4bdp: Difference between revisions
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<StructureSection load='4bdp' size='340' side='right'caption='[[4bdp]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='4bdp' size='340' side='right'caption='[[4bdp]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4bdp]] is a 3 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4bdp]] 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=4BDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BDP FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.8Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=4bdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bdp OCA], [https://pdbe.org/4bdp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bdp RCSB], [https://www.ebi.ac.uk/pdbsum/4bdp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bdp ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/DPO1_GEOSE DPO1_GEOSE] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity. | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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==See Also== | ==See Also== | ||
*[[DNA polymerase|DNA polymerase]] | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Geobacillus stearothermophilus]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Beese | [[Category: Beese LS]] | ||
[[Category: Kiefer | [[Category: Kiefer JR]] | ||
[[Category: Mao | [[Category: Mao C]] | ||
Latest revision as of 14:06, 2 August 2023
CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 11 BASE PAIRS OF DUPLEX DNA AFTER ADDITION OF TWO DATP RESIDUESCRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 11 BASE PAIRS OF DUPLEX DNA AFTER ADDITION OF TWO DATP RESIDUES
Structural highlights
FunctionDPO1_GEOSE In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedDNA polymerases copy DNA templates with remarkably high fidelity, checking for correct base-pair formation both at nucleotide insertion and at subsequent DNA extension steps. Despite extensive biochemical, genetic and structural studies, the mechanism by which nucleotides are correctly incorporated is not known. Here we present high-resolution crystal structures of a thermostable bacterial (Bacillus stearothermophilus) DNA polymerase I large fragments with DNA primer templates bound productively at the polymerase active site. The active site retains catalytic activity, allowing direct observation of the products of several rounds of nucleotide incorporation. The polymerase also retains its ability to discriminate between correct and incorrectly paired nucleotides in the crystal. Comparison of the structures of successively translocated complexes allows the structural features for the sequence-independent molecular recognition of correctly formed base pairs to be deduced unambiguously. These include extensive interactions with the first four to five base pairs in the minor groove, location of the terminal base pair in a pocket of excellent steric complementarity favouring correct base-pair formation, and a conformational switch from B-form to underwound A-form DNA at the polymerase active site. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal.,Kiefer JR, Mao C, Braman JC, Beese LS Nature. 1998 Jan 15;391(6664):304-7. PMID:9440698[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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