3ojs: Difference between revisions
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==Snapshots of the large fragment of DNA polymerase I from Thermus Aquaticus processing C5 modified thymidines== | |||
<StructureSection load='3ojs' size='340' side='right'caption='[[3ojs]], [[Resolution|resolution]] 1.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ojs]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OJS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OJS FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=XJS:2-DEOXY-5-[9-(3-{[4-(DIETHYLAMINO)-4-OXOBUTANOYL]AMINO}PROPYL)-18-ETHYL-5,8,14,17-TETRAOXO-4,9,13,18-TETRAAZAICOS-1-YN-1-YL]URIDINE+5-(TETRAHYDROGEN+TRIPHOSPHATE)'>XJS</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=3ojs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ojs OCA], [https://pdbe.org/3ojs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ojs RCSB], [https://www.ebi.ac.uk/pdbsum/3ojs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ojs ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Numerous 2'-deoxynucleoside triphosphates (dNTPs) that are functionalized with spacious modifications such as dyes and affinity tags like biotin are substrates for DNA polymerases. They are widely employed in many cutting-edge technologies like advanced DNA sequencing approaches, microarrays, and single molecule techniques. Modifications attached to the nucleobase are accepted by many DNA polymerases, and thus, dNTPs bearing nucleobase modifications are predominantly employed. When pyrimidines are used the modifications are almost exclusively at the C5 position to avoid disturbing of Watson-Crick base pairing ability. However, the detailed molecular mechanism by which C5 modifications are processed by a DNA polymerase is poorly understood. Here, we present the first crystal structures of a DNA polymerase from Thermus aquaticus processing two C5 modified substrates that are accepted by the enzyme with different efficiencies. The structures were obtained as ternary complex of the enzyme bound to primer/template duplex with the respective modified dNTP in position poised for catalysis leading to incorporation. Thus, the study provides insights into the incorporation mechanism of the modified nucleotides elucidating how bulky modifications are accepted by the enzyme. The structures show a varied degree of perturbation of the enzyme substrate complexes depending on the nature of the modifications suggesting design principles for future developments of modified substrates for DNA polymerases. | |||
Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase.,Obeid S, Baccaro A, Welte W, Diederichs K, Marx A Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21327-31. Epub 2010 Dec 1. PMID:21123743<ref>PMID:21123743</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3ojs" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[DNA polymerase|DNA polymerase]] | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Thermus aquaticus]] | [[Category: Thermus aquaticus]] | ||
[[Category: Diederichs | [[Category: Diederichs K]] | ||
[[Category: Marx | [[Category: Marx A]] | ||
[[Category: Obeid | [[Category: Obeid S]] | ||
Latest revision as of 12:40, 6 September 2023
Snapshots of the large fragment of DNA polymerase I from Thermus Aquaticus processing C5 modified thymidinesSnapshots of the large fragment of DNA polymerase I from Thermus Aquaticus processing C5 modified thymidines
Structural highlights
FunctionPublication Abstract from PubMedNumerous 2'-deoxynucleoside triphosphates (dNTPs) that are functionalized with spacious modifications such as dyes and affinity tags like biotin are substrates for DNA polymerases. They are widely employed in many cutting-edge technologies like advanced DNA sequencing approaches, microarrays, and single molecule techniques. Modifications attached to the nucleobase are accepted by many DNA polymerases, and thus, dNTPs bearing nucleobase modifications are predominantly employed. When pyrimidines are used the modifications are almost exclusively at the C5 position to avoid disturbing of Watson-Crick base pairing ability. However, the detailed molecular mechanism by which C5 modifications are processed by a DNA polymerase is poorly understood. Here, we present the first crystal structures of a DNA polymerase from Thermus aquaticus processing two C5 modified substrates that are accepted by the enzyme with different efficiencies. The structures were obtained as ternary complex of the enzyme bound to primer/template duplex with the respective modified dNTP in position poised for catalysis leading to incorporation. Thus, the study provides insights into the incorporation mechanism of the modified nucleotides elucidating how bulky modifications are accepted by the enzyme. The structures show a varied degree of perturbation of the enzyme substrate complexes depending on the nature of the modifications suggesting design principles for future developments of modified substrates for DNA polymerases. Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase.,Obeid S, Baccaro A, Welte W, Diederichs K, Marx A Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21327-31. Epub 2010 Dec 1. PMID:21123743[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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