This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
4ejz
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 4ejz is ON HOLD Authors: Jiang, T., Yu, H.J., Bi, L.J., Zhang, X.E., Yang, M.Z. Description: structure of MBOgg1 in complex with low affinity DNA l...) |
|||
| (7 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==Structure of MBOgg1 in complex with low affinity DNA ligand== | |
| + | <StructureSection load='4ejz' size='340' side='right'caption='[[4ejz]], [[Resolution|resolution]] 3.05Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[4ejz]] 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=4EJZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EJZ 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]] 3.05Å</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></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=4ejz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ejz OCA], [https://pdbe.org/4ejz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ejz RCSB], [https://www.ebi.ac.uk/pdbsum/4ejz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ejz ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q8R5T9_CALS4 Q8R5T9_CALS4] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == 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<ref>PMID:23246782</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 4ejz" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Caldanaerobacter subterraneus subsp. tengcongensis MB4]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Bi LJ]] | ||
| + | [[Category: Jiang T]] | ||
| + | [[Category: Yang MZ]] | ||
| + | [[Category: Yu HJ]] | ||
| + | [[Category: Zhang XE]] | ||
Current revision
Structure of MBOgg1 in complex with low affinity DNA ligand
| |||||||||||
