3imn

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Current revision (08:28, 20 March 2024) (edit) (undo)
 
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<StructureSection load='3imn' size='340' side='right'caption='[[3imn]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
<StructureSection load='3imn' size='340' side='right'caption='[[3imn]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3imn]] is a 1 chain structure with sequence from [https://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=3IMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IMN FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3imn]] 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=3IMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IMN FirstGlance]. <br>
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</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=SO4:SULFATE+ION'>SO4</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]] 1.81&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3in9|3in9]], [[3ina|3ina]]</div></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=SO4:SULFATE+ION'>SO4</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=3imn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3imn OCA], [https://pdbe.org/3imn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3imn RCSB], [https://www.ebi.ac.uk/pdbsum/3imn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3imn ProSAT]</span></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=3imn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3imn OCA], [https://pdbe.org/3imn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3imn RCSB], [https://www.ebi.ac.uk/pdbsum/3imn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3imn ProSAT]</span></td></tr>
</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 3imn" 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]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Han, Y H]]
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[[Category: Han YH]]
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[[Category: Jeon, Y H]]
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[[Category: Jeon YH]]
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[[Category: Ryu, K S]]
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[[Category: Ryu KS]]
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[[Category: Jelly roll]]
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[[Category: Lyase]]
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Current revision

Crystal structure of heparin lyase I from Bacteroides thetaiotaomicron

PDB ID 3imn

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OCA

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