3lwm

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{{Seed}}
 
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[[Image:3lwm.jpg|left|200px]]
 
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==Structure of the large fragment of thermus aquaticus DNA polymerase I in complex with a blunt-ended DNA and ddATP==
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The line below this paragraph, containing "STRUCTURE_3lwm", creates the "Structure Box" on the page.
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<StructureSection load='3lwm' size='340' side='right'caption='[[3lwm]], [[Resolution|resolution]] 2.19&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'>[[3lwm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LWM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LWM 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]] 2.186&#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=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DDS:2,3-DIDEOXYADENOSINE+TRIPHOSPHATE'>DDS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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{{STRUCTURE_3lwm| PDB=3lwm | 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=3lwm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lwm OCA], [https://pdbe.org/3lwm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lwm RCSB], [https://www.ebi.ac.uk/pdbsum/3lwm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lwm ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]
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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/lw/3lwm_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=3lwm 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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Abasic sites represent the most frequent DNA lesions in the genome that have high mutagenic potential and lead to mutations commonly found in human cancers. Although these lesions are devoid of the genetic information, adenine is most efficiently inserted when abasic sites are bypassed by DNA polymerases, a phenomenon termed A-rule. In this study, we present X-ray structures of a DNA polymerase caught while incorporating a nucleotide opposite an abasic site. We found that a functionally important tyrosine side chain directs for nucleotide incorporation rather than DNA. It fills the vacant space of the absent template nucleobase and thereby mimics a pyrimidine nucleobase directing for preferential purine incorporation opposite abasic residues because of enhanced geometric fit to the active site. This amino acid templating mechanism was corroborated by switching to pyrimidine specificity because of mutation of the templating tyrosine into tryptophan. The tyrosine is located in motif B and highly conserved throughout evolution from bacteria to humans indicating a general amino acid templating mechanism for bypass of non-instructive lesions by DNA polymerases at least from this sequence family.
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===Structure of the large fragment of thermus aquaticus DNA polymerase I in complex with a blunt-ended DNA and ddATP===
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Replication through an abasic DNA lesion: structural basis for adenine selectivity.,Obeid S, Blatter N, Kranaster R, Schnur A, Diederichs K, Welte W, Marx A EMBO J. 2010 May 19;29(10):1738-47. Epub 2010 Apr 16. PMID:20400942<ref>PMID:20400942</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3lwm" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_20400942}}, adds the Publication Abstract to the page
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 20400942 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20400942}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3LWM is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LWM OCA].
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==Reference==
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<ref group="xtra">PMID:20400942</ref><references group="xtra"/>
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Thermus aquaticus]]
[[Category: Thermus aquaticus]]
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[[Category: Diederichs, K.]]
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[[Category: Diederichs K]]
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[[Category: Marx, A.]]
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[[Category: Marx A]]
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[[Category: Obeid, S.]]
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[[Category: Obeid S]]
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[[Category: Amino acid-templating mechanism]]
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[[Category: Blunt-ended dna]]
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[[Category: Dna polymerase]]
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[[Category: Dna replication]]
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[[Category: Dna-binding]]
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[[Category: Dna-directed dna polymerase]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Template-independent dna synthesis]]
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[[Category: Template-independent nucleotide addition]]
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[[Category: Terminal deoxynucleotidyl transferase]]
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[[Category: Transferase]]
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[[Category: Transferase-dna complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 5 11:51:44 2010''
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Current revision

Structure of the large fragment of thermus aquaticus DNA polymerase I in complex with a blunt-ended DNA and ddATP

PDB ID 3lwm

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