1akz: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1akz.gif|left|200px]]<br />
-<applet load="1akz" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1akz, resolution 1.57&Aring;" />
-'''HUMAN URACIL-DNA GLYCOSYLASE'''<br />
-==Overview==
+==HUMAN URACIL-DNA GLYCOSYLASE==
-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.
+<StructureSection load='1akz' size='340' side='right'caption='[[1akz]], [[Resolution|resolution]] 1.57&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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>
+</table>
+== Disease ==
+[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>
-==Disease==
+==See Also==
-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]]
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-AKZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1AKZ OCA].
+__TOC__
+</StructureSection>
-==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://ispc.weizmann.ac.il//pmbin/getpm?pmid=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://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 15:59:24 2007''