6ajo

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Current revision (10:32, 27 March 2024) (edit) (undo)
 
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<StructureSection load='6ajo' size='340' side='right'caption='[[6ajo]], [[Resolution|resolution]] 2.27&Aring;' scene=''>
<StructureSection load='6ajo' size='340' side='right'caption='[[6ajo]], [[Resolution|resolution]] 2.27&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6ajo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AJO FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6ajo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis] and [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=6AJO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AJO 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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</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]] 2.269&#8491;</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=6ajo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ajo OCA], [http://pdbe.org/6ajo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ajo RCSB], [http://www.ebi.ac.uk/pdbsum/6ajo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ajo ProSAT]</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=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <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'>[https://proteopedia.org/fgij/fg.htm?mol=6ajo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ajo OCA], [https://pdbe.org/6ajo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ajo RCSB], [https://www.ebi.ac.uk/pdbsum/6ajo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ajo 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/A0QP43_MYCS2 A0QP43_MYCS2]
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Uracil DNA glycosylases (UDGs) are important DNA repair enzymes that excise uracil from DNA, yielding an abasic site. Recently, UdgX, an unconventional UDG with extremely tight binding to DNA containing uracil, was discovered. The structure of UdgX from Mycobacterium smegmatis in complex with DNA shows an overall similarity to that of family 4 UDGs except for a protruding loop at the entrance of the uracil-binding pocket. Surprisingly, H109 in the loop was found to make a covalent bond to the abasic site to form a stable intermediate, while the excised uracil remained in the pocket of the active site. H109 functions as a nucleophile to attack the oxocarbenium ion, substituting for the catalytic water molecule found in other UDGs. To our knowledge, this change from a catalytic water attack to a direct nucleophilic attack by the histidine residue is unprecedented. UdgX utilizes a unique mechanism of protecting cytotoxic abasic sites from exposure to the cellular environment.
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Covalent binding of uracil DNA glycosylase UdgX to abasic DNA upon uracil excision.,Ahn WC, Aroli S, Kim JH, Moon JH, Lee GS, Lee MH, Sang PB, Oh BH, Varshney U, Woo EJ Nat Chem Biol. 2019 Jun;15(6):607-614. doi: 10.1038/s41589-019-0289-3. Epub 2019 , May 17. PMID:31101917<ref>PMID:31101917</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 6ajo" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Ahn, W C]]
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[[Category: Mycolicibacterium smegmatis]]
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[[Category: Aroli, S]]
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[[Category: Mycolicibacterium smegmatis MC2 155]]
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[[Category: Varshney, U]]
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[[Category: Ahn WC]]
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[[Category: Woo, E J]]
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[[Category: Aroli S]]
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[[Category: Base excision]]
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[[Category: Varshney U]]
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[[Category: Dna binding protein]]
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[[Category: Woo EJ]]
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[[Category: Dna repair]]
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[[Category: Dna-protein crosslink]]
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Current revision

Complex form of Uracil DNA glycosylase X and uracil-DNA.

PDB ID 6ajo

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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