1akz: Difference between revisions

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-[[Image:1akz.gif|left|200px]]
- {{Structure
+==HUMAN URACIL-DNA GLYCOSYLASE==
-|PDB= 1akz |SIZE=350|CAPTION= <scene name='initialview01'>1akz</scene>, resolution 1.57&Aring;
+<StructureSection load='1akz' size='340' side='right'caption='[[1akz]], [[Resolution|resolution]] 1.57&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<table><tr><td colspan='2'>[[1akz]] is a 1 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=1AKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AKZ FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.57&#8491;</td></tr>
-|GENE=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1akz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akz OCA], [https://pdbe.org/1akz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1akz RCSB], [https://www.ebi.ac.uk/pdbsum/1akz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1akz ProSAT]</span></td></tr>
-|DOMAIN=
+</table>
-|RELATEDENTRY=
+== Disease ==
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1akz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akz OCA], [http://www.ebi.ac.uk/pdbsum/1akz PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1akz RCSB]</span>
+[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>
-}}
+== Function ==
+[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.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ak/1akz_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1akz ConSurf].
+<div style="clear:both"></div>
-'''HUMAN URACIL-DNA GLYCOSYLASE'''
+==See Also==
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
+== References ==
-==Overview==
+<references/>
-Crystal structures of the DNA repair enzyme human uracil-DNA glycosylase (UDG), combined with mutational analysis, reveal the structural basis for the specificity of the enzyme. Within the classic alpha/beta fold of UDG, sequence-conserved residues form a positively charged, active-site groove the width of duplex DNA, at the C-terminal edge of the central four-stranded parallel beta sheet. In the UDG-6-aminouracil complex, uracil binds at the base of the groove within a rigid preformed pocket that confers selectivity for uracil over other bases by shape complementary and by main chain and Asn-204 side chain hydrogen bonds. Main chain nitrogen atoms are positioned to stabilize the oxyanion intermediate generated by His-268 acting via nucleophilic attack or general base mechanisms. Specific binding of uracil flipped out from a DNA duplex provides a structural mechanism for damaged base recognition.
+__TOC__
+</StructureSection>
-==About this Structure==
-AKZ 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=1AKZ OCA].
-==Reference==
-Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis., Mol CD, Arvai AS, Slupphaug G, Kavli B, Alseth I, Krokan HE, Tainer JA, Cell. 1995 Mar 24;80(6):869-78. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7697717 7697717]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Tainer, C D.M J.A.]]
+[[Category: Mol CD]]
-[[Category: alpha/ beta protein]]
+[[Category: Tainer JA]]
-[[Category: dna repair]]
-[[Category: glycosidase]]
-[[Category: glycosylase]]
-[[Category: uracil removal from dna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:42:29 2008''