3hc7: Difference between revisions

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OCA

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 ==Crystal structure of lysin B from Mycobacteriophage D29==
-<StructureSection load='3hc7' size='340' side='right' caption='[[3hc7]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='3hc7' size='340' side='right'caption='[[3hc7]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3hc7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpmd2 Bpmd2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HC7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HC7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3hc7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_virus_D29 Mycobacterium virus D29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HC7 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">12, gp12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28369 BPMD2])</td></tr>
+</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&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3hc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hc7 OCA], [http://pdbe.org/3hc7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hc7 RCSB], [http://www.ebi.ac.uk/pdbsum/3hc7 PDBsum]</span></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=3hc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hc7 OCA], [https://pdbe.org/3hc7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hc7 RCSB], [https://www.ebi.ac.uk/pdbsum/3hc7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hc7 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LYSB_BPMD2 LYSB_BPMD2] Endolysin that degrades the junction between mycolic acid and peptidoglycans in the host cell wall and participates with the holin protein in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the mycolic acid-rich outer membrane. Cleaves the ester linkage joining the mycolic acid-rich outer membrane to arabinogalactan, releasing free mycolic acids.<ref>PMID:19555454</ref>
 == 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/hc/3hc7_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hc/3hc7_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 16: / Line 19: @@
 </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=3hc7 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Mycobacteriophages encounter a unique problem among phages of Gram-positive bacteria, in that lysis must not only degrade the peptidoglycan layer but also circumvent a mycolic acid-rich outer membrane covalently attached to the arabinogalactan-peptidoglycan complex. Mycobacteriophages accomplish this by producing two lysis enzymes, Lysin A (LysA) that hydrolyses peptidoglycan, and Lysin B (LysB), a novel mycolylarabinogalactan esterase, that cleaves the mycolylarabinogalactan bond to release free mycolic acids. The D29 LysB structure shows an alpha/beta hydrolase organization with a catalytic triad common to cutinases, but which contains an additional four-helix domain implicated in the binding of lipid substrates. Whereas LysA is essential for mycobacterial lysis, a Giles DeltalysB mutant mycobacteriophage is viable, but defective in the normal timing, progression and completion of host cell lysis. We propose that LysB facilitates lysis by compromising the integrity of the mycobacterial outer membrane linkage to the arabinogalactan-peptidoglycan layer.
-Mycobacteriophage Lysin B is a novel mycolylarabinogalactan esterase.,Payne K, Sun Q, Sacchettini J, Hatfull GF Mol Microbiol. 2009 Aug;73(3):367-81. Epub 2009 Jun 22. PMID:19555454<ref>PMID:19555454</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Lysin 3D structures|Lysin 3D structures]]
-<div class="pdbe-citations 3hc7" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bpmd2]]
+[[Category: Large Structures]]
-[[Category: Sacchettini, J C]]
+[[Category: Mycobacterium virus D29]]
-[[Category: Sun, Q]]
+[[Category: Sacchettini JC]]
-[[Category: Alpha/beta sandwich]]
+[[Category: Sun Q]]
-[[Category: Cell adhesion]]