1xc9

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[[Image:1xc9.gif|left|200px]]
 
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==Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication==
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The line below this paragraph, containing "STRUCTURE_1xc9", creates the "Structure Box" on the page.
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<StructureSection load='1xc9' size='340' side='right'caption='[[1xc9]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1xc9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XC9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XC9 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_1xc9| PDB=1xc9 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xc9 OCA], [https://pdbe.org/1xc9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xc9 RCSB], [https://www.ebi.ac.uk/pdbsum/1xc9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xc9 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPO1_GEOSE DPO1_GEOSE] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xc/1xc9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xc9 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Of the carcinogens to which humans are most frequently exposed, the polycyclic aromatic hydrocarbon benzo[a]pyrene (BP) is one of the most ubiquitous. BP is a byproduct of grilled foods and tobacco and fuel combustion and has long been linked to various human cancers, particularly lung and skin. BP is metabolized to diol epoxides that covalently modify DNA bases to form bulky adducts that block DNA synthesis by replicative or high fidelity DNA polymerases. Here we present the structure of a high fidelity polymerase from a thermostable strain of Bacillus stearothermophilus (Bacillus fragment) bound to the most common BP-derived N2-guanine adduct base-paired with cytosine. The BP adduct adopts a conformation that places the polycyclic BP moiety in the nascent DNA minor groove and is the first structure of a minor groove adduct bound to a polymerase. Orientation of the BP moiety into the nascent DNA minor groove results in extensive disruption to the interactions between the adducted DNA duplex and the polymerase. The disruptions revealed by the structure of Bacillus fragment bound to a BP adduct provide a molecular basis for rationalizing the potent blocking effect on replication exerted by BP adducts.
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'''Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication'''
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Structure of a high fidelity DNA polymerase bound to a benzo[a]pyrene adduct that blocks replication.,Hsu GW, Huang X, Luneva NP, Geacintov NE, Beese LS J Biol Chem. 2005 Feb 4;280(5):3764-70. Epub 2004 Nov 16. PMID:15548515<ref>PMID:15548515</ref>
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==Overview==
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Of the carcinogens to which humans are most frequently exposed, the polycyclic aromatic hydrocarbon benzo[a]pyrene (BP) is one of the most ubiquitous. BP is a byproduct of grilled foods and tobacco and fuel combustion and has long been linked to various human cancers, particularly lung and skin. BP is metabolized to diol epoxides that covalently modify DNA bases to form bulky adducts that block DNA synthesis by replicative or high fidelity DNA polymerases. Here we present the structure of a high fidelity polymerase from a thermostable strain of Bacillus stearothermophilus (Bacillus fragment) bound to the most common BP-derived N2-guanine adduct base-paired with cytosine. The BP adduct adopts a conformation that places the polycyclic BP moiety in the nascent DNA minor groove and is the first structure of a minor groove adduct bound to a polymerase. Orientation of the BP moiety into the nascent DNA minor groove results in extensive disruption to the interactions between the adducted DNA duplex and the polymerase. The disruptions revealed by the structure of Bacillus fragment bound to a BP adduct provide a molecular basis for rationalizing the potent blocking effect on replication exerted by BP adducts.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XC9 OCA].
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</div>
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<div class="pdbe-citations 1xc9" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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Structure of a high fidelity DNA polymerase bound to a benzo[a]pyrene adduct that blocks replication., Hsu GW, Huang X, Luneva NP, Geacintov NE, Beese LS, J Biol Chem. 2005 Feb 4;280(5):3764-70. Epub 2004 Nov 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15548515 15548515]
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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[[Category: DNA-directed DNA polymerase]]
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== References ==
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[[Category: Beese, L S.]]
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<references/>
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[[Category: Geacintov, N E.]]
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__TOC__
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[[Category: Hsu, G W.]]
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</StructureSection>
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[[Category: Huang, X.]]
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[[Category: Geobacillus stearothermophilus]]
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[[Category: Luneva, N P.]]
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[[Category: Large Structures]]
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[[Category: Benzopyrene]]
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[[Category: Beese LS]]
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[[Category: Dna lesion]]
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[[Category: Geacintov NE]]
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[[Category: Dna polymerase i]]
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[[Category: Hsu GW]]
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[[Category: Dna replication]]
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[[Category: Huang X]]
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[[Category: Klenow fragment]]
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[[Category: Luneva NP]]
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[[Category: Translation replication]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 14:50:39 2008''
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Current revision

Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication

PDB ID 1xc9

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