3s5a: Difference between revisions

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 <StructureSection load='3s5a' size='340' side='right'caption='[[3s5a]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3s5a]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S5A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S5A FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3s5a]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S5A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S5A FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XL3:PROPANE-1-THIOL'>XL3</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]] 1.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3bty|3bty]], [[3s57|3s57]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XL3:PROPANE-1-THIOL'>XL3</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ABH2, ALKBH2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3s5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s5a OCA], [https://pdbe.org/3s5a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s5a RCSB], [https://www.ebi.ac.uk/pdbsum/3s5a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s5a ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/ALKB2_HUMAN ALKB2_HUMAN]] Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. Can also repair alkylated DNA containing 1-ethenoadenine (in vitro). Has strong preference for double-stranded DNA. Has low efficiency with single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron.<ref>PMID:12486230</ref> <ref>PMID:12594517</ref> <ref>PMID:16174769</ref> <ref>PMID:18519673</ref> <ref>PMID:18432238</ref>
+[https://www.uniprot.org/uniprot/ALKB2_HUMAN ALKB2_HUMAN] Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. Can also repair alkylated DNA containing 1-ethenoadenine (in vitro). Has strong preference for double-stranded DNA. Has low efficiency with single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron.<ref>PMID:12486230</ref> <ref>PMID:12594517</ref> <ref>PMID:16174769</ref> <ref>PMID:18519673</ref> <ref>PMID:18432238</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-ALKBH2 is a direct DNA repair dioxygenase guarding the mammalian genome against N(1)-methyladenine, N(3)-methylcytosine and 1,N(6)-ethenoadenine damage. A prerequisite for repair is to identify these lesions in the genome. Here we present crystal structures of human ALKBH2 bound to different duplex DNAs. Together with computational and biochemical analyses, our results suggest that DNA interrogation by ALKBH2 has two previously unknown features: (i) ALKBH2 probes base-pair stability and detects base pairs with reduced stability, and (ii) ALKBH2 does not have nor need a damage-checking site, which is critical for preventing spurious base cleavage for several glycosylases. The demethylation mechanism of ALKBH2 insures that only cognate lesions are oxidized and reversed to normal bases, and that a flipped, non-substrate base remains intact in the active site. Overall, the combination of duplex interrogation and oxidation chemistry allows ALKBH2 to detect and process diverse lesions efficiently and correctly.
-Duplex interrogation by a direct DNA repair protein in search of base damage.,Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C Nat Struct Mol Biol. 2012 Jun 3;19(7):671-6. doi: 10.1038/nsmb.2320. PMID:22659876<ref>PMID:22659876</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3s5a" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 27: / Line 17: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Chen, B]]
+[[Category: Chen B]]
-[[Category: Dinner, A R]]
+[[Category: Dinner AR]]
-[[Category: He, C]]
+[[Category: He C]]
-[[Category: Jia, G]]
+[[Category: Jia G]]
-[[Category: Li, C Q]]
+[[Category: Li CQ]]
-[[Category: Qi, B]]
+[[Category: Qi B]]
-[[Category: Ramirez, B]]
+[[Category: Ramirez B]]
-[[Category: Yang, C G]]
+[[Category: Yang C-G]]
-[[Category: Yi, C]]
+[[Category: Yi C]]
-[[Category: Zhang, L]]
+[[Category: Zhang L]]
-[[Category: Zhang, W]]
+[[Category: Zhang W]]
-[[Category: Cross-linking]]
-[[Category: Dioxygenase]]
-[[Category: Dna binding]]
-[[Category: Double helix]]
-[[Category: Jelly-roll fold]]
-[[Category: Oxidoreductase-dna complex]]
-[[Category: Protein-dna complex]]