1e6p: Difference between revisions

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-{{Seed}}
-[[Image:1e6p.png|left|200px]]
-<!--
+==Chitinase B from Serratia marcescens inactive mutant E144Q==
-The line below this paragraph, containing "STRUCTURE_1e6p", creates the "Structure Box" on the page.
+<StructureSection load='1e6p' size='340' side='right'caption='[[1e6p]], [[Resolution|resolution]] 1.70&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'>[[1e6p]] 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=1E6P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E6P 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]] 1.7&#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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1e6p|  PDB=1e6p  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1e6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6p OCA], [https://pdbe.org/1e6p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e6p RCSB], [https://www.ebi.ac.uk/pdbsum/1e6p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6p 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/e6/1e6p_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=1e6p 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 INACTIVE MUTANT E144Q===
+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>
+<div class="pdbe-citations 1e6p" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11481469}}, adds the Publication Abstract to the page
+*[[Chitinase 3D structures|Chitinase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11481469 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11481469}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-E6P is a [[Single protein]] structure of 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=1E6P OCA].
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/11481469 11481469]
 [[Category: Serratia marcescens]]
-[[Category: Single protein]]
+[[Category: Eijsink VGH]]
-[[Category: Aalten, D M.F Van.]]
+[[Category: Komander D]]
-[[Category: Eijsink, V G.H.]]
+[[Category: Synstad B]]
-[[Category: Komander, D.]]
+[[Category: Van Aalten DMF]]
-[[Category: Synstad, B.]]
-[[Category: Chitin degradation]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 00:14:40 2008''