2xy7: Difference between revisions

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-[[Image:2xy7.png|left|200px]]
-<!--
+==Crystal structure of a salicylic aldehyde base in the pre-insertion site of fragment DNA polymerase I from Bacillus stearothermophilus==
-The line below this paragraph, containing "STRUCTURE_2xy7", creates the "Structure Box" on the page.
+<StructureSection load='2xy7' size='340' side='right'caption='[[2xy7]], [[Resolution|resolution]] 3.05&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2xy7]] 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=2XY7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XY7 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.05&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</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></td></tr>
-{{STRUCTURE_2xy7|  PDB=2xy7  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xy7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xy7 OCA], [https://pdbe.org/2xy7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xy7 RCSB], [https://www.ebi.ac.uk/pdbsum/2xy7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xy7 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.
-===CRYSTAL STRUCTURE OF A SALICYLIC ALDEHYDE BASE IN THE PRE-INSERTION SITE OF FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS===
+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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2xy7" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[2xy7]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XY7 OCA].
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-[[Category: DNA-directed DNA polymerase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Carell, T.]]
+[[Category: Large Structures]]
-[[Category: Kaul, C.]]
+[[Category: Synthetic construct]]
-[[Category: Mueller, M.]]
+[[Category: Carell T]]
-[[Category: Schneider, S.]]
+[[Category: Kaul C]]
-[[Category: Wagner, M.]]
+[[Category: Mueller M]]
-[[Category: Metal basepair]]
+[[Category: Schneider S]]
-[[Category: Replication]]
+[[Category: Wagner M]]
-[[Category: Salen complex]]
-[[Category: Synthetic biology]]
-[[Category: Transferase-dna complex]]