1q3f

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[[Image:1q3f.gif|left|200px]]
 
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{{Structure
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==Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA==
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|PDB= 1q3f |SIZE=350|CAPTION= <scene name='initialview01'>1q3f</scene>, resolution 1.9&Aring;
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<StructureSection load='1q3f' size='340' side='right'caption='[[1q3f]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene> and <scene name='pdbligand=URA:URACIL'>URA</scene>
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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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|ACTIVITY=
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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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|GENE= UNG OR DGU OR UNG15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
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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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}}
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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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'''Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-contianing DNA'''
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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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==Overview==
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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 ==
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.
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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==Disease==
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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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Known diseases associated with this structure: Immunodeficiency with hyper IgM, type 4 OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191525 191525]]
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1Q3F is a [[Single protein]] structure of sequence 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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</div>
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<div class="pdbe-citations 1q3f" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/14580190 14580190]
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Amzel, L M.]]
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[[Category: Amzel LM]]
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[[Category: Bianchet, M A.]]
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[[Category: Bianchet MA]]
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[[Category: Ichikawa, Y.]]
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[[Category: Ichikawa Y]]
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[[Category: Jiang, Y L.]]
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[[Category: Jiang YL]]
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[[Category: Seiple, L A.]]
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[[Category: Seiple LA]]
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[[Category: Stivers, J T.]]
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[[Category: Stivers JT]]
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[[Category: PO4]]
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[[Category: URA]]
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[[Category: dna repair]]
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[[Category: udg]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:32:27 2008''
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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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