1zyq

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[[Image:1zyq.gif|left|200px]]
 
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{{Structure
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==T7 DNA polymerase in complex with 8oG and incoming ddATP==
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|PDB= 1zyq |SIZE=350|CAPTION= <scene name='initialview01'>1zyq</scene>, resolution 2.70&Aring;
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<StructureSection load='1zyq' size='340' side='right'caption='[[1zyq]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=8OG:8-OXO-2&#39;-DEOXY-GUANOSINE-5&#39;-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DAD:2&#39;,3&#39;-DIDEOXYADENOSINE-5&#39;-TRIPHOSPHATE'>DAD</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DDG:2&#39;,3&#39;-DIDEOXY-GUANOSINE-5&#39;-MONOPHOSPHATE'>DDG</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
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<table><tr><td colspan='2'>[[1zyq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZYQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZYQ FirstGlance]. <br>
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|ACTIVITY= <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>
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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]] 2.7&#8491;</td></tr>
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|GENE= 5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 Enterobacteria phage T7]), trxA, fipA, tsnC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=DAD:2,3-DIDEOXYADENOSINE-5-TRIPHOSPHATE'>DAD</scene>, <scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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|DOMAIN=
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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=1zyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zyq OCA], [https://pdbe.org/1zyq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zyq RCSB], [https://www.ebi.ac.uk/pdbsum/1zyq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zyq ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1t7p|1T7P]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zyq OCA], [http://www.ebi.ac.uk/pdbsum/1zyq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zyq RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/DPOL_BPT7 DPOL_BPT7] Replicates viral genomic DNA. Non-processive DNA polymerase that achieves processivity by binding to host thioredoxin (TrxA). This interaction increases the rate of dNTP incorporation to yield a processivity of approximately 800 nucleotides (nt) per binding event. Interacts with DNA helicase gp4 to coordinate nucleotide polymerization with unwinding of the DNA. The leading strand is synthesized continuously while synthesis of the lagging strand requires the synthesis of oligoribonucleotides by the primase domain of gp4.<ref>PMID:9218486</ref> <ref>PMID:21606333</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/zy/1zyq_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=1zyq ConSurf].
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<div style="clear:both"></div>
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'''T7 DNA polymerase in complex with 8oG and incoming ddATP'''
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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*[[Thioredoxin 3D structures|Thioredoxin 3D structures]]
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==Overview==
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== References ==
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8-oxo-7,8-dihydroguanosine (8oG) is a highly mutagenic DNA lesion that stably pairs with adenosine, forming 8oG(syn).dA(anti) Hoogsteen base pairs. DNA polymerases show different propensities to insert dCMP or dAMP opposite 8oG, but the molecular mechanisms that determine faithful or mutagenic bypass are poorly understood. Here, we report kinetic and structural data providing evidence that, in T7 DNA polymerase, residue Lys536 is responsible for attenuating the miscoding potential of 8oG. The Lys536Ala polymerase shows a significant increase in mutagenic 8oG bypass versus wild-type polymerase, and a crystal structure of the Lys536Ala mutant reveals a closed complex with an 8oG(syn).dATP mismatch in the polymerase active site, in contrast to the unproductive, open complex previously obtained by using wild-type polymerase. We propose that Lys536 acts as a steric and/or electrostatic filter that attenuates the miscoding potential of 8oG by normally interfering with the binding of 8oG in a syn conformation that pairs with dATP.
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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1ZYQ is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZYQ OCA].
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==Reference==
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A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine., Brieba LG, Kokoska RJ, Bebenek K, Kunkel TA, Ellenberger T, Structure. 2005 Nov;13(11):1653-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16271888 16271888]
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Enterobacteria phage t7]]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Protein complex]]
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[[Category: Escherichia phage T7]]
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[[Category: Bebenek, K.]]
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[[Category: Large Structures]]
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[[Category: Brieba, L G.]]
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[[Category: Bebenek K]]
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[[Category: Ellenberger, T.]]
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[[Category: Brieba LG]]
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[[Category: Kokoska, R J.]]
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[[Category: Ellenberger T]]
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[[Category: Kunkel, T A.]]
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[[Category: Kokoska RJ]]
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[[Category: 8og]]
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[[Category: Kunkel TA]]
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[[Category: fidelity]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:43:25 2008''
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Current revision

T7 DNA polymerase in complex with 8oG and incoming ddATP

PDB ID 1zyq

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