|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Structure of MBOgg1 in complex with high affinity DNA ligand== | | ==Structure of MBOgg1 in complex with high affinity DNA ligand== |
| - | <StructureSection load='4ejy' size='340' side='right' caption='[[4ejy]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='4ejy' size='340' side='right'caption='[[4ejy]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ejy]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis Caldanaerobacter subterraneus subsp. tengcongensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EJY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EJY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ejy]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis_MB4 Caldanaerobacter subterraneus subsp. tengcongensis MB4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EJY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EJY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ejz|4ejz]]</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=4ejy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ejy OCA], [https://pdbe.org/4ejy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ejy RCSB], [https://www.ebi.ac.uk/pdbsum/4ejy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ejy ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AlkA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273068 Caldanaerobacter subterraneus subsp. tengcongensis])</td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ejy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ejy OCA], [http://pdbe.org/4ejy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ejy RCSB], [http://www.ebi.ac.uk/pdbsum/4ejy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ejy ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q8R5T9_CALS4 Q8R5T9_CALS4] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 21: |
Line 21: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[DNA glycosylase|DNA glycosylase]] | + | *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Caldanaerobacter subterraneus subsp. tengcongensis]] | + | [[Category: Caldanaerobacter subterraneus subsp. tengcongensis MB4]] |
| - | [[Category: Bi, L J]] | + | [[Category: Large Structures]] |
| - | [[Category: Jiang, T]] | + | [[Category: Bi LJ]] |
| - | [[Category: Yang, M Z]] | + | [[Category: Jiang T]] |
| - | [[Category: Yu, H J]] | + | [[Category: Yang MZ]] |
| - | [[Category: Zhang, X E]] | + | [[Category: Yu HJ]] |
| - | [[Category: 8-oxoguanine dna glycosylase]] | + | [[Category: Zhang XE]] |
| - | [[Category: Hydrolase-dna complex]]
| + | |
| Structural highlights
Function
Q8R5T9_CALS4
Publication Abstract from PubMed
7,8-Dihydro-8-oxoguanine (8-oxoG) is one of the most common oxidative DNA lesions. 8-oxoguanine DNA glycosylases (Oggs) detect and excise 8-oxoG through a multiple-step process. To better understand the basis for estranged base recognition, we have solved the crystal structures of MBOgg1, the 8-oxoguanine DNA glycosylase of Thermoanaerobacter tengcongensis, in complex with DNA containing a tetrahydrofuranyl site (THF, a stable abasic site analog) paired with an estranged cytosine (MBOgg1/DNA(THF:C)) or thymine (MBOgg1/DNA(THF:T)). Different states of THF (extrahelical or intrahelical) are observed in the two complexes of the ASU of MBOgg1/DNA(THF:C) structure. Analyses of their different interaction modes reveal that variable contacts on the 5' region flanking the THF abasic site are correlated with the states of the THF. Comparison of MBOgg1/DNA(THF:T) with MBOgg1/DNA(THF:C) indicates that the non-preferred estranged T may affect MBOgg1's contacts with the 5' flank of the lesion strand. Furthermore, we identified a region in MBOgg1 that is rich in positive charges and interacts with the 5' region flanking the lesion. This region is conserved only in non-eukaryotic Oggs, and additional mutagenesis and biochemical assays reveal that it may contribute to the distinct estranged base specificities between eukaryotic and non-eukaryotic Oggs.
Crystal structures of MBOgg1 in complex with two abasic DNA ligands.,Yu H, Yang M, Zhang XE, Bi L, Jiang T J Struct Biol. 2013 Mar;181(3):252-63. doi: 10.1016/j.jsb.2012.12.003. Epub 2012 , Dec 12. PMID:23246782[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yu H, Yang M, Zhang XE, Bi L, Jiang T. Crystal structures of MBOgg1 in complex with two abasic DNA ligands. J Struct Biol. 2013 Mar;181(3):252-63. doi: 10.1016/j.jsb.2012.12.003. Epub 2012 , Dec 12. PMID:23246782 doi:http://dx.doi.org/10.1016/j.jsb.2012.12.003
|
