4ds5: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4ds5]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DS5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DS5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4ds5]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DS5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DS5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 1.68&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=4ds5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ds5 OCA], [https://pdbe.org/4ds5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ds5 RCSB], [https://www.ebi.ac.uk/pdbsum/4ds5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ds5 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=4ds5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ds5 OCA], [https://pdbe.org/4ds5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ds5 RCSB], [https://www.ebi.ac.uk/pdbsum/4ds5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ds5 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/Q5KWC1_GEOKA Q5KWC1_GEOKA]]
[https://www.uniprot.org/uniprot/Q5KWC1_GEOKA Q5KWC1_GEOKA]  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In addition to discriminating against base-pair mismatches, DNA polymerases exhibit a high degree of selectivity for deoxyribonucleotides over ribo- or dideoxy nucleotides. It has been proposed that a single active site residue (steric gate) blocks productive binding of nucleotides containing 2' hydroxyls. Although this steric gate plays a role in sugar moiety discrimination, its interactions do not account fully for the observed behavior of mutants. Here we present ten high-resolution crystal structures and enzyme kinetic analyses of Bacillus DNA polymerase I large fragment (BF) variants complexed with deoxy-, ribo-, dideoxy-nucleotides, and a DNA substrate. Taken together, these data present a more nuanced and general mechanism for nucleotide discrimination in which ensembles of intermediate conformations in the active site trap non-cognate substrates. It is known that the active site O-helix transitions from an open state in the absence of nucleotide substrates to a ternary complex closed state in which the reactive groups are aligned for catalysis. Substrate misalignment in the closed state plays a fundamental part in preventing non-cognate nucleotide misincorpation. The structures presented here show that additional O-helix conformations intermediate between the open and closed state extremes create an ensemble of binding sites that trap and misalign non-cognate nucleotides. Water-mediated interactions, absent in the fully closed state, play an important role in formation of these binding sites, and can be remodeled to accommodate different non-cognate substrates. This mechanism may extend also to base-pair discrimination.


Structural factors that determine selectivity of a high-fidelity DNA polymerase for deoxy-, dideoxy-, and ribo-nucleotides.,Wang W, Wu EY, Hellinga HW, Beese LS J Biol Chem. 2012 May 30. PMID:22648417<ref>PMID:22648417</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 4ds5" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>

Latest revision as of 17:43, 14 March 2024

Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and rCTP in presence of Mg2+Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and rCTP in presence of Mg2+

Structural highlights

4ds5 is a 6 chain structure with sequence from Geobacillus kaustophilus HTA426. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.68Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q5KWC1_GEOKA

See Also

4ds5, resolution 1.68Å

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