3ikw: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
==Structure of Heparinase I from Bacteroides thetaiotaomicron==
==Structure of Heparinase I from Bacteroides thetaiotaomicron==
<StructureSection load='3ikw' size='340' side='right' caption='[[3ikw]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
<StructureSection load='3ikw' size='340' side='right'caption='[[3ikw]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ikw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IKW FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ikw]] 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=3IKW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IKW FirstGlance]. <br>
</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></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]] 1.3&#8491;</td></tr>
<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 Bacteroides thetaiotaomicron])</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=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
<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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ikw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikw OCA], [https://pdbe.org/3ikw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ikw RCSB], [https://www.ebi.ac.uk/pdbsum/3ikw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikw ProSAT]</span></td></tr>
<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=3ikw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ikw RCSB], [http://www.ebi.ac.uk/pdbsum/3ikw PDBsum]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/Q89YQ6_BACTN Q89YQ6_BACTN]
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacteroides thetaiotaomicron]]
[[Category: Bacteroides thetaiotaomicron]]
[[Category: Heparin lyase]]
[[Category: Large Structures]]
[[Category: Cygler, M]]
[[Category: Cygler M]]
[[Category: Garron, M L]]
[[Category: Garron ML]]
[[Category: Shaya, D]]
[[Category: Shaya D]]
[[Category: Beta-jelly roll]]
[[Category: Heparin]]
[[Category: Lyase]]
[[Category: Polysaccharide lyase]]

Latest revision as of 10:05, 21 February 2024

Structure of Heparinase I from Bacteroides thetaiotaomicron

3ikw, resolution 1.30Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=3ikw&oldid=4065621"