3hl8: Difference between revisions

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-{{Seed}}
-[[Image:3hl8.jpg|left|200px]]
-<!--
+==Crystal structure of exonuclease I in complex with inhibitor BCBP==
-The line below this paragraph, containing "STRUCTURE_3hl8", creates the "Structure Box" on the page.
+<StructureSection load='3hl8' size='340' side='right'caption='[[3hl8]], [[Resolution|resolution]] 1.55&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'>[[3hl8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HL8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HL8 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]] 1.55&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BBP:(5R)-3-TERT-BUTYL-1-(6-CHLORO-1,3-BENZOTHIAZOL-2-YL)-4,5-DIHYDRO-1H-PYRAZOL-5-OL'>BBP</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_3hl8|  PDB=3hl8  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hl8 OCA], [https://pdbe.org/3hl8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hl8 RCSB], [https://www.ebi.ac.uk/pdbsum/3hl8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hl8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/EX1_ECOLI EX1_ECOLI] Also functions as a DNA deoxyribophosphodiesterase that releases deoxyribose-phosphate moieties following the cleavage DNA at an apurinic/apyrimidinic (AP) site by either an AP endonuclease AP lyase.
+== 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/hl/3hl8_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=3hl8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Bacterial single-stranded DNA-binding proteins (SSBs) help to recruit a diverse array of genome maintenance enzymes to their sites of action through direct protein interactions. For all cases examined to date, these interactions are mediated by the evolutionarily conserved C terminus of SSB (SSB-Ct). The essential nature of SSB protein interactions makes inhibitors that block SSB complex formation valuable biochemical tools and attractive potential antibacterial agents. Here, we identify four small molecules that disrupt complexes formed between Escherichia coli SSB and Exonuclease I (ExoI), a well-studied SSB-interacting enzyme. Each compound disrupts ExoI/SSB-Ct peptide complexes and abrogates SSB stimulation of ExoI nuclease activity. Structural and biochemical studies support a model for three of the compounds in which they compete with SSB for binding to ExoI. The fourth appears to rely on an allosteric mechanism to disrupt ExoI/SSB complexes. Subsets of the inhibitors block SSB-Ct complex formation with two other SSB-interaction partners as well, which highlights their utility as reagents for investigating the roles of SSB/protein interactions in diverse DNA replication, recombination, and repair reactions.
-===Crystal structure of exonuclease I in complex with inhibitor BCBP===
+Small-molecule tools for dissecting the roles of SSB/protein interactions in genome maintenance.,Lu D, Bernstein DA, Satyshur KA, Keck JL Proc Natl Acad Sci U S A. 2010 Jan 12;107(2):633-8. Epub 2009 Dec 16. PMID:20018747<ref>PMID:20018747</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3hl8" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20018747}}, adds the Publication Abstract to the page
+*[[Exonuclease 3D structures|Exonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20018747 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20018747}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli K-12]]
-HL8 is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HL8 OCA].
+[[Category: Large Structures]]
+[[Category: Satyshur KA]]
-==Reference==
-<ref group="xtra">PMID:20018747</ref><references group="xtra"/>
-[[Category: Escherichia coli k-12]]
-[[Category: Exodeoxyribonuclease I]]
-[[Category: Satyshur, K A.]]
-[[Category: Dna damage]]
-[[Category: Dna repair]]
-[[Category: Exonuclease]]
-[[Category: Genome maintenance]]
-[[Category: Hydrolase]]
-[[Category: Nuclease]]
-[[Category: Ssb]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 20 15:45:54 2010''