spacer
spacer

PDBsum entry 1unn
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Beta-clamp PDB id
1unn

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
366 a.a. *
111 a.a. *
Ligands
SO4 ×2
Waters ×947
* Residue conservation analysis
PDB id:
1unn
Name: Beta-clamp
Title: Complex of beta-clamp processivity factor and little finger domain of poliv
Structure: DNA polymerase iii beta subunit. Chain: a, b. Engineered: yes. DNA polymerase iv. Chain: c, d. Fragment: little finger, residues 243-351. Synonym: pol iv. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
1.90Å     R-factor:   0.179     R-free:   0.240
Authors: K.A.Bunting,S.M.Roe,L.H.Pearl
Key ref: K.A.Bunting et al. (2003). Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp. Embo J, 22, 5883-5892. PubMed id: 14592985
Date:
11-Sep-03     Release date:   06-Nov-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A988  (DPO3B_ECOLI) -  Beta sliding clamp from Escherichia coli (strain K12)
Seq:
Struc: 		366 a.a.
366 a.a.
Protein chains
Pfam   ArchSchema ?
Q47155  (DPO4_ECOLI) -  DNA polymerase IV from Escherichia coli (strain K12)
Seq:
Struc: 		351 a.a.
111 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains C, 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    
 
 
Embo J 22:5883-5892 (2003)
PubMed id: 14592985  
 
 
Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp.
K.A.Bunting, S.M.Roe, L.H.Pearl.
 
  ABSTRACT  
 
Y-family DNA polymerases can extend primer strands across template strand lesions that stall replicative polymerases. The poor processivity and fidelity of these enzymes, key to their biological role, requires that their access to the primer-template junction is both facilitated and regulated in order to minimize mutations. These features are believed to be provided by interaction with processivity factors, beta-clamp or proliferating cell nuclear antigen (PCNA), which are also essential for the function of replicative DNA polymerases. The basis for this interaction is revealed by the crystal structure of the complex between the 'little finger' domain of the Y-family DNA polymerase Pol IV and the beta-clamp processivity factor, both from Escherichia coli. The main interaction involves a C-terminal peptide of Pol IV, and is similar to interactions seen between isolated peptides and other processivity factors. However, this first structure of an entire domain of a binding partner with an assembled clamp reveals a substantial secondary interface, which maintains the polymerase in an inactive orientation, and may regulate the switch between replicative and Y-family DNA polymerases in response to a template strand lesion.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21320186 T.E.Sladewski, K.M.Hetrick, and P.L.Foster (2011).
Escherichia coli Rep DNA helicase and error-prone DNA polymerase IV interact physically and functionally.
  Mol Microbiol, 80, 524-541.  
21265749 T.R.Beattie, and S.D.Bell (2011).
The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes.
  Biochem Soc Trans, 39, 70-76.  
20305653 B.D.Freudenthal, L.Gakhar, S.Ramaswamy, and M.T.Washington (2010).
Structure of monoubiquitinated PCNA and implications for translesion synthesis and DNA polymerase exchange.
  Nat Struct Mol Biol, 17, 479-484.
PDB codes: 3l0w 3l0x 3l10
20139184 B.D.Kana, G.L.Abrahams, N.Sung, D.F.Warner, B.G.Gordhan, E.E.Machowski, L.Tsenova, J.C.Sacchettini, N.G.Stoker, G.Kaplan, and V.Mizrahi (2010).
Role of the DinB homologs Rv1537 and Rv3056 in Mycobacterium tuberculosis.
  J Bacteriol, 192, 2220-2227.  
20123134 J.D.Pata (2010).
Structural diversity of the Y-family DNA polymerases.
  Biochim Biophys Acta, 1804, 1124-1135.  
  20936072 J.N.Ollivierre, J.Fang, and P.J.Beuning (2010).
The Roles of UmuD in Regulating Mutagenesis.
  J Nucleic Acids, 2010, 0.  
21190558 M.D.Sutton, J.M.Duzen, and S.K.Scouten Ponticelli (2010).
A single hydrophobic cleft in the Escherichia coli processivity clamp is sufficient to support cell viability and DNA damage-induced mutagenesis in vivo.
  BMC Mol Biol, 11, 102.  
19540941 M.D.Sutton (2010).
Coordinating DNA polymerase traffic during high and low fidelity synthesis.
  Biochim Biophys Acta, 1804, 1167-1179.  
20453097 N.M.Dupes, B.W.Walsh, A.D.Klocko, J.S.Lenhart, H.L.Peterson, D.A.Gessert, C.E.Pavlick, and L.A.Simmons (2010).
Mutations in the Bacillus subtilis beta clamp that separate its roles in DNA replication from mismatch repair.
  J Bacteriol, 192, 3452-3463.  
20523737 P.J.Hastings, M.N.Hersh, P.C.Thornton, N.C.Fonville, A.Slack, R.L.Frisch, M.P.Ray, R.S.Harris, S.M.Leal, and S.M.Rosenberg (2010).
Competition of Escherichia coli DNA polymerases I, II and III with DNA Pol IV in stressed cells.
  PLoS One, 5, e10862.  
  20936174 S.Chandani, C.Jacobs, and E.L.Loechler (2010).
Architecture of y-family DNA polymerases relevant to translesion DNA synthesis as revealed in structural and molecular modeling studies.
  J Nucleic Acids, 2010, 0.  
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.  
19703395 A.R.Parks, Z.Li, Q.Shi, R.M.Owens, M.M.Jin, and J.E.Peters (2009).
Transposition into replicating DNA occurs through interaction with the processivity factor.
  Cell, 138, 685-695.  
19019142 E.Curti, J.P.McDonald, S.Mead, and R.Woodgate (2009).
DNA polymerase switching: effects on spontaneous mutagenesis in Escherichia coli.
  Mol Microbiol, 71, 315-331.  
19881914 F.J.López de Saro (2009).
Regulation of interactions with sliding clamps during DNA replication and repair.
  Curr Genomics, 10, 206-215.  
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.  
19698123 J.A.Winter, P.Christofi, S.Morroll, and K.A.Bunting (2009).
The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation.
  BMC Struct Biol, 9, 55.
PDB code: 3ifv
19617571 J.M.Heltzel, R.W.Maul, S.K.Scouten Ponticelli, and M.D.Sutton (2009).
A model for DNA polymerase switching involving a single cleft and the rim of the sliding clamp.
  Proc Natl Acad Sci U S A, 106, 12664-12669.  
19361435 J.M.Heltzel, S.K.Scouten Ponticelli, L.H.Sanders, J.M.Duzen, V.Cody, J.Pace, E.H.Snell, and M.D.Sutton (2009).
Sliding clamp-DNA interactions are required for viability and contribute to DNA polymerase management in Escherichia coli.
  J Mol Biol, 387, 74-91.
PDB code: 3f1v
19843218 J.Wagner, H.Etienne, R.P.Fuchs, A.Cordonnier, and D.Burnouf (2009).
Distinct beta-clamp interactions govern the activities of the Y family PolIV DNA polymerase.
  Mol Microbiol, 74, 1143-1151.  
19633075 P.J.Beuning, S.Chan, L.S.Waters, H.Addepalli, J.N.Ollivierre, and G.C.Walker (2009).
Characterization of novel alleles of the Escherichia coli umuDC genes identifies additional interaction sites of UmuC with the beta clamp.
  J Bacteriol, 191, 5910-5920.  
19000695 Q.Xu, D.McMullan, P.Abdubek, T.Astakhova, D.Carlton, C.Chen, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, M.A.Elsliger, J.Feuerhelm, J.Hale, G.W.Han, L.Jaroszewski, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, P.Kozbial, S.Sri Krishna, A.Kumar, D.Marciano, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, C.Trame, H.van den Bedem, D.Weekes, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2009).
A structural basis for the regulatory inactivation of DnaA.
  J Mol Biol, 385, 368-380.
PDB code: 3bos
19706415 S.Fujii, and R.P.Fuchs (2009).
Biochemical basis for the essential genetic requirements of RecA and the beta-clamp in Pol V activation.
  Proc Natl Acad Sci U S A, 106, 14825-14830.  
19279187 S.K.Scouten Ponticelli, J.M.Duzen, and M.D.Sutton (2009).
Contributions of the individual hydrophobic clefts of the Escherichia coli beta sliding clamp to clamp loading, DNA replication and clamp recycling.
  Nucleic Acids Res, 37, 2796-2809.  
18308729 A.Furukohri, M.F.Goodman, and H.Maki (2008).
A dynamic polymerase exchange with Escherichia coli DNA polymerase IV replacing DNA polymerase III on the sliding clamp.
  J Biol Chem, 283, 11260-11269.  
19053247 B.D.Freudenthal, S.Ramaswamy, M.M.Hingorani, and M.T.Washington (2008).
Structure of a mutant form of proliferating cell nuclear antigen that blocks translesion DNA synthesis.
  Biochemistry, 47, 13354-13361.
PDB code: 3f1w
18761688 K.Uchida, A.Furukohri, Y.Shinozaki, T.Mori, D.Ogawara, S.Kanaya, T.Nohmi, H.Maki, and M.Akiyama (2008).
Overproduction of Escherichia coli DNA polymerase DinB (Pol IV) inhibits replication fork progression and is lethal.
  Mol Microbiol, 70, 608-622.  
18280235 L.A.Simmons, B.W.Davies, A.D.Grossman, and G.C.Walker (2008).
Beta clamp directs localization of mismatch repair in Bacillus subtilis.
  Mol Cell, 29, 291-301.  
18931783 N.Y.Yao, and M.O'Donnell (2008).
Replisome dynamics and use of DNA trombone loops to bypass replication blocks.
  Mol Biosyst, 4, 1075-1084.  
18691598 R.A.Wing, S.Bailey, and T.A.Steitz (2008).
Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit.
  J Mol Biol, 382, 859-869.
PDB code: 3e0d
18678908 R.E.Georgescu, O.Yurieva, S.S.Kim, J.Kuriyan, X.P.Kong, and M.O'Donnell (2008).
Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp.
  Proc Natl Acad Sci U S A, 105, 11116-11121.
PDB codes: 3d1e 3d1f 3d1g
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
18703842 V.Hlinkova, G.Xing, J.Bauer, Y.J.Shin, I.Dionne, K.R.Rajashankar, S.D.Bell, and H.Ling (2008).
Structures of monomeric, dimeric and trimeric PCNA: PCNA-ring assembly and opening.
  Acta Crystallogr D Biol Crystallogr, 64, 941-949.
PDB codes: 2ijx 2io4 2nti
  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.  
18385374 Z.Zhuang, R.E.Johnson, L.Haracska, L.Prakash, S.Prakash, and S.J.Benkovic (2008).
Regulation of polymerase exchange between Poleta and Poldelta by monoubiquitination of PCNA and the movement of DNA polymerase holoenzyme.
  Proc Natl Acad Sci U S A, 105, 5361-5366.  
17720921 A.B.Williams, and P.L.Foster (2007).
The Escherichia coli histone-like protein HU has a role in stationary phase adaptive mutation.
  Genetics, 177, 723-735.  
17551516 K.Schlacher, and M.F.Goodman (2007).
Lessons from 50 years of SOS DNA-damage-induced mutagenesis.
  Nat Rev Mol Cell Biol, 8, 587-594.  
17609212 P.McInerney, and M.O'Donnell (2007).
Replisome fate upon encountering a leading strand block and clearance from DNA by recombination proteins.
  J Biol Chem, 282, 25903-25916.  
17635192 R.W.Maul, S.K.Ponticelli, J.M.Duzen, and M.D.Sutton (2007).
Differential binding of Escherichia coli DNA polymerases to the beta-sliding clamp.
  Mol Microbiol, 65, 811-827.  
17707225 S.T.Lovett (2007).
Polymerase switching in DNA replication.
  Mol Cell, 27, 523-526.  
18158902 V.G.Godoy, D.F.Jarosz, S.M.Simon, A.Abyzov, V.Ilyin, and G.C.Walker (2007).
UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB.
  Mol Cell, 28, 1058-1070.  
17898175 W.Yang, and R.Woodgate (2007).
What a difference a decade makes: insights into translesion DNA synthesis.
  Proc Natl Acad Sci U S A, 104, 15591-15598.  
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
16407313 D.Murat, P.Bance, I.Callebaut, and E.Dassa (2006).
ATP hydrolysis is essential for the function of the Uup ATP-binding cassette ATPase in precise excision of transposons.
  J Biol Chem, 281, 6850-6859.  
16546997 F.J.López de Saro, M.G.Marinus, P.Modrich, and M.O'Donnell (2006).
The beta sliding clamp binds to multiple sites within MutL and MutS.
  J Biol Chem, 281, 14340-14349.  
16608433 J.L.Beck, T.Urathamakul, S.J.Watt, M.M.Sheil, P.M.Schaeffer, and N.E.Dixon (2006).
Proteomic dissection of DNA polymerization.
  Expert Rev Proteomics, 3, 197-211.  
16855240 K.Kongsuwan, P.Josh, M.J.Picault, G.Wijffels, and B.Dalrymple (2006).
The plasmid RK2 replication initiator protein (TrfA) binds to the sliding clamp beta subunit of DNA polymerase III: implication for the toxicity of a peptide derived from the amino-terminal portion of 33-kilodalton TrfA.
  J Bacteriol, 188, 5501-5509.  
16421093 M.O'Donnell (2006).
Replisome architecture and dynamics in Escherichia coli.
  J Biol Chem, 281, 10653-10656.  
16390442 P.J.Beuning, D.Sawicka, D.Barsky, and G.C.Walker (2006).
Two processivity clamp interactions differentially alter the dual activities of UmuC.
  Mol Microbiol, 59, 460-474.  
16464848 P.J.Beuning, S.M.Simon, A.Zemla, D.Barsky, and G.C.Walker (2006).
A non-cleavable UmuD variant that acts as a UmuD' mimic.
  J Biol Chem, 281, 9633-9640.  
16719715 T.Nohmi (2006).
Environmental stress and lesion-bypass DNA polymerases.
  Annu Rev Microbiol, 60, 231-253.  
16322565 Y.Wang, K.Arora, and T.Schlick (2006).
Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass.
  Protein Sci, 15, 135-151.  
15952889 A.Johnson, and M.O'Donnell (2005).
Cellular DNA replicases: components and dynamics at the replication fork.
  Annu Rev Biochem, 74, 283-315.  
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.  
16223720 J.Cramer, and T.Restle (2005).
Pre-steady-state kinetic characterization of the DinB homologue DNA polymerase of Sulfolobus solfataricus.
  J Biol Chem, 280, 40552-40558.  
15752198 M.D.Sutton, J.M.Duzen, and R.W.Maul (2005).
Mutant forms of the Escherichia colibeta sliding clamp that distinguish between its roles in replication and DNA polymerase V-dependent translesion DNA synthesis.
  Mol Microbiol, 55, 1751-1766.  
15719018 M.Newman, J.Murray-Rust, J.Lally, J.Rudolf, A.Fadden, P.P.Knowles, M.F.White, and N.Q.McDonald (2005).
Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition.
  EMBO J, 24, 895-905.
PDB codes: 2bgw 2bhn
15611053 M.Su'etsugu, T.R.Shimuta, T.Ishida, H.Kawakami, and T.Katayama (2005).
Protein associations in DnaA-ATP hydrolysis mediated by the Hda-replicase clamp complex.
  J Biol Chem, 280, 6528-6536.  
15886391 R.S.Galhardo, R.P.Rocha, M.V.Marques, and C.F.Menck (2005).
An SOS-regulated operon involved in damage-inducible mutagenesis in Caulobacter crescentus.
  Nucleic Acids Res, 33, 2603-2614.  
16045613 S.Duigou, S.D.Ehrlich, P.Noirot, and M.F.Noirot-Gros (2005).
DNA polymerase I acts in translesion synthesis mediated by the Y-polymerases in Bacillus subtilis.
  Mol Microbiol, 57, 678-690.  
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
15342632 A.E.Vidal, P.Kannouche, V.N.Podust, W.Yang, A.R.Lehmann, and R.Woodgate (2004).
Proliferating cell nuclear antigen-dependent coordination of the biological functions of human DNA polymerase iota.
  J Biol Chem, 279, 48360-48368.  
15196456 B.S.Plosky, and R.Woodgate (2004).
Switching from high-fidelity replicases to low-fidelity lesion-bypass polymerases.
  Curr Opin Genet Dev, 14, 113-119.  
15159531 C.M.Joyce (2004).
T4 replication: what does "processivity" really mean?
  Proc Natl Acad Sci U S A, 101, 8255-8256.  
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
15210708 J.G.Bertram, L.B.Bloom, M.O'Donnell, and M.F.Goodman (2004).
Increased dNTP binding affinity reveals a nonprocessive role for Escherichia coli beta clamp with DNA polymerase IV.
  J Biol Chem, 279, 33047-33050.  
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.  
15466025 M.D.Sutton (2004).
The Escherichia coli dnaN159 mutant displays altered DNA polymerase usage and chronic SOS induction.
  J Bacteriol, 186, 6738-6748.  
15150238 M.Kurz, B.Dalrymple, G.Wijffels, and K.Kongsuwan (2004).
Interaction of the sliding clamp beta-subunit and Hda, a DnaA-related protein.
  J Bacteriol, 186, 3508-3515.  
15149598 P.L.Kannouche, J.Wing, and A.R.Lehmann (2004).
Interaction of human DNA polymerase eta with monoubiquitinated PCNA: a possible mechanism for the polymerase switch in response to DNA damage.
  Mol Cell, 14, 491-500.  
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 codes are shown on the right.

 

spacer
spacer