2d5j

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:46, 13 March 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[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>
-
}}
+
</table>
-
 
+
== Function ==
-
'''Unsaturated Glucuronyl Hydrolase Triggers Hydration of Vinyl Ether Group but not of Glycosidic Bond'''
+
[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]]
-
==Overview==
+
Check<jmol>
-
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.
+
<jmolCheckbox>
-
 
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d5/2d5j_consurf.spt"</scriptWhenChecked>
-
==About this Structure==
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
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].
+
<text>to colour the structure by Evolutionary Conservation</text>
-
 
+
</jmolCheckbox>
-
==Reference==
+
</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].
-
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]
+
<div style="clear:both"></div>
-
[[Category: Bacillus sp.]]
+
== References ==
-
[[Category: Single protein]]
+
<references/>
-
[[Category: Hashimoto, W.]]
+
__TOC__
-
[[Category: Itoh, T.]]
+
</StructureSection>
-
[[Category: Mikami, B.]]
+
[[Category: Bacillus sp. GL1]]
-
[[Category: Murata, K.]]
+
[[Category: Large Structures]]
-
[[Category: alpha/alpha barrel]]
+
[[Category: Hashimoto W]]
-
[[Category: unsaturated glucuronyl hydrolase]]
+
[[Category: Itoh T]]
-
 
+
[[Category: Mikami B]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:23:35 2008''
+
[[Category: Murata K]]

Current revision

Unsaturated Glucuronyl Hydrolase Triggers Hydration of Vinyl Ether Group but not of Glycosidic Bond

PDB ID 2d5j

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2d5j"
Personal tools