3ilr

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==Structure of Heparinase I from Bacteroides thetaiotaomicron in complex with tetrasaccharide product==
==Structure of Heparinase I from Bacteroides thetaiotaomicron in complex with tetrasaccharide product==
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<StructureSection load='3ilr' size='340' side='right' caption='[[3ilr]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
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<StructureSection load='3ilr' size='340' side='right'caption='[[3ilr]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3ilr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_thetaiotaomicron"_distaso_1912 "bacillus thetaiotaomicron" distaso 1912]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ILR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ILR FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3ilr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ILR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ILR FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IXD:4-DEOXY-2-O-SULFO-BETA-D-ERYTHRO-HEX-4-ENOPYRANURONIC+ACID'>IXD</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ikw|3ikw]]</td></tr>
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<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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IXD:4-DEOXY-2-O-SULFO-BETA-D-ERYTHRO-HEX-4-ENOPYRANURONIC+ACID'>IXD</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BT_4675 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 "Bacillus thetaiotaomicron" Distaso 1912])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ilr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ilr OCA], [https://pdbe.org/3ilr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ilr RCSB], [https://www.ebi.ac.uk/pdbsum/3ilr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ilr ProSAT]</span></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heparin_lyase Heparin lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.7 4.2.2.7] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ilr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ilr OCA], [http://pdbe.org/3ilr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ilr RCSB], [http://www.ebi.ac.uk/pdbsum/3ilr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ilr ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q89YQ6_BACTN Q89YQ6_BACTN]
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Heparin lyase I (heparinase I) specifically depolymerizes heparin, cleaving the glycosidic linkage next to iduronic acid. Here, we show the crystal structures of heparinase I from Bacteroides thetaiotaomicron at various stages of the reaction with heparin oligosaccharides before and just after cleavage and product disaccharide. The heparinase I structure is comprised of a beta-jellyroll domain harboring a long and deep substrate binding groove and an unusual thumb-resembling extension. This thumb, decorated with many basic residues, is of particular importance in activity especially on short heparin oligosaccharides. Unexpected structural similarity of the active site to that of heparinase II with an (alpha/alpha)(6) fold is observed. Mutational studies and kinetic analysis of this enzyme provide insights into the catalytic mechanism, the substrate recognition, and processivity.
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Structural snapshots of heparin depolymerization by heparin lyase I.,Han YH, Garron ML, Kim HY, Kim WS, Zhang Z, Ryu KS, Shaya D, Xiao Z, Cheong C, Kim YS, Linhardt RJ, Jeon YH, Cygler M J Biol Chem. 2009 Dec 4;284(49):34019-27. Epub 2009 Oct 2. PMID:19801541<ref>PMID:19801541</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3ilr" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus thetaiotaomicron distaso 1912]]
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[[Category: Bacteroides thetaiotaomicron]]
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[[Category: Heparin lyase]]
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[[Category: Large Structures]]
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[[Category: Cygler, M]]
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[[Category: Cygler M]]
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[[Category: Garron, M L]]
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[[Category: Garron ML]]
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[[Category: Shaya, D]]
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[[Category: Shaya D]]
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[[Category: Beta-jelly roll]]
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[[Category: Heparin]]
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[[Category: Lyase]]
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[[Category: Polysaccharide lyase]]
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Current revision

Structure of Heparinase I from Bacteroides thetaiotaomicron in complex with tetrasaccharide product

PDB ID 3ilr

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