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.


6ajp

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:20, 20 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='6ajp' size='340' side='right'caption='[[6ajp]], [[Resolution|resolution]] 1.33&Aring;' scene=''>
<StructureSection load='6ajp' size='340' side='right'caption='[[6ajp]], [[Resolution|resolution]] 1.33&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[6ajp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AJP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AJP FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[6ajp]] 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=6AJP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AJP FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 1.334&#8491;</td></tr>
-
<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=6ajp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ajp OCA], [http://pdbe.org/6ajp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ajp RCSB], [http://www.ebi.ac.uk/pdbsum/6ajp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ajp ProSAT]</span></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=6ajp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ajp OCA], [https://pdbe.org/6ajp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ajp RCSB], [https://www.ebi.ac.uk/pdbsum/6ajp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ajp ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/A0QP43_MYCS2 A0QP43_MYCS2]
-
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.
+
-
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>
+
==See Also==
-
 
+
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 6ajp" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Ahn, W C]]
+
[[Category: Mycolicibacterium smegmatis MC2 155]]
-
[[Category: Aroli, S]]
+
[[Category: Ahn WC]]
-
[[Category: Varshney, U]]
+
[[Category: Aroli S]]
-
[[Category: Woo, E J]]
+
[[Category: Varshney U]]
-
[[Category: Base excision]]
+
[[Category: Woo EJ]]
-
[[Category: Dna binding protein]]
+
-
[[Category: Dna repair]]
+
-
[[Category: Dna-protein crosslink]]
+

Current revision

Complex form of Uracil DNA glycosylase X and deoxyuridine monophosphate.

PDB ID 6ajp

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6ajp"
Personal tools