1nk5

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[[Image:1nk5.jpg|left|200px]]
 
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{{Structure
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==ADENINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE==
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|PDB= 1nk5 |SIZE=350|CAPTION= <scene name='initialview01'>1nk5</scene>, resolution 2.10&Aring;
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<StructureSection load='1nk5' size='340' side='right'caption='[[1nk5]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene>
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<table><tr><td colspan='2'>[[1nk5]] 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=1NK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NK5 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]] 2.1&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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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|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=1nk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nk5 OCA], [https://pdbe.org/1nk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nk5 RCSB], [https://www.ebi.ac.uk/pdbsum/1nk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nk5 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1njw|1NJW]], [[1njx|1NJX]], [[1njy|1NJY]], [[1njz|1NJZ]], [[1nk0|1NK0]], [[1nk4|1NK4]], [[1nk6|1NK6]], [[1nk7|1NK7]], [[1nk8|1NK8]], [[1nk9|1NK9]], [[1nkb|1NKB]], [[1nkc|1NKC]], [[1nke|1NKE]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nk5 OCA], [http://www.ebi.ac.uk/pdbsum/1nk5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nk5 RCSB]</span>
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== Function ==
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}}
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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/nk/1nk5_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=1nk5 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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Accurate DNA replication is essential for genomic stability. One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. Here we a present a structural characterization of all 12 possible mismatches captured at the growing primer terminus in the active site of a polymerase. Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. Furthermore, we have observed the effects of extending a mismatch up to six base pairs from the primer terminus and find that long-range distortions in the DNA transmit the presence of the mismatch back to the enzyme active site, suggesting the structural basis for the short-term memory of replication errors.
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'''ADENINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE'''
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Structures of mismatch replication errors observed in a DNA polymerase.,Johnson SJ, Beese LS Cell. 2004 Mar 19;116(6):803-16. PMID:15035983<ref>PMID:15035983</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 1nk5" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Accurate DNA replication is essential for genomic stability. One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. Here we a present a structural characterization of all 12 possible mismatches captured at the growing primer terminus in the active site of a polymerase. Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. Furthermore, we have observed the effects of extending a mismatch up to six base pairs from the primer terminus and find that long-range distortions in the DNA transmit the presence of the mismatch back to the enzyme active site, suggesting the structural basis for the short-term memory of replication errors.
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1NK5 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NK5 OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Structures of mismatch replication errors observed in a DNA polymerase., Johnson SJ, Beese LS, Cell. 2004 Mar 19;116(6):803-16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15035983 15035983]
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Beese, L S.]]
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[[Category: Beese LS]]
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[[Category: Johnson, S J.]]
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[[Category: Johnson SJ]]
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[[Category: dna mismatch]]
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[[Category: dna polymerase i]]
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[[Category: dna replication]]
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[[Category: klenow fragment]]
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[[Category: protein-dna complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:31:28 2008''
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Current revision

ADENINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE

PDB ID 1nk5

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