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PDBsum entry 2r8k
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protein dna_rna ligands metals Protein-protein interface(s) links
Replication, transferase/DNA PDB id
2r8k

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
511 a.a. *
DNA/RNA
Ligands
CPT ×2
DTP ×2
Metals
_CA ×4
* Residue conservation analysis
PDB id:
2r8k
Name: Replication, transferase/DNA
Title: Structure of the eukaryotic DNA polymerase eta in complex with 1,2- d(gpg)-cisplatin containing DNA
Structure: 5'-d( Dgp Dtp Dgp Dgp Dtp Dgp Dap Dgp Dc)-3'. Chain: q, p. Engineered: yes. 5'-d(p Dgp Dgp Dcp Dtp Dcp Dap Dcp Dcp Dap Dc)-3'. Chain: u, t. Engineered: yes. DNA polymerase eta. Chain: a, b. Fragment: catalytic domain.
Source: Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: yph499 (atcc 76625). Gene: rad30, dbh1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.30Å     R-factor:   0.230     R-free:   0.267
Authors: T.Carell,A.Alt,K.Lammens
Key ref:
A.Alt et al. (2007). Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta. Science, 318, 967-970. PubMed id: 17991862 DOI: 10.1126/science.1148242
Date:
11-Sep-07     Release date:   11-Dec-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q04049  (POLH_YEAST) -  DNA polymerase eta from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		632 a.a.
511 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  G-T-G-G-T-G-A-G-C 9 bases
  G-G-C-T-C-A-C-C-A-C 10 bases
  G-T-G-G-T-G-A-G-C 9 bases
  G-G-C-T-C-A-C-C-A-C 10 bases

 Enzyme reactions 
   Enzyme class: 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: 10.1126/science.1148242 Science 318:967-970 (2007)
PubMed id: 17991862  
 
 
Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta.
A.Alt, K.Lammens, C.Chiocchini, A.Lammens, J.C.Pieck, D.Kuch, K.P.Hopfner, T.Carell.
 
  ABSTRACT  
 
DNA polymerase eta (Pol eta) is a eukaryotic lesion bypass polymerase that helps organisms to survive exposure to ultraviolet (UV) radiation, and tumor cells to gain resistance against cisplatin-based chemotherapy. It allows cells to replicate across cross-link lesions such as 1,2-d(GpG) cisplatin adducts (Pt-GG) and UV-induced cis-syn thymine dimers. We present structural and biochemical analysis of how Pol eta copies Pt-GG-containing DNA. The damaged DNA is bound in an open DNA binding rim. Nucleotidyl transfer requires the DNA to rotate into an active conformation, driven by hydrogen bonding of the templating base to the dNTP. For the 3'dG of the Pt-GG, this step is accomplished by a Watson-Crick base pair to dCTP and is biochemically efficient and accurate. In contrast, bypass of the 5'dG of the Pt-GG is less efficient and promiscuous for dCTP and dATP as a result of the presence of the rigid Pt cross-link. Our analysis reveals the set of structural features that enable Pol eta to replicate across strongly distorting DNA lesions.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Pol structure in ternary complex with lesion containing DNA. (A) In the 3'dG elongation complex, the cisplatin (magenta) is shown with the platinum anomalous electron density contoured at 10 . The primer and template strands of the DNA (brown) and the Watson-Crick H-bonded dCTP (magenta) are depicted as sticks. The two metal ions are shown as gray spheres. (B) View of the 1,2-d(GpG) cisplatin lesion superimposed with the simulated annealed composit-omit density map contoured at 1.0 sigma. (C) The catalytic residues in the active site. R73 orients the dCTP for H-bonding with the 3'desoxyguanine of the lesion. (D) Schematics of protein-DNA contacts representing the pre-elongation, 3'dG elongation, and 5'dG elongation complex. Direct hydrogen-bonds are indicated by solid lines. DNA contacts with the symmetry-related molecule are not shown. 		Figure 2.
Fig. 2. The 3'dG elongation process of Pol (A) The catalytic residues, the metal ions and the dCTP are shown for the pre-elongation complex. Phe^35 stacks upon the dNTPs deoxyribose. The dNTP is unpaired. (B) Detailed view of the lesion in the pre-elongation complex (cyan) superpositioned with the lesion in the 3'dG elongation state (magenta). For clarity, the finger domain has been omitted and the DNA molecules (cyan and magenta) are viewed in a simplified form. Watson-Crick base pairing revolves the DNA to position the 3'OH of the primer for nucleophilic attack on the -phosphate of the dNTP. (C) The DNA revolves from the pre-elongation state into the first elongation state, forming a Watson-Crick base pair. This aligns the 3'OH of the primer for nucleotidyl transfer. The protein of the pre-elongation complex is omitted for clarity, and the protein of the 3'dG elongation state is depicted in gray. The DNA molecules are color coded as in Fig. 2B.
 
  The above figures are reprinted by permission from the AAAs: Science (2007, 318, 967-970) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22562137 A.Ummat, O.Rechkoblit, R.Jain, J.Roy Choudhury, R.E.Johnson, T.D.Silverstein, A.Buku, S.Lone, L.Prakash, S.Prakash, and A.K.Aggarwal (2012).
Structural basis for cisplatin DNA damage tolerance by human polymerase η during cancer chemotherapy.
  Nat Struct Mol Biol, 19, 628-632.
PDB code: 4eey
20846959 S.M.Sherrer, K.A.Fiala, J.D.Fowler, S.A.Newmister, J.M.Pryor, and Z.Suo (2011).
Quantitative analysis of the efficiency and mutagenic spectra of abasic lesion bypass catalyzed by human Y-family DNA polymerases.
  Nucleic Acids Res, 39, 609-622.  
  20811617 A.Basu, and S.Krishnamurthy (2010).
Cellular responses to Cisplatin-induced DNA damage.
  J Nucleic Acids, 2010, 0.  
19939936 A.Katafuchi, A.Sassa, N.Niimi, P.Grúz, H.Fujimoto, C.Masutani, F.Hanaoka, T.Ohta, and T.Nohmi (2010).
Critical amino acids in human DNA polymerases eta and kappa involved in erroneous incorporation of oxidized nucleotides.
  Nucleic Acids Res, 38, 859-867.  
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
20647037 B.Köberle, M.T.Tomicic, S.Usanova, and B.Kaina (2010).
Cisplatin resistance: preclinical findings and clinical implications.
  Biochim Biophys Acta, 1806, 172-182.  
20577208 C.Biertümpfel, Y.Zhao, Y.Kondo, S.Ramón-Maiques, M.Gregory, J.Y.Lee, C.Masutani, A.R.Lehmann, F.Hanaoka, and W.Yang (2010).
Structure and mechanism of human DNA polymerase eta.
  Nature, 465, 1044-1048.
PDB codes: 3mr2 3mr3 3mr4 3mr5 3mr6 3si8
  20798853 J.A.Brown, L.Zhang, S.M.Sherrer, J.S.Taylor, P.M.Burgers, and Z.Suo (2010).
Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase Eta.
  J Nucleic Acids, 2010, 0.  
20123134 J.D.Pata (2010).
Structural diversity of the Y-family DNA polymerases.
  Biochim Biophys Acta, 1804, 1124-1135.  
20028736 J.K.Hicks, C.L.Chute, M.T.Paulsen, R.L.Ragland, N.G.Howlett, Q.Guéranger, T.W.Glover, and C.E.Canman (2010).
Differential roles for DNA polymerases eta, zeta, and REV1 in lesion bypass of intrastrand versus interstrand DNA cross-links.
  Mol Cell Biol, 30, 1217-1230.  
20173781 J.Xie, R.Litman, S.Wang, M.Peng, S.Guillemette, T.Rooney, and S.B.Cantor (2010).
Targeting the FANCJ-BRCA1 interaction promotes a switch from recombination to poleta-dependent bypass.
  Oncogene, 29, 2499-2508.  
19616647 M.T.Washington, K.D.Carlson, B.D.Freudenthal, and J.M.Pryor (2010).
Variations on a theme: eukaryotic Y-family DNA polymerases.
  Biochim Biophys Acta, 1804, 1113-1123.  
20154704 O.Rechkoblit, A.Kolbanovskiy, L.Malinina, N.E.Geacintov, S.Broyde, and D.J.Patel (2010).
Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4.
  Nat Struct Mol Biol, 17, 379-388.
PDB codes: 3khg 3khh 3khl 3khr
  20936119 R.L.Eoff, J.Y.Choi, and F.P.Guengerich (2010).
Mechanistic Studies with DNA Polymerases Reveal Complex Outcomes following Bypass of DNA Damage.
  J Nucleic Acids, 2010, 0.  
20577203 S.Broyde, and D.J.Patel (2010).
DNA repair: How to accurately bypass damage.
  Nature, 465, 1023-1024.  
  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.  
20015866 S.Chijiwa, C.Masutani, F.Hanaoka, S.Iwai, and I.Kuraoka (2010).
Polymerization by DNA polymerase eta is blocked by cis-diamminedichloroplatinum(II) 1,3-d(GpTpG) cross-link: implications for cytotoxic effects in nucleotide excision repair-negative tumor cells.
  Carcinogenesis, 31, 388-393.  
21076032 S.Schorr, S.Schneider, K.Lammens, K.P.Hopfner, and T.Carell (2010).
Mechanism of replication blocking and bypass of Y-family polymerase {eta} by bulky acetylaminofluorene DNA adducts.
  Proc Natl Acad Sci U S A, 107, 20720-20725.
PDB codes: 2xgp 2xgq
21064171 S.Schorr, and T.Carell (2010).
Mechanism of acetylaminofluorene-dG induced frameshifting by polymerase η.
  Chembiochem, 11, 2534-2537.  
20577207 T.D.Silverstein, R.E.Johnson, R.Jain, L.Prakash, S.Prakash, and A.K.Aggarwal (2010).
Structural basis for the suppression of skin cancers by DNA polymerase eta.
  Nature, 465, 1039-1043.
PDB codes: 3mfh 3mfi
20129057 T.Sekimoto, T.Oda, F.M.Pozo, Y.Murakumo, C.Masutani, F.Hanaoka, and T.Yamashita (2010).
The molecular chaperone Hsp90 regulates accumulation of DNA polymerase eta at replication stalling sites in UV-irradiated cells.
  Mol Cell, 37, 79-89.  
19542228 A.Irimia, R.L.Eoff, F.P.Guengerich, and M.Egli (2009).
Structural and functional elucidation of the mechanism promoting error-prone synthesis by human DNA polymerase kappa opposite the 7,8-dihydro-8-oxo-2'-deoxyguanosine adduct.
  J Biol Chem, 284, 22467-22480.
PDB codes: 2w7o 2w7p
19446518 J.J.Perry, K.Hitomi, and J.A.Tainer (2009).
Flexibility promotes fidelity.
  Structure, 17, 633-634.  
19072536 K.Donny-Clark, R.Shapiro, and S.Broyde (2009).
Accommodation of an N-(deoxyguanosin-8-yl)-2-acetylaminofluorene adduct in the active site of human DNA polymerase iota: Hoogsteen or Watson-Crick base pairing?
  Biochemistry, 48, 7.  
19440206 K.N.Kirouac, and H.Ling (2009).
Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota.
  EMBO J, 28, 1644-1654.
PDB codes: 3gv5 3gv7 3gv8
19607844 K.Y.Seo, J.Yin, P.Donthamsetti, S.Chandani, C.H.Lee, and E.L.Loechler (2009).
Amino acid architecture that influences dNTP insertion efficiency in Y-family DNA polymerase V of E. coli.
  J Mol Biol, 392, 270-282.  
19258535 L.S.Waters, B.K.Minesinger, M.E.Wiltrout, S.D'Souza, R.V.Woodruff, and G.C.Walker (2009).
Eukaryotic translesion polymerases and their roles and regulation in DNA damage tolerance.
  Microbiol Mol Biol Rev, 73, 134-154.  
18984581 M.G.Pence, P.Blans, C.N.Zink, T.Hollis, J.C.Fishbein, and F.W.Perrino (2009).
Lesion bypass of N2-ethylguanine by human DNA polymerase iota.
  J Biol Chem, 284, 1732-1740.
PDB codes: 3epg 3epi
19449361 O.Nováková, J.Malina, J.Kaspárková, A.Halámiková, V.Bernard, F.Intini, G.Natile, and V.Brabec (2009).
Energetics, conformation, and recognition of DNA duplexes modified by methylated analogues of [PtCl(dien)]+.
  Chemistry, 15, 6211-6221.  
19446528 O.Rechkoblit, L.Malinina, Y.Cheng, N.E.Geacintov, S.Broyde, and D.J.Patel (2009).
Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases.
  Structure, 17, 725-736.
PDB codes: 3gii 3gij 3gik 3gil 3gim
19515847 R.L.Eoff, R.Sanchez-Ponce, and F.P.Guengerich (2009).
Conformational changes during nucleotide selection by Sulfolobus solfataricus DNA polymerase Dpo4.
  J Biol Chem, 284, 21090-21099.  
19188081 S.Chandani, and E.L.Loechler (2009).
Y-Family DNA polymerases may use two different dNTP shapes for insertion: a hypothesis and its implications.
  J Mol Graph Model, 27, 759-769.  
19153606 S.Shachar, O.Ziv, S.Avkin, S.Adar, J.Wittschieben, T.Reissner, S.Chaney, E.C.Friedberg, Z.Wang, T.Carell, N.Geacintov, and Z.Livneh (2009).
Two-polymerase mechanisms dictate error-free and error-prone translesion DNA synthesis in mammals.
  EMBO J, 28, 383-393.  
19428373 T.J.O'Brien, P.Witcher, B.Brooks, and S.R.Patierno (2009).
DNA polymerase zeta is essential for hexavalent chromium-induced mutagenesis.
  Mutat Res, 663, 77-83.  
18499711 J.A.Brown, S.A.Newmister, K.A.Fiala, and Z.Suo (2008).
Mechanism of double-base lesion bypass catalyzed by a Y-family DNA polymerase.
  Nucleic Acids Res, 36, 3867-3878.  
18399510 J.Cramer, G.Rangam, A.Marx, and T.Restle (2008).
Varied active-site constraints in the klenow fragment of E. coli DNA polymerase I and the lesion-bypass Dbh DNA polymerase.
  Chembiochem, 9, 1243-1250.  
18931375 L.Jia, N.E.Geacintov, and S.Broyde (2008).
The N-clasp of human DNA polymerase kappa promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions.
  Nucleic Acids Res, 36, 6571-6584.  
18407502 S.Broyde, L.Wang, O.Rechkoblit, N.E.Geacintov, and D.J.Patel (2008).
Lesion processing: high-fidelity versus lesion-bypass DNA polymerases.
  Trends Biochem Sci, 33, 209-219.  
19111656 S.H.Kim, and W.M.Michael (2008).
Regulated proteolysis of DNA polymerase eta during the DNA-damage response in C. elegans.
  Mol Cell, 32, 757-766.  
18598057 S.Kumar, M.Bakhtina, and M.D.Tsai (2008).
Altered order of substrate binding by DNA polymerase X from African Swine Fever virus.
  Biochemistry, 47, 7875-7887.  
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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