3ct5: Difference between revisions

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 ==Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail==
-<StructureSection load='3ct5' size='340' side='right' caption='[[3ct5]], [[Resolution|resolution]] 1.37&Aring;' scene=''>
+<StructureSection load='3ct5' size='340' side='right'caption='[[3ct5]], [[Resolution|resolution]] 1.37&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ct5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_phi-29 Bacteriophage phi-29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CT5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CT5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ct5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_phage_phi29 Bacillus phage phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CT5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CT5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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]] 1.37&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3csq|3csq]], [[3csr|3csr]], [[3csz|3csz]], [[3ct0|3ct0]], [[3ct1|3ct1]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900017:triacetyl-beta-chitotriose'>PRD_900017</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 Bacteriophage phi-29])</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=3ct5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ct5 OCA], [https://pdbe.org/3ct5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ct5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ct5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ct5 ProSAT]</span></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=3ct5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ct5 OCA], [http://pdbe.org/3ct5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ct5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ct5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ct5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VG13_BPPH2 VG13_BPPH2]] Essential for tail assembly and the production of infectious particles. Degrades the peptidoglycan layer of the host cell wall and thereby facilitates infection of host bacteria. Acts probably as multifunctional enzyme that degrades N-acetylglucosamine polymers (in vitro) and cleaves the peptide cross-links of the host cell wall (Probable).<ref>PMID:18394643</ref> <ref>PMID:18606992</ref>
+[https://www.uniprot.org/uniprot/GP13_BPPH2 GP13_BPPH2] May serve as a plug to restrain the highly pressurized packaged genome and thus would be the first virion protein to contact the host cell wall, degrading the peptidoglycan layer and thereby facilitating viral genome entry into the host bacteria. Acts probably as a multifunctional enzyme that degrades N-acetylglucosamine polymers (in vitro) and cleaves the peptide cross-links of the host cell wall. Essential for the tail assembly.<ref>PMID:18394643</ref> <ref>PMID:18606992</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/ct/3ct5_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ct/3ct5_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 21: / Line 20: @@
 </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=3ct5 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The small bacteriophage phi29 must penetrate the approximately 250-A thick external peptidoglycan cell wall and cell membrane of the Gram-positive Bacillus subtilis, before ejecting its dsDNA genome through its tail into the bacterial cytoplasm. The tail of bacteriophage phi29 is noncontractile and approximately 380 A long. A 1.8-A resolution crystal structure of gene product 13 (gp13) shows that this tail protein has spatially well separated N- and C-terminal domains, whose structures resemble lysozyme-like enzymes and metallo-endopeptidases, respectively. CryoEM reconstructions of the WT bacteriophage and mutant bacteriophages missing some or most of gp13 shows that this enzyme is located at the distal end of the phi29 tail knob. This finding suggests that gp13 functions as a tail-associated, peptidoglycan-degrading enzyme able to cleave both the polysaccharide backbone and peptide cross-links of the peptidoglycan cell wall. Comparisons of the gp13(-) mutants with the phi29 mature and emptied phage structures suggest the sequence of events that occur during the penetration of the tail through the peptidoglycan layer.
-Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail.,Xiang Y, Morais MC, Cohen DN, Bowman VD, Anderson DL, Rossmann MG Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9552-7. Epub 2008 Jul 7. PMID:18606992<ref>PMID:18606992</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3ct5" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacteriophage phi-29]]
+[[Category: Bacillus phage phi29]]
-[[Category: Rossmann, M G]]
+[[Category: Large Structures]]
-[[Category: Xiang, Y]]
+[[Category: Rossmann MG]]
-[[Category: Cell wall]]
+[[Category: Xiang Y]]
-[[Category: Hydrolase]]
-[[Category: Infection]]
-[[Category: Late protein]]
-[[Category: Phi29]]