3b01: 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: @@
-[[Image:3b01.jpg|left|200px]]
-<!--
+==Crystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8==
-The line below this paragraph, containing "STRUCTURE_3b01", creates the "Structure Box" on the page.
+<StructureSection load='3b01' size='340' side='right'caption='[[3b01]], [[Resolution|resolution]] 1.87&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'>[[3b01]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B01 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]] 1.87&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3b01|  PDB=3b01  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3b01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b01 OCA], [https://pdbe.org/3b01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b01 RCSB], [https://www.ebi.ac.uk/pdbsum/3b01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b01 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9WXN1_THEMA Q9WXN1_THEMA]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Laminarinases hydrolyzing the beta-1,3-linkage of glucans play essential roles in microbial saccharide degradation. Here we report the crystal structures at 1.65-1.82 A resolution of the catalytic domain of laminarinase from the thermophile Thermotoga maritima with various space groups in the ligand-free form or in the presence of inhibitors gluconolactone and cetyltrimethylammonium. Ligands were bound at the cleft of the active site near an enclosure formed by Trp232 and a flexible GASIG loop. A closed configuration at the active site cleft was observed in some molecules. The loop flexibility in the enzyme may contribute to the regulation of endo- or exo-activity of the enzyme and a preference to release laminaritrioses in long chain carbohydrate hydrolysis. Glu137 and Glu132 are proposed to serve as the proton donor and nucleophile, respectively, in the retaining catalysis of hydrolyzation. Calcium ions in the crystallization media are found to accelerate crystal growth. Comparison of laminarinase and endoglucanase structures revealed the subtle difference of key residues in the active site for the selection of beta-1,3-glucan and beta-1,4-glucan substrates, respectively. Arg85 may be pivotal to beta-1,3 glucan substrate selection. The similarity of the structures between the laminarinase catalytic domain and its carbohydrate-binding (CBM) modules may have evolutionary relevance due to similarities in their folds.
-===Crystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8===
+Crystal structures of the laminarinase catalytic domain from Thermotoga maritima MSB8 in complex with inhibitors: essential residues for beta-1,3 and beta-1,4 glucan selection.,Jeng WY, Wang NC, Lin CT, Shyur LF, Wang AH J Biol Chem. 2011 Nov 7. PMID:22065588<ref>PMID:22065588</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3b01" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_22065588}}, adds the Publication Abstract to the page
+*[[Laminarase 3D structures|Laminarase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 22065588 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22065588}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3b01]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B01 OCA].
+[[Category: Thermotoga maritima MSB8]]
+[[Category: Jeng WY]]
-==Reference==
+[[Category: Wang AHJ]]
-<ref group="xtra">PMID:022065588</ref><references group="xtra"/>
+[[Category: Wang NC]]
-[[Category: Glucan endo-1,3-beta-D-glucosidase]]
-[[Category: Thermotoga maritima]]
-[[Category: Jeng, W Y.]]
-[[Category: Wang, A H.J.]]
-[[Category: Wang, N C.]]
-[[Category: 3-beta-glucanase]]
-[[Category: Beta-jelly roll fold]]
-[[Category: Endo-1]]
-[[Category: Glycosyl hydrolase family 16]]
-[[Category: Hydrolase]]
-[[Category: Laminarinase]]