2waf: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2waf.png|left|200px]]
-<!--
+==PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN R6)==
-The line below this paragraph, containing "STRUCTURE_2waf", creates the "Structure Box" on the page.
+<StructureSection load='2waf' size='340' side='right'caption='[[2waf]], [[Resolution|resolution]] 3.29&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'>[[2waf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_R6 Streptococcus pneumoniae R6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WAF 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]] 3.29&#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></td></tr>
-{{STRUCTURE_2waf|  PDB=2waf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2waf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2waf OCA], [https://pdbe.org/2waf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2waf RCSB], [https://www.ebi.ac.uk/pdbsum/2waf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2waf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PBP2_STRR6 PBP2_STRR6]
+== 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/wa/2waf_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=2waf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Penicillin-binding proteins (PBPs), the main targets of beta-lactam antibiotics, are membrane-associated enzymes that catalyze the two last steps in the biosynthesis of peptidoglycan. In Streptococcus pneumoniae, a major human pathogen, the surge in resistance to such antibiotics is a direct consequence of the proliferation of mosaic PBP-encoding genes, which give rise to proteins containing tens of mutations. PBP2b is a major drug resistance target, and its modification is essential for the development of high levels of resistance to piperacillin. In this work, we have solved the crystal structures of PBP2b from a wild-type pneumococcal strain, as well as from a highly drug-resistant clinical isolate displaying 58 mutations. Although mutations are present throughout the entire PBP structure, those surrounding the active site influence the total charge and the polar character of the region, while those in close proximity to the catalytic nucleophile impart flexibility onto the beta3/beta4 loop area, which encapsulates the cleft. The wealth of structural data on pneumococcal PBPs now underlines the importance of high malleability in active site regions of drug-resistant strains, suggesting that active site "breathing" could be a common mechanism employed by this pathogen to prevent targeting by beta-lactams.
-===PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN R6)===
+PBP active site flexibility as the key mechanism for beta-lactam resistance in pneumococci.,Contreras-Martel C, Dahout-Gonzalez C, Martins Ados S, Kotnik M, Dessen A J Mol Biol. 2009 Apr 10;387(4):899-909. Epub 2009 Feb 20. PMID:19233207<ref>PMID:19233207</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2waf" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19233207}}, adds the Publication Abstract to the page
+*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19233207 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19233207}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-WAF is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WAF OCA].
+[[Category: Streptococcus pneumoniae R6]]
+[[Category: Contreras-Martel C]]
-==Reference==
+[[Category: Dahout-Gonzalez C]]
-<ref group="xtra">PMID:19233207</ref><ref group="xtra">PMID:15105143</ref><references group="xtra"/>
+[[Category: Dessen A]]
-[[Category: Streptococcus pneumoniae]]
+[[Category: Dos-Santos-Martins A]]
-[[Category: Contreras-Martel, C.]]
+[[Category: Kotnik M]]
-[[Category: Dahout-Gonzalez, C.]]
-[[Category: Dessen, A.]]
-[[Category: Dos-Santos-Martins, A.]]
-[[Category: Kotnik, M.]]
-[[Category: Antibiotic]]
-[[Category: Antibiotic resistance]]
-[[Category: Cell membrane]]
-[[Category: Cell shape]]
-[[Category: Cell wall biogenesis/degradation]]
-[[Category: Infection]]
-[[Category: Membrane]]
-[[Category: Penicillin-binding protein]]
-[[Category: Peptide binding protein]]
-[[Category: Peptidoglycan]]
-[[Category: Peptidoglycan synthesis]]
-[[Category: Resistance]]
-[[Category: Transmembrane]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  8 20:10:51 2009''