This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

6lja

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal Structure of exoHep from Bacteroides intestinalis DSM 17393 complexed with disaccharide product

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6lja"

@@ Line 3: / Line 3: @@
 <StructureSection load='6lja' size='340' side='right'caption='[[6lja]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6lja]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_intestinalis_341 Bacteroides intestinalis 341]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LJA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6lja]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_intestinalis_DSM_17393 Bacteroides intestinalis DSM 17393]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LJA FirstGlance]. <br>
-</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=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.978&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UAP:4-DEOXY-2-O-SULFO-ALPHA-L-THREO-HEX-4-ENOPYRANURONIC+ACID'>UAP</scene></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=PRD_900026:HEPARIN+DISACCHARIDE+I-S,'>PRD_900026</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene>, <scene name='pdbligand=UAP:4-DEOXY-2-O-SULFO-ALPHA-L-THREO-HEX-4-ENOPYRANURONIC+ACID'>UAP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BACINT_00178 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=471870 Bacteroides intestinalis 341])</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=6lja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lja OCA], [https://pdbe.org/6lja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lja RCSB], [https://www.ebi.ac.uk/pdbsum/6lja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lja ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/B3C5J6_9BACE B3C5J6_9BACE]
-Heparinases (Hepases) are critical tools for the studies of highly heterogeneous heparin (HP)/heparan sulfate (HS). However, exolytic heparinases urgently needed for the sequencing of HP/HS chains remain undiscovered. Herein, a type of exolytic heparinases (exoHepases) is identified from the genomes of different bacteria. These exoHepases share almost no homology with known Hepases and prefer to digest HP rather than HS chains by sequentially releasing unsaturated disaccharides from their reducing ends. The structural study of an exoHepase (BIexoHep) shows that an N-terminal conserved DUF4962 superfamily domain is essential to the enzyme activities of these exoHepases, which is involved in the formation of a unique L-shaped catalytic cavity controlling the sequential digestion of substrates through electrostatic interactions. Further, several HP octasaccharides have been preliminarily sequenced by using BIexoHep. Overall, this study fills the research gap of exoHepases and provides urgently needed tools for the structural and functional studies of HP/HS chains.
-Discovery of exolytic heparinases and their catalytic mechanism and potential application.,Zhang Q, Cao HY, Wei L, Lu D, Du M, Yuan M, Shi D, Chen X, Wang P, Chen XL, Chi L, Zhang YZ, Li F Nat Commun. 2021 Feb 24;12(1):1263. doi: 10.1038/s41467-021-21441-8. PMID:33627653<ref>PMID:33627653</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6lja" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacteroides intestinalis 341]]
+[[Category: Bacteroides intestinalis DSM 17393]]
 [[Category: Large Structures]]
-[[Category: Cao, H Y]]
+[[Category: Cao HY]]
-[[Category: Li, F C]]
+[[Category: Li FC]]
-[[Category: Wei, L]]
+[[Category: Wei L]]
-[[Category: Zhang, Q D]]
+[[Category: Zhang QD]]
-[[Category: Zhang, Y Z]]
+[[Category: Zhang YZ]]
-[[Category: Heparan sulfate]]
-[[Category: Heparin]]
-[[Category: Heparinase]]
-[[Category: Lyase]]

6lja

From Proteopedia

Current revision

Crystal Structure of exoHep from Bacteroides intestinalis DSM 17393 complexed with disaccharide product

Structural highlights

Function

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox