3in9
From Proteopedia
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| - | {{STRUCTURE_3in9| PDB=3in9 | SCENE= }} | ||
| - | ===Crystal structure of heparin lyase I complexed with disaccharide heparin=== | ||
| - | {{ABSTRACT_PUBMED_19801541}} | ||
| - | == | + | ==Crystal structure of heparin lyase I complexed with disaccharide heparin== |
| - | [[3in9]] is a 1 chain structure with sequence from [ | + | <StructureSection load='3in9' size='340' side='right'caption='[[3in9]], [[Resolution|resolution]] 2.00Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3in9]] 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=3IN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IN9 FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3in9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3in9 OCA], [https://pdbe.org/3in9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3in9 RCSB], [https://www.ebi.ac.uk/pdbsum/3in9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3in9 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q89YQ6_BACTN Q89YQ6_BACTN] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 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. | ||
| - | + | 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> | |
| - | <ref | + | |
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 3in9" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
[[Category: Bacteroides thetaiotaomicron]] | [[Category: Bacteroides thetaiotaomicron]] | ||
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: | + | [[Category: Han YH]] |
| - | [[Category: | + | [[Category: Jeon YH]] |
| - | [[Category: | + | [[Category: Kim HY]] |
| - | [[Category: | + | [[Category: Ryu KS]] |
| - | + | ||
Current revision
Crystal structure of heparin lyase I complexed with disaccharide heparin
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