2yg8: Difference between revisions

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-[[Image:2yg8.png|left|200px]]
-{{STRUCTURE_2yg8|  PDB=2yg8  |  SCENE=  }}
+==Structure of an unusual 3-Methyladenine DNA Glycosylase II (Alka) from Deinococcus radiodurans==
+<StructureSection load='2yg8' size='340' side='right'caption='[[2yg8]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2yg8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YG8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YG8 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=2yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yg8 OCA], [https://pdbe.org/2yg8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yg8 RCSB], [https://www.ebi.ac.uk/pdbsum/2yg8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yg8 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+-Methyladenine DNA glycosylase II (AlkA) is a DNA-repair enzyme that removes alkylated bases in DNA via the base-excision repair (BER) pathway. The enzyme belongs to the helix-hairpin-helix (HhH) superfamily of DNA glycosylases and possesses broad substrate specificity. In the genome of Deinococcus radiodurans, two genes encoding putative AlkA have been identified (Dr_2074 and Dr_2584). Dr_2074 is a homologue of human AlkA (MPG or AAG) and Dr_2584 is a homologue of bacterial AlkAs. Here, the three-dimensional structure of Dr_2584 (DrAlkA2) is presented and compared with the previously determined structure of Escherichia coli AlkA (EcAlkA). The results show that the enzyme consists of two helical-bundle domains separated by a wide DNA-binding cleft and contains an HhH motif. Overall, the protein fold is similar to the two helical-bundle domains of EcAlkA, while the third N-terminal mixed alpha/beta domain observed in EcAlkA is absent. Substrate-specificity analyses show that DrAlkA2, like EcAlkA, is able to remove both 3-methyladenine (3meA) and 7-methylguanine (7meG) from DNA; however, the enzyme possesses no activity towards 1,N(6)-ethenoadenine (A) and hypoxanthine (Hx). In addition, it shows activity towards the AlkB dioxygenase substrates 3-methylcytosine (3meC) and 1-methyladenine (1meA). Thus, the enzyme seems to preferentially repair methylated bases with weakened N-glycosidic bonds; this is an unusual specificity for a bacterial AlkA protein and is probably dictated by a combination of the wide DNA-binding cleft and a highly accessible specificity pocket.
-===Structure of an unusual 3-METHYLADENINE DNA GLYCOSYLASE II (ALKA) FROM DEINOCOCCUS RADIODURANS===
+Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans.,Moe E, Hall DR, Leiros I, Monsen VT, Timmins J, McSweeney S Acta Crystallogr D Biol Crystallogr. 2012 Jun;68(Pt 6):703-12. Epub 2012 May 17. PMID:22683793<ref>PMID:22683793</ref>
-{{ABSTRACT_PUBMED_22683793}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2yg8" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[2yg8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YG8 OCA].
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:022683793</ref><references group="xtra"/>
+__TOC__
-[[Category: Hall, D R.]]
+</StructureSection>
-[[Category: Leiros, I.]]
+[[Category: Deinococcus radiodurans]]
-[[Category: Mcsweeney, S.]]
+[[Category: Large Structures]]
-[[Category: Moe, E.]]
+[[Category: Hall DR]]
-[[Category: Talstad, V.]]
+[[Category: Leiros I]]
-[[Category: Timmins, J.]]
+[[Category: McSweeney S]]
-[[Category: Dna repair]]
+[[Category: Moe E]]
-[[Category: Hydrolase]]
+[[Category: Talstad V]]
+[[Category: Timmins J]]