4hug: Difference between revisions

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-{{STRUCTURE_4hug|  PDB=4hug  |  SCENE=  }}
-===Structure of 5-chlorouracil modified A:U base pairs===
-{{ABSTRACT_PUBMED_23275540}}
-==Function==
+==Structure of 5-chlorouracil modified A:U base pairs==
-[[http://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
+<StructureSection load='4hug' size='340' side='right'caption='[[4hug]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4hug]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans_C-125 Alkalihalobacillus halodurans C-125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HUG 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]] 1.64&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UCL:5-CHLORO-2-DEOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UCL</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=4hug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hug OCA], [https://pdbe.org/4hug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hug RCSB], [https://www.ebi.ac.uk/pdbsum/4hug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hug ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli strain relies on the four building blocks 5-chloro-2'-deoxyuridine (ClU), A, C and G instead of the standard T, A, C, G alphabet [Marliere,P., Patrouix,J., Doring,V., Herdewijn,P., Tricot,S., Cruveiller,S., Bouzon,M. and Mutzel,R. (2011) Chemical evolution of a bacterium's genome. Angew. Chem. Int. Ed., 50, 7109-7114]. The residual fraction of T in the DNA of adapted bacteria was &lt;2% and the switch from T to ClU was accompanied by a massive number of mutations, including &gt;1500 A to G or G to A transitions in a culture. The former is most likely due to wobble base pairing between ClU and G, which may be more common for ClU than T. To identify potential changes in the geometries of base pairs and duplexes as a result of replacement of T by ClU, we determined four crystal structures of a B-form DNA dodecamer duplex containing ClU:A or ClU:G base pairs. The structures reveal nearly identical geometries of these pairs compared with T:A or T:G, respectively, and no consequences for stability and cleavage by an endonuclease (EcoRI). The lack of significant changes in the geometry of ClU:A and ClU:G base pairs relative to the corresponding native pairs is consistent with the sustained unlimited self-reproduction of E. coli strains with virtually complete T--&gt;ClU genome substitution.
-==About this Structure==
+Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs.,Patra A, Harp J, Pallan PS, Zhao L, Abramov M, Herdewijn P, Egli M Nucleic Acids Res. 2012 Dec 28. PMID:23275540<ref>PMID:23275540</ref>
-[[4hug]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans_c-125 Bacillus halodurans c-125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HUG OCA].
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4hug" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Ribonuclease|Ribonuclease]]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-[[Category: Bacillus halodurans c-125]]
+== References ==
-[[Category: Ribonuclease H]]
+<references/>
-[[Category: Egli, M.]]
+__TOC__
-[[Category: Patra, A.]]
+</StructureSection>
-[[Category: 5-chloro-2'-deoxyuridine]]
+[[Category: Alkalihalobacillus halodurans C-125]]
-[[Category: Double helix]]
+[[Category: Large Structures]]
-[[Category: Hydrolase-dna complex]]
+[[Category: Egli M]]
-[[Category: W-c base pair]]
+[[Category: Patra A]]
-[[Category: Watson-crick base pairing pattern]]
-[[Category: Wobble base pair]]