4cis
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==Structure of MutM in complex with carbocyclic 8-oxo-G containing DNA== | ==Structure of MutM in complex with carbocyclic 8-oxo-G containing DNA== | ||
| - | <StructureSection load='4cis' size='340' side='right' caption='[[4cis]], [[Resolution|resolution]] 2.05Å' scene=''> | + | <StructureSection load='4cis' size='340' side='right'caption='[[4cis]], [[Resolution|resolution]] 2.05Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[4cis]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CIS OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[4cis]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_cremoris Lactococcus cremoris] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CIS FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[ | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[ | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=68Z:1R,2S,4R)-4-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-2-OXIDANYL-CYCLOPENTYL]METHYL+DIHYDROGEN+PHOSPHATE'>68Z</scene>, <scene name='pdbligand=BU3:(R,R)-2,3-BUTANEDIOL'>BU3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4cis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cis OCA], [https://pdbe.org/4cis PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cis RCSB], [https://www.ebi.ac.uk/pdbsum/4cis PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cis ProSAT]</span></td></tr> | |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | </table> |
| - | <table> | + | == Function == |
| + | [https://www.uniprot.org/uniprot/Q031W6_LACLS Q031W6_LACLS] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS000191_004_120556] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Living organisms protect the genome against external influences by recognizing and repairing damaged DNA. A common source of gene mutation is the oxidized guanine, which undergoes base excision repair through cleavage of the glycosidic bond between the ribose and the nucleobase of the lesion. We unravel the repair mechanism utilized by bacterial glycosylase, MutM, using quantum-chemical calculations involving more than 1000 atoms of the catalytic site. In contrast to the base-protonated pathway currently favored in the literature, we show that the initial protonation of the lesion's ribose paves the way for an almost barrier-free glycosidic cleavage. The combination of theoretical and experimental data provides further insight into the selectivity and discrimination of MutM's binding site toward various substrates. | ||
| + | |||
| + | Ribose-Protonated DNA Base Excision Repair: A Combined Theoretical and Experimental Study.,Sadeghian K, Flaig D, Blank ID, Schneider S, Strasser R, Stathis D, Winnacker M, Carell T, Ochsenfeld C Angew Chem Int Ed Engl. 2014 Jul 25. doi: 10.1002/anie.201403334. PMID:25065673<ref>PMID:25065673</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 4cis" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Lactococcus cremoris]] |
| - | [[Category: Blank | + | [[Category: Large Structures]] |
| - | [[Category: Carell | + | [[Category: Synthetic construct]] |
| - | [[Category: Flaig | + | [[Category: Blank ID]] |
| - | [[Category: Ochsenfeld | + | [[Category: Carell T]] |
| - | [[Category: Sadeghian | + | [[Category: Flaig D]] |
| - | [[Category: Schneider | + | [[Category: Ochsenfeld C]] |
| - | [[Category: Stathis | + | [[Category: Sadeghian K]] |
| - | [[Category: Strasser | + | [[Category: Schneider S]] |
| - | [[Category: Winnacker | + | [[Category: Stathis D]] |
| - | + | [[Category: Strasser R]] | |
| - | + | [[Category: Winnacker M]] | |
| - | + | ||
Current revision
Structure of MutM in complex with carbocyclic 8-oxo-G containing DNA
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