2z2n: Difference between revisions

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-{{Seed}}
-[[Image:2z2n.png|left|200px]]
-<!--
+==Crystal Structure of selenomethionine substituted virginiamycin B lyase from Staphylococcus aureus==
-The line below this paragraph, containing "STRUCTURE_2z2n", creates the "Structure Box" on the page.
+<StructureSection load='2z2n' size='340' side='right'caption='[[2z2n]], [[Resolution|resolution]] 1.65&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'>[[2z2n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z2N 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]] 1.65&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2z2n|  PDB=2z2n  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2z2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z2n OCA], [https://pdbe.org/2z2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z2n RCSB], [https://www.ebi.ac.uk/pdbsum/2z2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z2n ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VGB_STAAU VGB_STAAU] Inactivates the type B streptogramin antibiotics by linearizing the lactone ring at the ester linkage, generating a free phenylglycine carboxylate and converting the threonyl moiety into 2-amino-butenoic acid.<ref>PMID:11467949</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/z2/2z2n_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2z2n ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The streptogramin combination therapy of quinupristin-dalfopristin (Synercid) is used to treat infections caused by bacterial pathogens, such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. However, the effectiveness of this therapy is being compromised because of an increased incidence of streptogramin resistance. One of the clinically observed mechanisms of resistance is enzymatic inactivation of the type B streptogramins, such as quinupristin, by a streptogramin B lyase, i.e., virginiamycin B lyase (Vgb). The enzyme catalyzes the linearization of the cyclic antibiotic via a cleavage that requires a divalent metal ion. Here, we present crystal structures of Vgb from S. aureus in its apoenzyme form and in complex with quinupristin and Mg2+ at 1.65- and 2.8-A resolution, respectively. The fold of the enzyme is that of a seven-bladed beta-propeller, although the sequence reveals no similarity to other known members of this structural family. Quinupristin binds to a large depression on the surface of the enzyme, where it predominantly forms van der Waals interactions. Validated by site-directed mutagenesis studies, a reaction mechanism is proposed in which the initial abstraction of a proton is facilitated by a Mg2+ -linked conjugated system. Analysis of the Vgb-quinupristin structure and comparison with the complex between quinupristin and its natural target, the 50S ribosomal subunit, reveals features that can be exploited for developing streptogramins that are impervious to Vgb-mediated resistance.
-===Crystal Structure of selenomethionine substituted virginiamycin B lyase from Staphylococcus aureus===
+Structural basis for streptogramin B resistance in Staphylococcus aureus by virginiamycin B lyase.,Korczynska M, Mukhtar TA, Wright GD, Berghuis AM Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10388-93. Epub 2007 Jun 11. PMID:17563376<ref>PMID:17563376</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17563376}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2z2n" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17563376 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17563376}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Z2N is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z2N OCA].
-==Reference==
-<ref group="xtra">PMID:17563376</ref><references group="xtra"/>
 [[Category: Staphylococcus aureus]]
-[[Category: Berghuis, A M.]]
+[[Category: Berghuis AM]]
-[[Category: Korczynska, M.]]
+[[Category: Korczynska M]]
-[[Category: Antibiotic resistance]]
-[[Category: Enzyme mechanism]]
-[[Category: Lyase]]
-[[Category: Seven-bladed beta-propeller]]
-[[Category: Streptogramin]]
-[[Category: Virginiamycin b hydrolase]]
-[[Category: Virginiamycin b lyase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 23:12:43 2009''