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| | <StructureSection load='3sav' size='340' side='right'caption='[[3sav]], [[Resolution|resolution]] 2.12Å' scene=''> | | <StructureSection load='3sav' size='340' side='right'caption='[[3sav]], [[Resolution|resolution]] 2.12Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3sav]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SAV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3sav]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SAV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.125Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CX2:2-DEOXY-5-O-{(R)-HYDROXY[(2-SULFANYLETHYL)AMINO]PHOSPHORYL}CYTIDINE'>CX2</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CX2:2-DEOXY-5-O-{(R)-HYDROXY[(2-SULFANYLETHYL)AMINO]PHOSPHORYL}CYTIDINE'>CX2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3sar|3sar]], [[3sas|3sas]], [[3sat|3sat]], [[3sau|3sau]], [[3saw|3saw]], [[3sbj|3sbj]]</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=3sav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sav OCA], [https://pdbe.org/3sav PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sav RCSB], [https://www.ebi.ac.uk/pdbsum/3sav PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sav ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MUTM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </span></td></tr>
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| - | <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=3sav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sav OCA], [http://pdbe.org/3sav PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3sav RCSB], [http://www.ebi.ac.uk/pdbsum/3sav PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3sav ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] 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:SAAS020629_004_120556] | + | [https://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE] 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:SAAS020629_004_120556] |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search process. Considerable interest surrounds the question of how DNA glycosylases translocate efficiently along DNA while maintaining their vigilance for target damaged sites. Here, we report the observation of strandwise translocation of 8-oxoguanine DNA glycosylase, MutM, along undamaged DNA. In these complexes, the protein is observed to translocate by one nucleotide on one strand while remaining untranslocated on the complementary strand. We further report that alterations of single base-pairs or a single amino acid substitution (R112A) can induce strandwise translocation. Molecular dynamics simulations confirm that MutM can translocate along DNA in a strandwise fashion. These observations reveal a previously unobserved mode of movement for a DNA-binding protein along the surface of DNA.
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| - | | + | |
| - | Strandwise translocation of a DNA glycosylase on undamaged DNA.,Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1086-91. Epub 2012 Jan 4. PMID:22219368<ref>PMID:22219368</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 3sav" style="background-color:#fffaf0;"></div>
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| | | | |
| | ==See Also== | | ==See Also== |
| | *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]] | | *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]] |
| - | == References == | |
| - | <references/> | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 12980]] | + | [[Category: Geobacillus stearothermophilus]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Qi, Y]] | + | [[Category: Qi Y]] |
| - | [[Category: Spong, M C]] | + | [[Category: Spong MC]] |
| - | [[Category: Verdine, G L]] | + | [[Category: Verdine GL]] |
| - | [[Category: Damage search]]
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| - | [[Category: Disulfide crosslinking]]
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| - | [[Category: Dna damage]]
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| - | [[Category: Dna glycosylase]]
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| - | [[Category: Dna repair]]
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| - | [[Category: Dna-binding]]
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| - | [[Category: Glycosidase]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Hydrolase-dna complex]]
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| - | [[Category: Lyase]]
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| - | [[Category: Metal-binding]]
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| - | [[Category: Multifunctional enzyme]]
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| - | [[Category: Translocation]]
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| - | [[Category: Zinc-finger]]
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