View source for 5jmd


==Heparinase III-BT4657 gene product, Methylated Lysines==
<StructureSection load='5jmd' size='340' side='right'caption='[[5jmd]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5jmd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JMD 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]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</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=5jmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jmd OCA], [https://pdbe.org/5jmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jmd RCSB], [https://www.ebi.ac.uk/pdbsum/5jmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jmd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q89YS4_BACTN Q89YS4_BACTN] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Glycosaminoglycans (GAGs) are linear polysaccharides comprised of disaccharide repeat units, a hexuronic acid, glucuronic acid or iduronic acid, linked to a hexosamine, N-acetylglucosamine (GlcNAc) or N-acetylgalactosamine. GAGs undergo further modification such as epimerization and sulfation. These polysaccharides are abundant in the extracellular matrix and connective tissues. GAGs function in stabilization of the fibrillar extracellular matrix, control of hydration, regulation of tissue, organism development by controlling cell cycle, cell behavior, and differentiation. Niche adapted bacteria expresses enzymes called polysaccharide lyases, which degrade GAGs for their nutrient content. Polysaccharide lyases have been classified into 24 sequence-related families. Comparison of three-dimensional structures of the prototypic members of these families allowed identification of distant evolutionary relationships between lyases that were unrecognized at the sequence level and identified occurrences of convergent evolution. We have characterized structurally and enzymatically Heparinase III from Bacteroides thetaiotaomicron (BtHepIII; gene BT4657), which is classified within the PL12 family. BtHepIII is a 72.5KDa protein. We will present the X-Ray structures of two crystal forms of BtHepIII of resolution 1.8 A and 2.4 A. BtHepIII contains two domains, the N-terminal alpha-helical domain forming a toroid and the C-terminal beta-sheet domain. Comparison with recently determined structures of two other heparinases from the same PL12 family allowed us to identify structural flexibility in the arrangement of the domains indicating open-close movement. Based on comparison with other GAG lyases we identified Tyr301 as the main catalytic residue and confirmed this by site-directed mutagenesis. We have characterized substrate preference of BtHepIII toward sulfate-poor heparan sulfate substrate.

Conformational Flexibility of PL12 family Heparinases: Structure and Substrate Specificity of Heparinase III from Bacteroides thetaiotaomicron (BT4657).,Ulaganathan T, Shi R, Yao D, Gu RX, Garron ML, Cherney M, Tieleman DP, Sterner E, Li G, Li L, Linhardt RJ, Cygler M Glycobiology. 2016 Sep 12. pii: cww096. PMID:27621378<ref>PMID:27621378</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5jmd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacteroides thetaiotaomicron VPI-5482]]
[[Category: Large Structures]]
[[Category: Cherney M]]
[[Category: Cygler M]]
[[Category: Garron M-L]]
[[Category: Shi R]]
[[Category: Ulaganathan TS]]
[[Category: Yao D]]