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3gv5

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{{Seed}}
 
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[[Image:3gv5.jpg|left|200px]]
 
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<!--
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==Human DNA polymerase iota in complex with T template DNA and incoming ddADP==
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The line below this paragraph, containing "STRUCTURE_3gv5", creates the "Structure Box" on the page.
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<StructureSection load='3gv5' size='340' side='right'caption='[[3gv5]], [[Resolution|resolution]] 2.00&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'>[[3gv5]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GV5 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADI:2,3-DIDEOXYADENOSINE-5-DIPHOSPHATE'>ADI</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_3gv5| PDB=3gv5 | SCENE= }}
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gv7|3gv7]], [[3gv8|3gv8]]</div></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POLI, RAD30B ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
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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=3gv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gv5 OCA], [https://pdbe.org/3gv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gv5 RCSB], [https://www.ebi.ac.uk/pdbsum/3gv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gv5 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[[https://www.uniprot.org/uniprot/POLI_HUMAN POLI_HUMAN]] Error-prone 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. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.<ref>PMID:11013228</ref> <ref>PMID:11251121</ref> <ref>PMID:11387224</ref> <ref>PMID:12410315</ref> <ref>PMID:14630940</ref> <ref>PMID:15199127</ref> <ref>PMID:15254543</ref>
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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/gv/3gv5_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=3gv5 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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Human DNA polymerase iota (pol iota) is a unique member of Y-family polymerases, which preferentially misincorporates nucleotides opposite thymines (T) and halts replication at T bases. The structural basis of the high error rates remains elusive. We present three crystal structures of pol complexed with DNA containing a thymine base, paired with correct or incorrect incoming nucleotides. A narrowed active site supports a pyrimidine to pyrimidine mismatch and excludes Watson-Crick base pairing by pol. The template thymine remains in an anti conformation irrespective of incoming nucleotides. Incoming ddATP adopts a syn conformation with reduced base stacking, whereas incorrect dGTP and dTTP maintain anti conformations with normal base stacking. Further stabilization of dGTP by H-bonding with Gln59 of the finger domain explains the preferential T to G mismatch. A template 'U-turn' is stabilized by pol and the methyl group of the thymine template, revealing the structural basis of T stalling. Our structural and domain-swapping experiments indicate that the finger domain is responsible for pol's high error rates on pyrimidines and determines the incorporation specificity.
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===Human DNA polymerase iota in complex with T template DNA and incoming ddADP===
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Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota.,Kirouac KN, Ling H EMBO J. 2009 Jun 3;28(11):1644-54. PMID:19440206<ref>PMID:19440206</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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The line below this paragraph, {{ABSTRACT_PUBMED_19440206}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3gv5" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19440206 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19440206}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3GV5 is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GV5 OCA].
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==Reference==
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<ref group="xtra">PMID:19440206</ref><references group="xtra"/>
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[[Category: DNA-directed DNA polymerase]]
[[Category: DNA-directed DNA polymerase]]
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[[Category: Homo sapiens]]
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[[Category: Human]]
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[[Category: Kirouac, K N.]]
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[[Category: Large Structures]]
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[[Category: Ling, H.]]
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[[Category: Kirouac, K N]]
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[[Category: Ling, H]]
[[Category: Dna damage]]
[[Category: Dna damage]]
[[Category: Dna repair]]
[[Category: Dna repair]]
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[[Category: Nucleus]]
[[Category: Nucleus]]
[[Category: Polymerase iota]]
[[Category: Polymerase iota]]
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[[Category: Polymorphism]]
 
[[Category: Schiff base]]
[[Category: Schiff base]]
[[Category: Transferase]]
[[Category: Transferase]]
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[[Category: Transferase/dna complex]]
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[[Category: Transferase-dna complex]]
[[Category: Y-family polymerase]]
[[Category: Y-family polymerase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 4 07:22:52 2009''
 

Current revision

Human DNA polymerase iota in complex with T template DNA and incoming ddADP

PDB ID 3gv5

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