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| | <StructureSection load='2yg9' size='340' side='right'caption='[[2yg9]], [[Resolution|resolution]] 1.95Å' scene=''> | | <StructureSection load='2yg9' size='340' side='right'caption='[[2yg9]], [[Resolution|resolution]] 1.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2yg9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YG9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2yg9]] 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=2YG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YG9 FirstGlance]. <br> |
| - | </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=NI:NICKEL+(II)+ION'>NI</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]] 1.95Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2yg8|2yg8]]</div></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=NI:NICKEL+(II)+ION'>NI</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR_2584 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=2yg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yg9 OCA], [https://pdbe.org/2yg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yg9 RCSB], [https://www.ebi.ac.uk/pdbsum/2yg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yg9 ProSAT]</span></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=2yg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yg9 OCA], [https://pdbe.org/2yg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yg9 RCSB], [https://www.ebi.ac.uk/pdbsum/2yg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yg9 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q9RRB0_DEIRA Q9RRB0_DEIRA] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Micrococcus radiodurans raj et al. 1960]] | + | [[Category: Deinococcus radiodurans]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hall, D R]] | + | [[Category: Hall DR]] |
| - | [[Category: Leiros, I]] | + | [[Category: Leiros I]] |
| - | [[Category: McSweeney, S]] | + | [[Category: McSweeney S]] |
| - | [[Category: Moe, E]] | + | [[Category: Moe E]] |
| - | [[Category: Talstad, V]] | + | [[Category: Talstad V]] |
| - | [[Category: Timmins, J]] | + | [[Category: Timmins J]] |
| - | [[Category: Dna repair]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
Q9RRB0_DEIRA
Publication Abstract from PubMed
3-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-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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Moe E, Hall DR, Leiros I, Monsen VT, Timmins J, McSweeney S. Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans. Acta Crystallogr D Biol Crystallogr. 2012 Jun;68(Pt 6):703-12. Epub 2012 May 17. PMID:22683793 doi:10.1107/S090744491200947X
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