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| | ==Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with d5SICS as templating nucleotide== | | ==Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with d5SICS as templating nucleotide== |
| - | <StructureSection load='4cch' size='340' side='right' caption='[[4cch]], [[Resolution|resolution]] 2.55Å' scene=''> | + | <StructureSection load='4cch' size='340' side='right'caption='[[4cch]], [[Resolution|resolution]] 2.55Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4cch]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CCH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4cch]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] 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=4CCH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CCH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.55Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=LHO:2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)-THIONE'>LHO</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LHO:2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)-THIONE'>LHO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://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=4cch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cch OCA], [https://pdbe.org/4cch PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cch RCSB], [https://www.ebi.ac.uk/pdbsum/4cch PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cch ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4cch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cch OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cch RCSB], [http://www.ebi.ac.uk/pdbsum/4cch PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4cch" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==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: Atcc 25104]] | + | [[Category: Large Structures]] |
| - | [[Category: DNA-directed DNA polymerase]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Betz, K]] | + | [[Category: Thermus aquaticus]] |
| - | [[Category: Diederichs, K]] | + | [[Category: Betz K]] |
| - | [[Category: Lavergne, T]] | + | [[Category: Diederichs K]] |
| - | [[Category: Malyshev, D A]] | + | [[Category: Lavergne T]] |
| - | [[Category: Marx, A]] | + | [[Category: Malyshev DA]] |
| - | [[Category: Romesberg, F E]] | + | [[Category: Marx A]] |
| - | [[Category: Welte, W]] | + | [[Category: Romesberg FE]] |
| - | [[Category: Artificial nucleotide]]
| + | [[Category: Welte W]] |
| - | [[Category: Binary complex]]
| + | |
| - | [[Category: Klentaq]]
| + | |
| - | [[Category: Transferase-dna complex]]
| + | |
| - | [[Category: Unnatural nucleotide]]
| + | |
| Structural highlights
4cch is a 3 chain structure with sequence from Thermus aquaticus and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.55Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
DPO1_THEAQ
Publication Abstract from PubMed
The genetic alphabet is composed of two base pairs, and the development of a third, unnatural base pair would increase the genetic and chemical potential of DNA. d5SICS-dNaM is one of the most efficiently replicated unnatural base pairs identified to date, but its pairing is mediated by only hydrophobic and packing forces, and in free duplex DNA it forms a cross-strand intercalated structure that makes its efficient replication difficult to understand. Recent studies of the KlenTaq DNA polymerase revealed that the insertion of d5SICSTP opposite dNaM proceeds via a mutually induced-fit mechanism, where the presence of the triphosphate induces the polymerase to form the catalytically competent closed structure, which in turn induces the pairing nucleotides of the developing unnatural base pair to adopt a planar Watson-Crick-like structure. To understand the remaining steps of replication, we now report the characterization of the prechemistry complexes corresponding to the insertion of dNaMTP opposite d5SICS, as well as multiple postchemistry complexes in which the already formed unnatural base pair is positioned at the postinsertion site. Unlike with the insertion of d5SICSTP opposite dNaM, addition of dNaMTP does not fully induce the formation of the catalytically competent closed state. The data also reveal that once synthesized and translocated to the postinsertion position, the unnatural nucleobases again intercalate. Two modes of intercalation are observed, depending on the nature of the flanking nucleotides, and are each stabilized by different interactions with the polymerase, and each appear to reduce the affinity with which the next correct triphosphate binds. Thus, continued primer extension is limited by deintercalation and rearrangements with the polymerase active site that are required to populate the catalytically active, triphosphate bound conformation.
Structural Insights into DNA Replication without Hydrogen Bonds.,Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A J Am Chem Soc. 2013 Nov 27. PMID:24283923[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A. Structural Insights into DNA Replication without Hydrogen Bonds. J Am Chem Soc. 2013 Nov 27. PMID:24283923 doi:http://dx.doi.org/10.1021/ja409609j
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