2ssp: Difference between revisions

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-{{Seed}}
-[[Image:2ssp.png|left|200px]]
-<!--
+==LEUCINE-272-ALANINE URACIL-DNA GLYCOSYLASE BOUND TO ABASIC SITE-CONTAINING DNA==
-The line below this paragraph, containing "STRUCTURE_2ssp", creates the "Structure Box" on the page.
+<StructureSection load='2ssp' size='340' side='right'caption='[[2ssp]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2ssp]] 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=2SSP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2SSP FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene></td></tr>
-{{STRUCTURE_2ssp|  PDB=2ssp  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ssp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ssp OCA], [https://pdbe.org/2ssp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ssp RCSB], [https://www.ebi.ac.uk/pdbsum/2ssp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ssp 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/ss/2ssp_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=2ssp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Three high-resolution crystal structures of DNA complexes with wild-type and mutant human uracil-DNA glycosylase (UDG), coupled kinetic characterizations and comparisons with the refined unbound UDG structure help resolve fundamental issues in the initiation of DNA base excision repair (BER): damage detection, nucleotide flipping versus extrahelical nucleotide capture, avoidance of apurinic/apyrimidinic (AP) site toxicity and coupling of damage-specific and damage-general BER steps. Structural and kinetic results suggest that UDG binds, kinks and compresses the DNA backbone with a 'Ser-Pro pinch' and scans the minor groove for damage. Concerted shifts in UDG simultaneously form the catalytically competent active site and induce further compression and kinking of the double-stranded DNA backbone only at uracil and AP sites, where these nucleotides can flip at the phosphate-sugar junction into a complementary specificity pocket. Unexpectedly, UDG binds to AP sites more tightly and more rapidly than to uracil-containing DNA, and thus may protect cells sterically from AP site toxicity. Furthermore, AP-endonuclease, which catalyzes the first damage-general step of BER, enhances UDG activity, most likely by inducing UDG release via shared minor groove contacts and flipped AP site binding. Thus, AP site binding may couple damage-specific and damage-general steps of BER without requiring direct protein-protein interactions.
-===LEUCINE-272-ALANINE URACIL-DNA GLYCOSYLASE BOUND TO ABASIC SITE-CONTAINING DNA===
+Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.,Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA EMBO J. 1998 Sep 1;17(17):5214-26. PMID:9724657<ref>PMID:9724657</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ssp" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9724657}}, adds the Publication Abstract to the page
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9724657 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9724657}}
+__TOC__
+</StructureSection>
-==About this Structure==
-SSP 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=2SSP OCA].
-==Reference==
-<ref group="xtra">PMID:9724657</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Uridine nucleosidase]]
+[[Category: Large Structures]]
-[[Category: Bharati, S.]]
+[[Category: Bharati S]]
-[[Category: Krokan, H E.]]
+[[Category: Krokan HE]]
-[[Category: Mol, C D.]]
+[[Category: Mol CD]]
-[[Category: Parikh, S S.]]
+[[Category: Parikh SS]]
-[[Category: Slupphaug, G.]]
+[[Category: Slupphaug G]]
-[[Category: Tainer, J A.]]
+[[Category: Tainer JA]]
-[[Category: Abasic site]]
-[[Category: Dna]]
-[[Category: Dna base excision repair]]
-[[Category: Dna glycosylase]]
-[[Category: Protein/dna]]
-[[Category: Uracil]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:31:30 2009''