1e6z: Difference between revisions

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-[[Image:1e6z.png|left|200px]]
-<!--
+==CHITINASE B FROM SERRATIA MARCESCENS WILDTYPE IN COMPLEX WITH CATALYTIC INTERMEDIATE==
-The line below this paragraph, containing "STRUCTURE_1e6z", creates the "Structure Box" on the page.
+<StructureSection load='1e6z' size='340' side='right'caption='[[1e6z]], [[Resolution|resolution]] 1.99&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'>[[1e6z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E6Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E6Z 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]] 1.99&#8491;</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=NGO:2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE'>NGO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1e6z|  PDB=1e6z  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1e6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6z OCA], [https://pdbe.org/1e6z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e6z RCSB], [https://www.ebi.ac.uk/pdbsum/1e6z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6z ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q54276_SERMA Q54276_SERMA]
+== 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/e6/1e6z_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=1e6z ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Chitinase B (ChiB) from Serratia marcescens is a family 18 exo-chitinase whose catalytic domain has a TIM-barrel fold with a tunnel-shaped active site. We have solved structures of three ChiB complexes that reveal details of substrate binding, substrate-assisted catalysis, and product displacement. The structure of an inactive ChiB mutant (E144Q) complexed with a pentameric substrate (binding in subsites -2 to +3) shows closure of the "roof" of the active site tunnel. It also shows that the sugar in the -1 position is distorted to a boat conformation, thus providing structural evidence in support of a previously proposed catalytic mechanism. The structures of the active enzyme complexed to allosamidin (an analogue of a proposed reaction intermediate) and of the active enzyme soaked with pentameric substrate show events after cleavage of the glycosidic bond. The latter structure shows reopening of the roof of the active site tunnel and enzyme-assisted product displacement in the +1 and +2 sites, allowing a water molecule to approach the reaction center. Catalysis is accompanied by correlated structural changes in the core of the TIM barrel that involve conserved polar residues whose functions were hitherto unknown. These changes simultaneously contribute to stabilization of the reaction intermediate and alternation of the pKa of the catalytic acid during the catalytic cycle.
-===CHITINASE B FROM SERRATIA MARCESCENS WILDTYPE IN COMPLEX WITH CATALYTIC INTERMEDIATE===
+Structural insights into the catalytic mechanism of a family 18 exo-chitinase.,van Aalten DM, Komander D, Synstad B, Gaseidnes S, Peter MG, Eijsink VG Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):8979-84. PMID:11481469<ref>PMID:11481469</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_11481469}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1e6z" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11481469 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_11481469}}
-==About this Structure==
-[[1e6z]] is a 2 chain structure of [[Chitinases]] with sequence from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E6Z OCA].
 ==See Also==
-*[[Chitinases]]
+*[[Chitinase 3D structures|Chitinase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:011481469</ref><references group="xtra"/>
+__TOC__
-[[Category: Chitinase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Serratia marcescens]]
-[[Category: Aalten, D M.F Van.]]
+[[Category: Eijsink VGH]]
-[[Category: Eijsink, V G.H.]]
+[[Category: Komander D]]
-[[Category: Komander, D.]]
+[[Category: Synstad B]]
-[[Category: Synstad, B.]]
+[[Category: Van Aalten DMF]]
-[[Category: Catalytic intermediate]]
-[[Category: Chitin degradation]]
-[[Category: Hydrolase]]

1e6z: Difference between revisions

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