7b0f: Difference between revisions
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==TgoT_6G12 Binary complex== | |||
<StructureSection load='7b0f' size='340' side='right'caption='[[7b0f]], [[Resolution|resolution]] 2.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7b0f]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7B0F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7B0F 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]] 2.797Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=7b0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7b0f OCA], [https://pdbe.org/7b0f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7b0f RCSB], [https://www.ebi.ac.uk/pdbsum/7b0f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7b0f ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DPOL_THEGO DPOL_THEGO] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Archaeal DNA polymerases from the B-family (polB) have found essential applications in biotechnology. In addition, some of their variants can accept a wide range of modified nucleotides or xenobiotic nucleotides, such as 1,5-anhydrohexitol nucleic acid (HNA), which has the unique ability to selectively cross-pair with DNA and RNA. This capacity is essential to allow the transmission of information between different chemistries of nucleic acid molecules. Variants of the archaeal polymerase from Thermococcus gorgonarius, TgoT, that can either generate HNA from DNA (TgoT_6G12) or DNA from HNA (TgoT_RT521) have been previously identified. To understand how DNA and HNA are recognized and selected by these two laboratory-evolved polymerases, we report six X-ray structures of these variants, as well as an in silico model of a ternary complex with HNA. Structural comparisons of the apo form of TgoT_6G12 together with its binary and ternary complexes with a DNA duplex highlight an ensemble of interactions and conformational changes required to promote DNA or HNA synthesis. MD simulations of the ternary complex suggest that the HNA-DNA hybrid duplex remains stable in the A-DNA helical form and help explain the presence of mutations in regions that would normally not be in contact with the DNA if it were not in the A-helical form. One complex with two incorporated HNA nucleotides is surprisingly found in a one nucleotide-backtracked form, which is new for a DNA polymerase. This information can be used for engineering a new generation of more efficient HNA polymerase variants. | |||
Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution.,Samson C, Legrand P, Tekpinar M, Rozenski J, Abramov M, Holliger P, Pinheiro VB, Herdwijn P, Delarue M Biomolecules. 2020 Dec 8;10(12). pii: biom10121647. doi: 10.3390/biom10121647. PMID:33302546<ref>PMID:33302546</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7b0f" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: Holliger | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Synthetic construct]] | |||
[[Category: Thermococcus gorgonarius]] | |||
[[Category: Abramov M]] | |||
[[Category: Delarue M]] | |||
[[Category: Herdewijn P]] | |||
[[Category: Holliger P]] | |||
[[Category: Legrand P]] | |||
[[Category: Pinheiro V]] | |||
[[Category: Rozenski J]] | |||
[[Category: Samson C]] | |||
[[Category: Tekpinar M]] | |||
Latest revision as of 15:20, 1 February 2024
TgoT_6G12 Binary complexTgoT_6G12 Binary complex
Structural highlights
FunctionDPOL_THEGO In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity. Publication Abstract from PubMedArchaeal DNA polymerases from the B-family (polB) have found essential applications in biotechnology. In addition, some of their variants can accept a wide range of modified nucleotides or xenobiotic nucleotides, such as 1,5-anhydrohexitol nucleic acid (HNA), which has the unique ability to selectively cross-pair with DNA and RNA. This capacity is essential to allow the transmission of information between different chemistries of nucleic acid molecules. Variants of the archaeal polymerase from Thermococcus gorgonarius, TgoT, that can either generate HNA from DNA (TgoT_6G12) or DNA from HNA (TgoT_RT521) have been previously identified. To understand how DNA and HNA are recognized and selected by these two laboratory-evolved polymerases, we report six X-ray structures of these variants, as well as an in silico model of a ternary complex with HNA. Structural comparisons of the apo form of TgoT_6G12 together with its binary and ternary complexes with a DNA duplex highlight an ensemble of interactions and conformational changes required to promote DNA or HNA synthesis. MD simulations of the ternary complex suggest that the HNA-DNA hybrid duplex remains stable in the A-DNA helical form and help explain the presence of mutations in regions that would normally not be in contact with the DNA if it were not in the A-helical form. One complex with two incorporated HNA nucleotides is surprisingly found in a one nucleotide-backtracked form, which is new for a DNA polymerase. This information can be used for engineering a new generation of more efficient HNA polymerase variants. Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution.,Samson C, Legrand P, Tekpinar M, Rozenski J, Abramov M, Holliger P, Pinheiro VB, Herdwijn P, Delarue M Biomolecules. 2020 Dec 8;10(12). pii: biom10121647. doi: 10.3390/biom10121647. PMID:33302546[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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