.  
16973545 G.Andrei, D.B.Gammon, P.Fiten, E.De Clercq, G.Opdenakker, R.Snoeck, and D.H.Evans (2006).
Cidofovir resistance in vaccinia virus is linked to diminished virulence in mice.
  J Virol, 80, 9391-9401.  
17071716 I.Ivanov, B.R.Chapados, J.A.McCammon, and J.A.Tainer (2006).
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications.
  Nucleic Acids Res, 34, 6023-6033.  
16403212 M.A.Argiriadi, E.R.Goedken, I.Bruck, M.O'Donnell, and J.Kuriyan (2006).
Crystal structure of a DNA polymerase sliding clamp from a Gram-positive bacterium.
  BMC Struct Biol, 6, 2.
PDB code: 2avt
16687658 M.Hogg, W.Cooper, L.Reha-Krantz, and S.S.Wallace (2006).
Kinetics of error generation in homologous B-family DNA polymerases.
  Nucleic Acids Res, 34, 2528-2535.  
16982794 R.S.Kornbluth, D.F.Smee, R.W.Sidwell, V.Snarsky, D.H.Evans, and K.Y.Hostetler (2006).
Mutations in the E9L polymerase gene of cidofovir-resistant vaccinia virus strain WR are associated with the drug resistance phenotype.
  Antimicrob Agents Chemother, 50, 4038-4043.  
16705640 R.Shi, A.Azzi, C.Gilbert, G.Boivin, and S.X.Lin (2006).
Three-dimensional modeling of cytomegalovirus DNA polymerase and preliminary analysis of drug resistance.
  Proteins, 64, 301-307.  
16638752 S.Liu, J.D.Knafels, J.S.Chang, G.A.Waszak, E.T.Baldwin, M.R.Deibel, D.R.Thomsen, F.L.Homa, P.A.Wells, M.C.Tory, R.A.Poorman, H.Gao, X.Qiu, and A.P.Seddon (2006).
Crystal structure of the herpes simplex virus 1 DNA polymerase.
  J Biol Chem, 281, 18193-18200.
PDB code: 2gv9
16881051 S.Sun, L.Geng, and Y.Shamoo (2006).
Structure and enzymatic properties of a chimeric bacteriophage RB69 DNA polymerase and single-stranded DNA binding protein with increased processivity.
  Proteins, 65, 231-238.
PDB codes: 2a1k 2atq
16407253 S.W.Nelson, J.Yang, and S.J.Benkovic (2006).
Site-directed mutations of T4 helicase loading protein (gp59) reveal multiple modes of DNA polymerase inhibition and the mechanism of unlocking by gp41 helicase.
  J Biol Chem, 281, 8697-8706.  
15952889 A.Johnson, and M.O'Donnell (2005).
Cellular DNA replicases: components and dynamics at the replication fork.
  Annu Rev Biochem, 74, 283-315.  
15680323 A.T.McGeoch, and S.D.Bell (2005).
Eukaryotic/archaeal primase and MCM proteins encoded in a bacteriophage genome.
  Cell, 120, 167-168.  
16168375 C.Indiani, P.McInerney, R.Georgescu, M.F.Goodman, and M.O'Donnell (2005).
A sliding-clamp toolbelt binds high- and low-fidelity DNA polymerases simultaneously.
  Mol Cell, 19, 805-815.  
16172520 H.Nishida, S.Ishino, T.Miyata, K.Morikawa, and Y.Ishino (2005).
Identification of the critical region in replication factor C from Pyrococcus furiosus for the stable complex formation with proliferating cell nuclear antigen and DNA.
  Genes Genet Syst, 80, 83-93.  
15845765 I.Rodríguez, J.M.Lázaro, L.Blanco, S.Kamtekar, A.J.Berman, J.Wang, T.A.Steitz, M.Salas, and M.de Vega (2005).
A specific subdomain in phi29 DNA polymerase confers both processivity and strand-displacement capacity.
  Proc Natl Acad Sci U S A, 102, 6407-6412.  
16140778 J.C.Randell, G.Komazin, C.Jiang, C.B.Hwang, and D.M.Coen (2005).
Effects of substitutions of arginine residues on the basic surface of herpes simplex virus UL42 support a role for DNA binding in processive DNA synthesis.
  J Virol, 79, 12025-12034.  
15659404 O.Gangisetty, C.E.Jones, M.Bhagwat, and N.G.Nossal (2005).
Maturation of bacteriophage T4 lagging strand fragments depends on interaction of T4 RNase H with T4 32 protein rather than the T4 gene 45 clamp.
  J Biol Chem, 280, 12876-12887.  
16169903 S.L.Kazmirski, Y.Zhao, G.D.Bowman, M.O'donnell, and J.Kuriyan (2005).
Out-of-plane motions in open sliding clamps: molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen.
  Proc Natl Acad Sci U S A, 102, 13801-13806.  
15616578 S.Sakurai, K.Kitano, H.Yamaguchi, K.Hamada, K.Okada, K.Fukuda, M.Uchida, E.Ohtsuka, H.Morioka, and T.Hakoshima (2005).
Structural basis for recruitment of human flap endonuclease 1 to PCNA.
  EMBO J, 24, 683-693.
PDB code: 1ul1
15308704 A.Loregian, B.A.Appleton, J.M.Hogle, and D.M.Coen (2004).
Specific residues in the connector loop of the human cytomegalovirus DNA polymerase accessory protein UL44 are crucial for interaction with the UL54 catalytic subunit.
  J Virol, 78, 9084-9092.  
15159531 C.M.Joyce (2004).
T4 replication: what does "processivity" really mean?
  Proc Natl Acad Sci U S A, 101, 8255-8256.  
15576024 D.Jeruzalmi (2004).
Chromosomal DNA replication on a protein "chip".
  Structure, 12, 2100-2102.  
15057282 E.Freisinger, A.P.Grollman, H.Miller, and C.Kisker (2004).
Lesion (in)tolerance reveals insights into DNA replication fidelity.
  EMBO J, 23, 1494-1505.
PDB codes: 1q9x 1q9y
15065653 F.López de Saro, R.E.Georgescu, F.Leu, and M.O'Donnell (2004).
Protein trafficking on sliding clamps.
  Philos Trans R Soc Lond B Biol Sci, 359, 25-30.  
15201901 G.D.Bowman, M.O'Donnell, and J.Kuriyan (2004).
Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex.
  Nature, 429, 724-730.
PDB code: 1sxj
15576034 J.B.Bruning, and Y.Shamoo (2004).
Structural and thermodynamic analysis of human PCNA with peptides derived from DNA polymerase-delta p66 subunit and flap endonuclease-1.
  Structure, 12, 2209-2219.
PDB codes: 1u76 1u7b
15292168 J.K.Kumar, E.T.Chiu, S.Tabor, and C.C.Richardson (2004).
A unique region in bacteriophage t7 DNA polymerase important for exonucleolytic hydrolysis of DNA.
  J Biol Chem, 279, 42018-42025.  
15148377 J.Yang, Z.Zhuang, R.M.Roccasecca, M.A.Trakselis, and S.J.Benkovic (2004).
The dynamic processivity of the T4 DNA polymerase during replication.
  Proc Natl Acad Sci U S A, 101, 8289-8294.  
14766746 K.Fien, Y.S.Cho, J.K.Lee, S.Raychaudhuri, I.Tappin, and J.Hurwitz (2004).
Primer utilization by DNA polymerase alpha-primase is influenced by its interaction with Mcm10p.
  J Biol Chem, 279, 16144-16153.  
15057283 M.Hogg, S.S.Wallace, and S.Doublié (2004).
Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site.
  EMBO J, 23, 1483-1493.
PDB codes: 1rv2 2p5o
15574501 S.Nechaev, M.Kamali-Moghaddam, E.André, J.P.Léonetti, and E.P.Geiduschek (2004).
The bacteriophage T4 late-transcription coactivator gp33 binds the flap domain of Escherichia coli RNA polymerase.
  Proc Natl Acad Sci U S A, 101, 17365-17370.  
15065652 T.A.Steitz, and Y.W.Yin (2004).
Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases.
  Philos Trans R Soc Lond B Biol Sci, 359, 17-23.  
15208692 T.Miyata, T.Oyama, K.Mayanagi, S.Ishino, Y.Ishino, and K.Morikawa (2004).
The clamp-loading complex for processive DNA replication.
  Nat Struct Mol Biol, 11, 632-636.  
15627374 V.M.Petrov, and J.D.Karam (2004).
Diversity of structure and function of DNA polymerase (gp43) of T4-related bacteriophages.
  Biochemistry (Mosc), 69, 1213-1218.  
15016374 Y.W.Yin, and T.A.Steitz (2004).
The structural mechanism of translocation and helicase activity in T7 RNA polymerase.
  Cell, 116, 393-404.
PDB codes: 1s76 1s77
14973201 Y.Wang, D.E.Prosen, L.Mei, J.C.Sullivan, M.Finney, and P.B.Vander Horn (2004).
A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro.
  Nucleic Acids Res, 32, 1197-1207.  
12730226 A.A.Sartori, and J.Jiricny (2003).
Enzymology of base excision repair in the hyperthermophilic archaeon Pyrobaculum aerophilum.
  J Biol Chem, 278, 24563-24576.  
12869690 A.Goel, R.D.Astumian, and D.Herschbach (2003).
Tuning and switching a DNA polymerase motor with mechanical tension.
  Proc Natl Acad Sci U S A, 100, 9699-9704.  
12832762 A.J.Oakley, P.Prosselkov, G.Wijffels, J.L.Beck, M.C.Wilce, and N.E.Dixon (2003).
Flexibility revealed by the 1.85 A crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III.
  Acta Crystallogr D Biol Crystallogr, 59, 1192-1199.
PDB code: 1mmi
12700227 E.Delagoutte, and P.H.Von Hippel (2003).
Function and assembly of the bacteriophage T4 DNA replication complex: interactions of the T4 polymerase with various model DNA constructs.
  J Biol Chem, 278, 25435-25447.  
12626685 E.S.Miller, E.Kutter, G.Mosig, F.Arisaka, T.Kunisawa, and W.Rüger (2003).
Bacteriophage T4 genome.
  Microbiol Mol Biol Rev, 67, 86.  
14633999 F.J.López de Saro, R.E.Georgescu, M.F.Goodman, and M.O'Donnell (2003).
Competitive processivity-clamp usage by DNA polymerases during DNA replication and repair.
  EMBO J, 22, 6408-6418.  
14630952 F.J.López de Saro, R.E.Georgescu, and M.O'Donnell (2003).
A peptide switch regulates DNA polymerase processivity.
  Proc Natl Acad Sci U S A, 100, 14689-14694.  
14592985 K.A.Bunting, S.M.Roe, and L.H.Pearl (2003).
Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp.
  EMBO J, 22, 5883-5892.
PDB code: 1unn
12496274 K.Wong, G.A.Kassavetis, J.P.Leonetti, and E.P.Geiduschek (2003).
Mutational and functional analysis of a segment of the sigma family bacteriophage T4 late promoter recognition protein gp55.
  J Biol Chem, 278, 7073-7080.  
12649440 S.Matsumiya, S.Ishino, Y.Ishino, and K.Morikawa (2003).
Intermolecular ion pairs maintain the toroidal structure of Pyrococcus furiosus PCNA.
  Protein Sci, 12, 823-831.
PDB codes: 1iz4 1iz5
12458197 S.Sun, and Y.Shamoo (2003).
Biochemical characterization of interactions between DNA polymerase and single-stranded DNA-binding protein in bacteriophage RB69.
  J Biol Chem, 278, 3876-3881.  
12134025 A.B.Brenkman, E.C.Breure, and P.C.van der Vliet (2002).
Molecular architecture of adenovirus DNA polymerase and location of the protein primer.
  J Virol, 76, 8200-8207.  
  12454051 A.Bebenek, G.T.Carver, H.K.Dressman, F.A.Kadyrov, J.K.Haseman, V.Petrov, W.H.Konigsberg, J.D.Karam, and J.W.Drake (2002).
Dissecting the fidelity of bacteriophage RB69 DNA polymerase: site-specific modulation of fidelity by polymerase accessory proteins.
  Genetics, 162, 1003-1018.  
11959500 D.Jeruzalmi, M.O'Donnell, and J.Kuriyan (2002).
Clamp loaders and sliding clamps.
  Curr Opin Struct Biol, 12, 217-224.  
12189135 E.Fidalgo da Silva, S.S.Mandal, and L.J.Reha-Krantz (2002).
Using 2-aminopurine fluorescence to measure incorporation of incorrect nucleotides by wild type and mutant bacteriophage T4 DNA polymerases.
  J Biol Chem, 277, 40640-40649.  
11927597 H.Yang, J.H.Chiang, S.Fitz-Gibbon, M.Lebel, A.A.Sartori, J.Jiricny, M.M.Slupska, and J.H.Miller (2002).
Direct interaction between uracil-DNA glycosylase and a proliferating cell nuclear antigen homolog in the crenarchaeon Pyrobaculum aerophilum.
  J Biol Chem, 277, 22271-22278.  
11988770 I.V.Shevelev, and U.Hübscher (2002).
The 3' 5' exonucleases.
  Nat Rev Mol Cell Biol, 3, 364-376.  
12124389 K.Shimizu, K.Hashimoto, J.M.Kirchner, W.Nakai, H.Nishikawa, M.A.Resnick, and A.Sugino (2002).
Fidelity of DNA polymerase epsilon holoenzyme from budding yeast Saccharomyces cerevisiae.
  J Biol Chem, 277, 37422-37429.  
11751576 N.Lenne-Samuel, J.Wagner, H.Etienne, and R.P.Fuchs (2002).
The processivity factor beta controls DNA polymerase IV traffic during spontaneous mutagenesis and translesion synthesis in vivo.
  EMBO Rep, 3, 45-49.  
12296822 S.Matsumiya, S.Ishino, Y.Ishino, and K.Morikawa (2002).
Physical interaction between proliferating cell nuclear antigen and replication factor C from Pyrococcus furiosus.
  Genes Cells, 7, 911-922.
PDB code: 1isq
12045093 U.Hubscher, G.Maga, and S.Spadari (2002).
Eukaryotic DNA polymerases.
  Annu Rev Biochem, 71, 133-163.  
12087102 V.M.Petrov, S.S.Ng, and J.D.Karam (2002).
Protein determinants of RNA binding by DNA polymerase of the T4-related bacteriophage RB69.
  J Biol Chem, 277, 33041-33048.  
12124382 V.P.Bermudez, S.A.MacNeill, I.Tappin, and J.Hurwitz (2002).
The influence of the Cdc27 subunit on the properties of the Schizosaccharomyces pombe DNA polymerase delta.
  J Biol Chem, 277, 36853-36862.  
11900537 W.C.Lam, E.H.Thompson, O.Potapova, X.C.Sun, C.M.Joyce, and D.P.Millar (2002).
3'-5' exonuclease of Klenow fragment: role of amino acid residues within the single-stranded DNA binding region in exonucleolysis and duplex DNA melting.
  Biochemistry, 41, 3943-3951.  
11986310 X.Lu, C.K.Tan, J.Q.Zhou, M.You, L.M.Carastro, K.M.Downey, and A.G.So (2002).
Direct interaction of proliferating cell nuclear antigen with the small subunit of DNA polymerase delta.
  J Biol Chem, 277, 24340-24345.  
11297928 A.Hillisch, M.Lorenz, and S.Diekmann (2001).
Recent advances in FRET: distance determination in protein-DNA complexes.
  Curr Opin Struct Biol, 11, 201-207.  
11573000 B.P.Dalrymple, K.Kongsuwan, G.Wijffels, N.E.Dixon, and P.A.Jennings (2001).
A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems.
  Proc Natl Acad Sci U S A, 98, 11627-11632.  
11525729 D.Jeruzalmi, M.O'Donnell, and J.Kuriyan (2001).
Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III.
  Cell, 106, 429-441.
PDB code: 1jr3
11525728 D.Jeruzalmi, O.Yurieva, Y.Zhao, M.Young, J.Stewart, M.Hingorani, M.O'Donnell, and J.Kuriyan (2001).
Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. coli DNA polymerase III.
  Cell, 106, 417-428.
PDB codes: 1jqj 1jql
11459968 G.Mosig, J.Gewin, A.Luder, N.Colowick, and D.Vo (2001).
Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer.
  Proc Natl Acad Sci U S A, 98, 8306-8311.  
11274057 H.E.Kleczkowska, G.Marra, T.Lettieri, and J.Jiricny (2001).
hMSH3 and hMSH6 interact with PCNA and colocalize with it to replication foci.
  Genes Dev, 15, 724-736.  
11172710 J.A.Carrodeguas, K.Theis, D.F.Bogenhagen, and C.Kisker (2001).
Crystal structure and deletion analysis show that the accessory subunit of mammalian DNA polymerase gamma, Pol gamma B, functions as a homodimer.
  Mol Cell, 7, 43-54.
PDB codes: 1g5h 1g5i
11551794 M.A.Trakselis, M.U.Mayer, F.T.Ishmael, R.M.Roccasecca, and S.J.Benkovic (2001).
Dynamic protein interactions in the bacteriophage T4 replisome.
  Trends Biochem Sci, 26, 566-572.  
11459977 M.A.Trakselis, S.C.Alley, E.Abel-Santos, and S.J.Benkovic (2001).
Creating a dynamic picture of the sliding clamp during T4 DNA polymerase holoenzyme assembly by using fluorescence resonance energy transfer.
  Proc Natl Acad Sci U S A, 98, 8368-8375.  
11709164 M.A.Trakselis, and S.J.Benkovic (2001).
Intricacies in ATP-dependent clamp loading: variations across replication systems.
  Structure, 9, 999.  
11719243 M.O'Donnell, D.Jeruzalmi, and J.Kuriyan (2001).
Clamp loader structure predicts the architecture of DNA polymerase III holoenzyme and RFC.
  Curr Biol, 11, R935-R946.  
11504721 S.C.Alley, M.A.Trakselis, M.U.Mayer, F.T.Ishmael, A.D.Jones, and S.J.Benkovic (2001).
Building a replisome solution structure by elucidation of protein-protein interactions in the bacteriophage T4 DNA polymerase holoenzyme.
  J Biol Chem, 276, 39340-39349.  
11395406 S.J.Benkovic, A.M.Valentine, and F.Salinas (2001).
Replisome-mediated DNA replication.
  Annu Rev Biochem, 70, 181-208.  
11266590 S.Matsumiya, Y.Ishino, and K.Morikawa (2001).
Crystal structure of an archaeal DNA sliding clamp: proliferating cell nuclear antigen from Pyrococcus furiosus.
  Protein Sci, 10, 17-23.
PDB code: 1ge8
11467934 T.C.Lin, C.X.Wang, C.M.Joyce, and W.H.Konigsberg (2001).
3'-5' Exonucleolytic activity of DNA polymerases: structural features that allow kinetic discrimination between ribo- and deoxyribonucleotide residues.
  Biochemistry, 40, 8749-8755.  
11572772 V.Ellison, and B.Stillman (2001).
Opening of the clamp: an intimate view of an ATP-driven biological machine.
  Cell, 106, 655-660.  
11309502 Y.H.Jin, R.Obert, P.M.Burgers, T.A.Kunkel, M.A.Resnick, and D.A.Gordenin (2001).
The 3'-->5' exonuclease of DNA polymerase delta can substitute for the 5' flap endonuclease Rad27/Fen1 in processing Okazaki fragments and preventing genome instability.
  Proc Natl Acad Sci U S A, 98, 5122-5127.  
10982878 A.F.Neuwald, and A.Poleksic (2000).
PSI-BLAST searches using hidden markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein.
  Nucleic Acids Res, 28, 3570-3580.  
11056476 E.Warbrick (2000).
The puzzle of PCNA's many partners.
  Bioessays, 22, 997.  
10882068 H.J.Zuccola, D.J.Filman, D.M.Coen, and J.M.Hogle (2000).
The crystal structure of an unusual processivity factor, herpes simplex virus UL42, bound to the C terminus of its cognate polymerase.
  Mol Cell, 5, 267-278.
PDB code: 1dml
10712935 J.L.Keck, and J.M.Berger (2000).
DNA replication at high resolution.
  Chem Biol, 7, R63-R71.  
10660290 M.M.Hingorani, and M.O'Donnell (2000).
Sliding clamps: a (tail)ored fit.
  Curr Biol, 10, R25-R29.  
10698951 N.Reynolds, E.Warbrick, P.A.Fantes, and S.A.MacNeill (2000).
Essential interaction between the fission yeast DNA polymerase delta subunit Cdc27 and Pcn1 (PCNA) mediated through a C-terminal p21(Cip1)-like PCNA binding motif.
  EMBO J, 19, 1108-1118.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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