5w2c: Difference between revisions

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'''Unreleased structure'''


The entry 5w2c is ON HOLD until Paper Publication
==Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and incoming dAMPNPP==
<StructureSection load='5w2c' size='340' side='right' caption='[[5w2c]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5w2c]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W2C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W2C FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LDG:'>LDG</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5w2a|5w2a]]</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5w2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w2c OCA], [http://pdbe.org/5w2c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w2c RCSB], [http://www.ebi.ac.uk/pdbsum/5w2c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w2c ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/POLK_HUMAN POLK_HUMAN]] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Depending on the context, it inserts the correct base, but causes frequent base transitions, transversions and frameshifts. Lacks 3'-5' proofreading exonuclease activity. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity.<ref>PMID:10620008</ref> <ref>PMID:11024016</ref> <ref>PMID:12145297</ref> <ref>PMID:12444249</ref> <ref>PMID:12952891</ref> <ref>PMID:14630940</ref> <ref>PMID:15533436</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA damage impinges on genetic information flow and has significant implications in human disease and aging. Lucidin-3-O-primeveroside (LuP) is an anthraquinone derivative present in madder root, which has been used as a coloring agent and food additive. LuP can be metabolically converted to genotoxic compound lucidin, which subsequently forms lucidin-specific N2-2'-deoxyguanosine (N2-dG) and N6-2'-deoxyadenosine (N6-dA) DNA adducts. Lucidin is mutagenic and carcinogenic in rodents, but has low carcinogenic risks in humans. To understand the molecular mechanism of low carcinogenicity of lucidin in humans, we performed DNA replication assays using site-specifically modified oligonucleotides containing a structural analogue (LdG) of lucidin-N2-dG DNA adduct and determined the crystal structures of DNA polymerase (pol) kappa in complex with LdG-bearing DNA and an incoming nucleotide. We examined four human pols (pol eta, pol iota, pol kappa, and Rev1) in their efficiency and accuracy during DNA replication with LdG; these pols are key players in DNA damage response. Our results demonstrate that pol kappa efficiently and accurately replicates past the LdG adduct, whereas DNA replication by pol eta, pol iota, and Rev1 is compromised to different extents. Two ternary crystal structures of pol kappa illustrate that the LdG adduct is accommodated by pol kappa at the enzyme active site during insertion and postlesion-extension steps. The unique open active site of pol kappa allows the adducted DNA to adapt a standard B-form for accurate DNA replication. Collectively, these biochemical and structural data provide mechanistic insights into the low carcinogenic risk of lucidin in humans.


Authors: Jha, V.K., Ling, H.
Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase kappa.,Yockey O, Jha V, Ghodke PP, Xu T, Xu W, Ling H, Pradeepkumar PI, Zhao L Chem Res Toxicol. 2017 Oct 3. doi: 10.1021/acs.chemrestox.7b00227. PMID:28972744<ref>PMID:28972744</ref>


Description: Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and incoming dAMPNPP
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Jha, V.K]]
<div class="pdbe-citations 5w2c" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: DNA-directed DNA polymerase]]
[[Category: Jha, V K]]
[[Category: Ling, H]]
[[Category: Ling, H]]
[[Category: Dna polymerase kappa]]
[[Category: Lucidin-derived dna adduct]]
[[Category: Mutagenesis]]
[[Category: Replication]]
[[Category: Translesion synthesis]]

Revision as of 10:06, 18 October 2017

Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and incoming dAMPNPPStructure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and incoming dAMPNPP

Structural highlights

5w2c is a 6 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , , ,
NonStd Res:
Activity:DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[POLK_HUMAN] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Depending on the context, it inserts the correct base, but causes frequent base transitions, transversions and frameshifts. Lacks 3'-5' proofreading exonuclease activity. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity.[1] [2] [3] [4] [5] [6] [7]

Publication Abstract from PubMed

DNA damage impinges on genetic information flow and has significant implications in human disease and aging. Lucidin-3-O-primeveroside (LuP) is an anthraquinone derivative present in madder root, which has been used as a coloring agent and food additive. LuP can be metabolically converted to genotoxic compound lucidin, which subsequently forms lucidin-specific N2-2'-deoxyguanosine (N2-dG) and N6-2'-deoxyadenosine (N6-dA) DNA adducts. Lucidin is mutagenic and carcinogenic in rodents, but has low carcinogenic risks in humans. To understand the molecular mechanism of low carcinogenicity of lucidin in humans, we performed DNA replication assays using site-specifically modified oligonucleotides containing a structural analogue (LdG) of lucidin-N2-dG DNA adduct and determined the crystal structures of DNA polymerase (pol) kappa in complex with LdG-bearing DNA and an incoming nucleotide. We examined four human pols (pol eta, pol iota, pol kappa, and Rev1) in their efficiency and accuracy during DNA replication with LdG; these pols are key players in DNA damage response. Our results demonstrate that pol kappa efficiently and accurately replicates past the LdG adduct, whereas DNA replication by pol eta, pol iota, and Rev1 is compromised to different extents. Two ternary crystal structures of pol kappa illustrate that the LdG adduct is accommodated by pol kappa at the enzyme active site during insertion and postlesion-extension steps. The unique open active site of pol kappa allows the adducted DNA to adapt a standard B-form for accurate DNA replication. Collectively, these biochemical and structural data provide mechanistic insights into the low carcinogenic risk of lucidin in humans.

Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase kappa.,Yockey O, Jha V, Ghodke PP, Xu T, Xu W, Ling H, Pradeepkumar PI, Zhao L Chem Res Toxicol. 2017 Oct 3. doi: 10.1021/acs.chemrestox.7b00227. PMID:28972744[8]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Ogi T, Kato T Jr, Kato T, Ohmori H. Mutation enhancement by DINB1, a mammalian homologue of the Escherichia coli mutagenesis protein dinB. Genes Cells. 1999 Nov;4(11):607-18. PMID:10620008
  2. ↑ Gerlach VL, Feaver WJ, Fischhaber PL, Friedberg EC. Purification and characterization of pol kappa, a DNA polymerase encoded by the human DINB1 gene. J Biol Chem. 2001 Jan 5;276(1):92-8. PMID:11024016 doi:http://dx.doi.org/10.1074/jbc.M004413200
  3. ↑ Fischhaber PL, Gerlach VL, Feaver WJ, Hatahet Z, Wallace SS, Friedberg EC. Human DNA polymerase kappa bypasses and extends beyond thymine glycols during translesion synthesis in vitro, preferentially incorporating correct nucleotides. J Biol Chem. 2002 Oct 4;277(40):37604-11. Epub 2002 Jul 26. PMID:12145297 doi:10.1074/jbc.M206027200
  4. ↑ Haracska L, Prakash L, Prakash S. Role of human DNA polymerase kappa as an extender in translesion synthesis. Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16000-5. Epub 2002 Nov 20. PMID:12444249 doi:10.1073/pnas.252524999
  5. ↑ Wolfle WT, Washington MT, Prakash L, Prakash S. Human DNA polymerase kappa uses template-primer misalignment as a novel means for extending mispaired termini and for generating single-base deletions. Genes Dev. 2003 Sep 1;17(17):2191-9. PMID:12952891 doi:http://dx.doi.org/10.1101/gad.1108603
  6. ↑ Haracska L, Prakash L, Prakash S. A mechanism for the exclusion of low-fidelity human Y-family DNA polymerases from base excision repair. Genes Dev. 2003 Nov 15;17(22):2777-85. PMID:14630940 doi:10.1101/gad.1146103
  7. ↑ Yasui M, Suzuki N, Miller H, Matsuda T, Matsui S, Shibutani S. Translesion synthesis past 2'-deoxyxanthosine, a nitric oxide-derived DNA adduct, by mammalian DNA polymerases. J Mol Biol. 2004 Nov 26;344(3):665-74. PMID:15533436 doi:S0022-2836(04)01222-7
  8. ↑ Yockey O, Jha V, Ghodke PP, Xu T, Xu W, Ling H, Pradeepkumar PI, Zhao L. Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase kappa. Chem Res Toxicol. 2017 Oct 3. doi: 10.1021/acs.chemrestox.7b00227. PMID:28972744 doi:http://dx.doi.org/10.1021/acs.chemrestox.7b00227

5w2c, resolution 2.50Å

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