6iob

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Current revision (10:34, 27 March 2024) (edit) (undo)
 
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<StructureSection load='6iob' size='340' side='right'caption='[[6iob]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='6iob' size='340' side='right'caption='[[6iob]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6iob]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IOB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IOB FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6iob]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IOB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IOB FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.002&#8491;</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-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></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=6iob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iob OCA], [http://pdbe.org/6iob PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iob RCSB], [http://www.ebi.ac.uk/pdbsum/6iob PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iob ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6iob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iob OCA], [https://pdbe.org/6iob PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iob RCSB], [https://www.ebi.ac.uk/pdbsum/6iob PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iob ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/I7F541_MYCS2 I7F541_MYCS2]
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A uracil DNA glycosylase (UDG) from Mycobacterium smegmatis (MsmUdgX) shares sequence similarity with family 4 UDGs and forms exceedingly stable complexes with single-stranded uracil-containing DNAs (ssDNA-Us) that are resistant to denaturants. However, MsmUdgX has been reported to be inactive in excising uracil from ssDNA-Us and the underlying structural basis is unclear. Here, we report high-resolution crystal structures of MsmUdgX in the free, uracil- and DNA-bound forms, respectively. The structural information, supported by mutational and biochemical analyses, indicates that the conserved residue His109 located on a characteristic loop forms an irreversible covalent linkage with the deoxyribose at the apyrimidinic site of ssDNA-U, thus rendering the enzyme unable to regenerate. By proposing the catalytic pathway and molecular mechanism for MsmUdgX, our studies provide an insight into family 4 UDGs and UDGs in general.
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Suicide inactivation of the uracil DNA glycosylase UdgX by covalent complex formation.,Tu J, Chen R, Yang Y, Cao W, Xie W Nat Chem Biol. 2019 Jun;15(6):615-622. doi: 10.1038/s41589-019-0290-x. Epub 2019 , May 17. PMID:31101915<ref>PMID:31101915</ref>
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==See Also==
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6iob" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: DNA-directed DNA polymerase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Tu, J]]
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[[Category: Mycolicibacterium smegmatis MC2 155]]
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[[Category: Xie, W]]
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[[Category: Tu J]]
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[[Category: Dna binding protein]]
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[[Category: Xie W]]
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[[Category: Dna repair]]
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[[Category: Iron-sulfur]]
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[[Category: Uracil dna glycosylase]]
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Current revision

The structure of the H109A mutant of UdgX in complex with uracil

PDB ID 6iob

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