2d5j: Difference between revisions

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[[Image:2d5j.gif|left|200px]]


{{Structure
==Unsaturated Glucuronyl Hydrolase Triggers Hydration of Vinyl Ether Group but not of Glycosidic Bond==
|PDB= 2d5j |SIZE=350|CAPTION= <scene name='initialview01'>2d5j</scene>, resolution 1.60&Aring;
<StructureSection load='2d5j' size='340' side='right'caption='[[2d5j]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[2d5j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._GL1 Bacillus sp. GL1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D5J FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
|GENE=  
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d5j OCA], [https://pdbe.org/2d5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d5j RCSB], [https://www.ebi.ac.uk/pdbsum/2d5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d5j ProSAT]</span></td></tr>
|DOMAIN=
</table>
|RELATEDENTRY=[[2ahf|2AHF]], [[2ahg|2AHG]], [[1vd5|1VD5]]
== Function ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d5j OCA], [http://www.ebi.ac.uk/pdbsum/2d5j PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2d5j RCSB]</span>
[https://www.uniprot.org/uniprot/UGL_BACGL UGL_BACGL] Catalyzes the hydrolysis of oligosaccharides with unsaturated glucuronyl residues at the non-reducing terminal, to a sugar or an amino sugar, and an unsaturated D-glucuronic acid (GlcA), which is nonenzymatically converted immediately to alpha-keto acid.<ref>PMID:10441389</ref> <ref>PMID:21147778</ref>
}}
== Evolutionary Conservation ==
 
[[Image:Consurf_key_small.gif|200px|right]]
'''Unsaturated Glucuronyl Hydrolase Triggers Hydration of Vinyl Ether Group but not of Glycosidic Bond'''
Check<jmol>
 
  <jmolCheckbox>
 
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d5/2d5j_consurf.spt"</scriptWhenChecked>
==Overview==
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
Unsaturated glucuronyl hydrolase (UGL), which is a member of glycoside hydrolase family GH-88, is a bacterial enzyme that degrades mammalian glycosaminoglycans and bacterial biofilms. The enzyme, which acts on unsaturated oligosaccharides with an alpha-glycoside bond produced by microbial polysaccharide lyases responsible for bacterial invasion of host cells, was believed to release 4-deoxy-l-threo-5-hexosulose-uronate (unsaturated glucuronic acid, or DeltaGlcA) and saccharide with a new nonreducing terminus by hydrolyzing the glycosidic bond. We detail the crystal structures of wild-type inactive mutant UGL of Bacillus sp. GL1 and its complex with a substrate (unsaturated chondroitin disaccharide), identify active site residues, and postulate a reaction mechanism catalyzed by UGL that triggers the hydration of the vinyl ether group in DeltaGlcA, based on the structural analysis of the enzyme-substrate complex and biochemical analysis. The proposed catalytic mechanism of UGL is a novel case among known glycosidases. Under the proposed mechanism, Asp-149 acts as a general acid and base catalyst to protonate the DeltaGlcA C4 atom and to deprotonate the water molecule. The deprotonated water molecule attacks the DeltaGlcA C5 atom to yield unstable hemiketal; this is followed by spontaneous conversion to an aldehyde (4-deoxy-l-threo-5-hexosulose-uronate) and saccharide through hemiacetal formation and cleavage of the glycosidic bond. UGL is the first clarified alpha(6)/alpha(6)-barrel enzyme using aspartic acid as the general acid/base catalyst.
    <text>to colour the structure by Evolutionary Conservation</text>
 
  </jmolCheckbox>
==About this Structure==
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d5j ConSurf].
2D5J is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D5J OCA].  
<div style="clear:both"></div>
 
== References ==
==Reference==
<references/>
Crystal structure of unsaturated glucuronyl hydrolase complexed with substrate: molecular insights into its catalytic reaction mechanism., Itoh T, Hashimoto W, Mikami B, Murata K, J Biol Chem. 2006 Oct 6;281(40):29807-16. Epub 2006 Aug 7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16893885 16893885]
__TOC__
[[Category: Bacillus sp.]]
</StructureSection>
[[Category: Single protein]]
[[Category: Bacillus sp. GL1]]
[[Category: Hashimoto, W.]]
[[Category: Large Structures]]
[[Category: Itoh, T.]]
[[Category: Hashimoto W]]
[[Category: Mikami, B.]]
[[Category: Itoh T]]
[[Category: Murata, K.]]
[[Category: Mikami B]]
[[Category: alpha/alpha barrel]]
[[Category: Murata K]]
[[Category: unsaturated glucuronyl hydrolase]]
 
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Retrieved from "https://proteopedia.org/2d5j"