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< | ==Crystal structure of an artificial salen-copper basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus== | ||
<StructureSection load='2xy5' size='340' side='right'caption='[[2xy5]], [[Resolution|resolution]] 2.22Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2xy5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] 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=2XY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XY5 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]] 2.22Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=EDN:ETHANE-1,2-DIAMINE'>EDN</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PRD_900032:surcrose+isoform'>PRD_900032</scene>, <scene name='pdbligand=SAY:[(2R,3S,5R)-3-HYDROXY-5-(3-HYDROXY-4-METHANOYL-PHENYL)OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>SAY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Z9N:alpha-D-fructofuranose'>Z9N</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=2xy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xy5 OCA], [https://pdbe.org/2xy5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xy5 RCSB], [https://www.ebi.ac.uk/pdbsum/2xy5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xy5 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/E1C9K5_GEOSE E1C9K5_GEOSE] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The universal genetic code relies on two hydrogen-bonded Watson-Crick base pairs that can form 64 triplet codons. This places a limit on the number of amino acids that can be encoded, which has motivated efforts to create synthetic base pairs that are orthogonal to the natural ones. An additional base pair would result in another 61 triplet codons. Artificial organic base pairs have been described in enzymatic incorporation studies, and inorganic T-Hg-T and C-Ag-C base pairs have been reported to form in primer extension studies. Here, we demonstrate a metal base pair that is fully orthogonal and can be replicated, and can even be amplified by polymerase chain reaction in the presence of the canonical pairs dA:dT and dG:dC. Crystal structures of a dS-Cu-dS base pair inside a polymerase show that reversible chemistry is possible directly inside the polymerase, which enables the efficient copying of the inorganic crosslink. The results open up the possibility of replicating and amplifying artificial inorganic DNA nanostructures by extending the genetic alphabet. | |||
Reversible bond formation enables the replication and amplification of a crosslinking salen complex as an orthogonal base pair.,Kaul C, Muller M, Wagner M, Schneider S, Carell T Nat Chem. 2011 Aug 28;3(10):794-800. doi: 10.1038/nchem.1117. PMID:21941252<ref>PMID:21941252</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2xy5" style="background-color:#fffaf0;"></div> | |||
== | |||
==See Also== | ==See Also== | ||
*[[DNA polymerase|DNA polymerase]] | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Geobacillus stearothermophilus]] | [[Category: Geobacillus stearothermophilus]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Synthetic construct]] | ||
[[Category: | [[Category: Carell T]] | ||
[[Category: | [[Category: Kaul C]] | ||
[[Category: | [[Category: Mueller M]] | ||
[[Category: | [[Category: Schneider S]] | ||
[[Category: | [[Category: Wagner M]] | ||
Latest revision as of 13:41, 20 December 2023
Crystal structure of an artificial salen-copper basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilusCrystal structure of an artificial salen-copper basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus
Structural highlights
FunctionPublication Abstract from PubMedThe universal genetic code relies on two hydrogen-bonded Watson-Crick base pairs that can form 64 triplet codons. This places a limit on the number of amino acids that can be encoded, which has motivated efforts to create synthetic base pairs that are orthogonal to the natural ones. An additional base pair would result in another 61 triplet codons. Artificial organic base pairs have been described in enzymatic incorporation studies, and inorganic T-Hg-T and C-Ag-C base pairs have been reported to form in primer extension studies. Here, we demonstrate a metal base pair that is fully orthogonal and can be replicated, and can even be amplified by polymerase chain reaction in the presence of the canonical pairs dA:dT and dG:dC. Crystal structures of a dS-Cu-dS base pair inside a polymerase show that reversible chemistry is possible directly inside the polymerase, which enables the efficient copying of the inorganic crosslink. The results open up the possibility of replicating and amplifying artificial inorganic DNA nanostructures by extending the genetic alphabet. Reversible bond formation enables the replication and amplification of a crosslinking salen complex as an orthogonal base pair.,Kaul C, Muller M, Wagner M, Schneider S, Carell T Nat Chem. 2011 Aug 28;3(10):794-800. doi: 10.1038/nchem.1117. PMID:21941252[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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