2wpg: Difference between revisions

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-[[Image:2wpg.png|left|200px]]
-<!--
+==Sucrose Hydrolase==
-The line below this paragraph, containing "STRUCTURE_2wpg", creates the "Structure Box" on the page.
+<StructureSection load='2wpg' size='340' side='right'caption='[[2wpg]], [[Resolution|resolution]] 1.90&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'>[[2wpg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris Xanthomonas campestris pv. campestris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WPG 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]] 1.9&#8491;</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=2wpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wpg OCA], [https://pdbe.org/2wpg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wpg RCSB], [https://www.ebi.ac.uk/pdbsum/2wpg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wpg ProSAT]</span></td></tr>
-{{STRUCTURE_2wpg|  PDB=2wpg  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8P5I2_XANCP Q8P5I2_XANCP]
+== 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/wp/2wpg_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=2wpg ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Glycoside hydrolase family 13 (GH-13) mainly contains starch-degrading or starch-modifying enzymes. Sucrose hydrolases utilize sucrose instead of amylose as the primary glucosyl donor. Here, the catalytic properties and X-ray structure of sucrose hydrolase from Xanthomonas campestris pv. campestris are reported. Sucrose hydrolysis catalyzed by the enzyme follows Michaelis-Menten kinetics, with a K(m) of 60.7 mM and a k(cat) of 21.7 s(-1). The structure of the enzyme was solved at a resolution of 1.9 A in the resting state with an empty active site. This represents the first apo structure from subfamily 4 of GH-13. Comparisons with structures of the highly similar sucrose hydrolase from X. axonopodis pv. glycines most notably showed that residues Arg516 and Asp138, which form a salt bridge in the X. axonopodis sucrose complex and define part of the subsite -1 glucosyl-binding determinants, are not engaged in salt-bridge formation in the resting X. campestris enzyme. In the absence of the salt bridge an opening is created which gives access to subsite -1 from the ;nonreducing' end. Binding of the glucosyl moiety in subsite -1 is therefore likely to induce changes in the conformation of the active-site cleft of the X. campestris enzyme. These changes lead to salt-bridge formation that shortens the groove. Additionally, this finding has implications for understanding the molecular mechanism of the closely related subfamily 4 glucosyl transferase amylosucrase, as it indicates that sucrose could enter the active site from the ;nonreducing' end during the glucan-elongation cycle.
-===Sucrose Hydrolase===
+The apo structure of sucrose hydrolase from Xanthomonas campestris pv. campestris shows an open active-site groove.,Champion E, Remaud-Simeon M, Skov LK, Kastrup JS, Gajhede M, Mirza O Acta Crystallogr D Biol Crystallogr. 2009 Dec;65(Pt 12):1309-14. Epub 2009 Nov, 17. PMID:19966417<ref>PMID:19966417</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_19966417}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2wpg" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19966417 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_19966417}}
-==About this Structure==
-[[2wpg]] is a 1 chain structure of [[Alpha-Amylase]] with sequence from [http://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris Xanthomonas campestris pv. campestris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WPG OCA].
 ==See Also==
-*[[Alpha-Amylase|Alpha-Amylase]]
+*[[Amylase 3D structures|Amylase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019966417</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Xanthomonas campestris pv. campestris]]
-[[Category: Champion, E.]]
+[[Category: Champion E]]
-[[Category: Gajhede, M.]]
+[[Category: Gajhede M]]
-[[Category: Kastrup, J S.]]
+[[Category: Kastrup JS]]
-[[Category: Mirza, O.]]
+[[Category: Mirza O]]
-[[Category: Remaud-Simeon, M.]]
+[[Category: Remaud-Simeon M]]
-[[Category: Skov, L K.]]
+[[Category: Skov LK]]
-[[Category: Enzyme]]
-[[Category: Glycosyl hydrolase family 13]]
-[[Category: Hydrolase]]
-[[Category: Sucrose hydrolysis]]