3tar: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3tar]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus Geobacillus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TAR FirstGlance]. <br>
<table><tr><td colspan='2'>[[3tar]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus Geobacillus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TAR FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3tan|3tan]], [[3tap|3tap]], [[3taq|3taq]], [[3thv|3thv]], [[3ti0|3ti0]]</div></td></tr>
<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>
<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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3tar FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tar OCA], [https://pdbe.org/3tar PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tar RCSB], [https://www.ebi.ac.uk/pdbsum/3tar PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tar ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3tar FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tar OCA], [https://pdbe.org/3tar PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tar RCSB], [https://www.ebi.ac.uk/pdbsum/3tar PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tar ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that catalyzes replication in crystals, we observe that a C*A mismatch can mimic the shape of cognate base pairs at the site of incorporation. This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such that a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. These observations provide structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis, a long-standing concept that has been difficult to demonstrate directly.


Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.,Wang W, Hellinga HW, Beese LS Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17644-8. Epub 2011 Oct 17. PMID:22006298<ref>PMID:22006298</ref>
==See Also==
 
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3tar" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: DNA-directed DNA polymerase]]
[[Category: Geobacillus]]
[[Category: Geobacillus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Beese, L S]]
[[Category: Beese LS]]
[[Category: Wang, W]]
[[Category: Wang W]]
[[Category: Dna polymerase i]]
[[Category: Protein-dna complex]]
[[Category: Transferase-dna complex]]

Latest revision as of 16:22, 14 March 2024

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-6) PositionCrystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-6) Position

Structural highlights

3tar is a 3 chain structure with sequence from Geobacillus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

3tar, resolution 1.60Å

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