1q3f

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{{Seed}}
 
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[[Image:1q3f.png|left|200px]]
 
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==Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA==
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The line below this paragraph, containing "STRUCTURE_1q3f", creates the "Structure Box" on the page.
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<StructureSection load='1q3f' size='340' side='right'caption='[[1q3f]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1q3f]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q3F FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.9&#8491;</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=NRI:PHOSPHORIC+ACID+MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL)+ESTER'>NRI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
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{{STRUCTURE_1q3f| PDB=1q3f | SCENE= }}
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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=1q3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3f OCA], [https://pdbe.org/1q3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q3f RCSB], [https://www.ebi.ac.uk/pdbsum/1q3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q3f ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref>
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== Function ==
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[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q3/1q3f_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1q3f ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The DNA repair enzyme uracil DNA glycosylase has been crystallized with a cationic 1-aza-2'-deoxyribose-containing DNA that mimics the ultimate transition state of the reaction in which the water nucleophile attacks the anomeric center of the oxacarbenium ion-uracil anion reaction intermediate. Comparison with substrate and product structures, and the previous structure of the intermediate determined by kinetic isotope effects, reveals an exquisite example of geometric strain, least atomic motion, and electrophile migration in biological catalysis. This structure provides a rare opportunity to reconstruct the detailed structural transformations that occur along an enzymatic reaction coordinate.
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===Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-contianing DNA===
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Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase.,Bianchet MA, Seiple LA, Jiang YL, Ichikawa Y, Amzel LM, Stivers JT Biochemistry. 2003 Nov 4;42(43):12455-60. PMID:14580190<ref>PMID:14580190</ref>
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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 1q3f" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_14580190}}, adds the Publication Abstract to the page
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 14580190 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_14580190}}
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__TOC__
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</StructureSection>
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==About this Structure==
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1Q3F is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3F OCA].
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==Reference==
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<ref group="xtra">PMID:14580190</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Amzel, L M.]]
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[[Category: Large Structures]]
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[[Category: Bianchet, M A.]]
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[[Category: Amzel LM]]
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[[Category: Ichikawa, Y.]]
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[[Category: Bianchet MA]]
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[[Category: Jiang, Y L.]]
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[[Category: Ichikawa Y]]
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[[Category: Seiple, L A.]]
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[[Category: Jiang YL]]
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[[Category: Stivers, J T.]]
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[[Category: Seiple LA]]
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[[Category: Dna repair]]
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[[Category: Stivers JT]]
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[[Category: Udg]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:42:58 2009''
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Current revision

Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA

PDB ID 1q3f

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