2vw0: Difference between revisions

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-{{Seed}}
-[[Image:2vw0.png|left|200px]]
-<!--
+==Crystal structure of the NanB sialidase from Streptococcus pneumoniae==
-The line below this paragraph, containing "STRUCTURE_2vw0", creates the "Structure Box" on the page.
+<StructureSection load='2vw0' size='340' side='right'caption='[[2vw0]], [[Resolution|resolution]] 2.30&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'>[[2vw0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VW0 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-{{STRUCTURE_2vw0|  PDB=2vw0  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vw0 OCA], [https://pdbe.org/2vw0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vw0 RCSB], [https://www.ebi.ac.uk/pdbsum/2vw0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vw0 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NANB_STRPN NANB_STRPN]
+== 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/vw/2vw0_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=2vw0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The Streptococcus pneumoniae genomes encode up to three sialidases (or neuraminidases), NanA, NanB and NanC, which are believed to be involved in removing sialic acid from host cell surface glycans, thereby promoting colonization of the upper respiratory tract. Here, we present the crystal structure of NanB to 1.7 A resolution derived from a crystal grown in the presence of the buffer Ches (2-N-cyclohexylaminoethanesulfonic acid). Serendipitously, Ches was found bound to NanB at the enzyme active site, and was found to inhibit NanB with a K(i) of approximately 0.5 mM. In addition, we present the structure to 2.4 A resolution of NanB in complex with the transition-state analogue Neu5Ac2en (2-deoxy-2,3-dehydro-N-acetyl neuraminic acid), which inhibits NanB with a K(i) of approximately 0.3 mM. The sulphonic acid group of Ches and carboxylic acid group of Neu5Ac2en interact with the arginine triad of the active site. The cyclohexyl group of Ches binds in the hydrophobic pocket of NanB occupied by the acetamidomethyl group of Neu5Ac2en. The topology around the NanB active site suggests that the enzyme would have a preference for alpha2,3-linked sialoglycoconjugates, which is confirmed by a kinetic analysis of substrate binding. NMR studies also confirm this preference and show that, like the leech sialidase, NanB acts as an intramolecular trans-sialidase releasing Neu2,7-anhydro5Ac. All three pneumoccocal sialidases possess a carbohydrate-binding domain that is predicted to bind sialic acid. These studies provide support for a possible differential role for NanB compared to NanA in pneumococcal virulence.
-===CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM STREPTOCOCCUS PNEUMONIAE===
+Crystal structure of the NanB sialidase from Streptococcus pneumoniae.,Xu G, Potter JA, Russell RJ, Oggioni MR, Andrew PW, Taylor GL J Mol Biol. 2008 Dec 12;384(2):436-49. Epub 2008 Sep 21. PMID:18835278<ref>PMID:18835278</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vw0" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18835278}}, adds the Publication Abstract to the page
+*[[Neuraminidase 3D structures|Neuraminidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18835278 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18835278}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-VW0 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=2VW0 OCA].
-==Reference==
-Crystal structure of the NanB sialidase from Streptococcus pneumoniae., Xu G, Potter JA, Russell RJ, Oggioni MR, Andrew PW, Taylor GL, J Mol Biol. 2008 Dec 12;384(2):436-49. Epub 2008 Sep 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18835278 18835278]
-[[Category: Exo-alpha-sialidase]]
 [[Category: Streptococcus pneumoniae]]
-[[Category: Andrew, P W.]]
+[[Category: Andrew PW]]
-[[Category: Oggioni, M R.]]
+[[Category: Oggioni MR]]
-[[Category: Potter, J A.]]
+[[Category: Potter JA]]
-[[Category: Russell, R J.M.]]
+[[Category: Russell RJM]]
-[[Category: Taylor, G L.]]
+[[Category: Taylor GL]]
-[[Category: Xu, G.]]
+[[Category: Xu G]]
-[[Category: Drug design]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Neuraminidase]]
-[[Category: Sialidase]]
-[[Category: Virulence factor]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Nov 20 07:53:26 2008''