3khu

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:05, 6 November 2024) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3khu.png|left|200px]]
 
-
<!--
+
==Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate==
-
The line below this paragraph, containing "STRUCTURE_3khu", creates the "Structure Box" on the page.
+
<StructureSection load='3khu' size='340' side='right'caption='[[3khu]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3khu]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KHU FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>
-
{{STRUCTURE_3khu| PDB=3khu | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3khu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khu OCA], [https://pdbe.org/3khu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3khu RCSB], [https://www.ebi.ac.uk/pdbsum/3khu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3khu ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/UGDH_HUMAN UGDH_HUMAN] Involved in the biosynthesis of glycosaminoglycans; hyaluronan, chondroitin sulfate, and heparan sulfate.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kh/3khu_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=3khu ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Biosynthesis of UDP-glucuronic acid by UDP-glucose 6-dehydrogenase (UGDH)5 occurs through four-electron oxidation of the C6 primary alcohol of UDP-glucose in two NAD+-dependent steps. The catalytic reaction of UGDH is thought to involve a Cys nucleophile that promotes formation of a thiohemiacetal enzyme intermediate in the course of the first oxidation step. The thiohemiacetal undergoes further oxidation into a thioester, and hydrolysis of the thioester completes the catalytic cycle. Herein we present crystallographic and kinetic evidence for the human form of UGDH that clarifies participation of covalent catalysis in the enzymatic mechanism. Substitution of the putative catalytic base for water attack on thioester (Glu161) by an incompetent analog (Gln161) gave a UGDH variant (E161Q) in which the hydrolysis step had become completely rate limiting so that a thioester enzyme intermediate accumulated at steady state. Using crystallization of E161Q in the presence of 5 mM UDP-glucose and 2 mM NAD+, we succeeded in intercepting a thiohemiacetal enzyme intermediate and determined its structure at 2.3 Angstrom resolution. Cys276 was covalently modified in the structure, establishing a role for it as catalytic nucelophile of the reaction. The reactive C6 of thiohemiacetal was in a position suitable to become further oxidized by hydride transfer to NAD+. The proposed catalytic mechanism of human UGDH involves Lys220 as general base for alcohol oxidation on UDP-glucose and as oxyanion stabilizer during formation and breakdown of the thiohemiacetal and thioester enzyme intermediates. Water bonded to Asp280 deprotonates Cys276 for function as aldehyde trap and also provides oxyanion stabilization. Glu161 is the Bronsted base catalytically promoting the thioester hydrolysis.
-
===Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate===
+
Structural and kinetic evidence that the catalytic reaction of human UDP-glucose 6-dehydrogenase involves covalent thiohemiacetal and thioester enzyme intermediates.,Egger S, Chaikuad A, Klimacek M, Kavanagh KL, Oppermann U, Nidetzky B J Biol Chem. 2011 Nov 28. PMID:22123821<ref>PMID:22123821</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_22123821}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3khu" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 22123821 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_22123821}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
[[3khu]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHU OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:022123821</ref><references group="xtra"/>
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: UDP-glucose 6-dehydrogenase]]
+
[[Category: Large Structures]]
-
[[Category: Arrowsmith, C H.]]
+
[[Category: Arrowsmith CH]]
-
[[Category: Bountra, C.]]
+
[[Category: Bountra C]]
-
[[Category: Chaikuad, A.]]
+
[[Category: Chaikuad A]]
-
[[Category: Delft, F von.]]
+
[[Category: Edwards AM]]
-
[[Category: Edwards, A M.]]
+
[[Category: Egger S]]
-
[[Category: Egger, S.]]
+
[[Category: Filippakopoulos P]]
-
[[Category: Filippakopoulos, P.]]
+
[[Category: Guo K]]
-
[[Category: Guo, K.]]
+
[[Category: Kavanagh KL]]
-
[[Category: Kavanagh, K L.]]
+
[[Category: Muniz JRC]]
-
[[Category: Muniz, J R.C.]]
+
[[Category: Nidetzky B]]
-
[[Category: Nidetzky, B.]]
+
[[Category: Oppermann U]]
-
[[Category: Oppermann, U.]]
+
[[Category: Sethi R]]
-
[[Category: SGC, Structural Genomics Consortium.]]
+
[[Category: Weigelt J]]
-
[[Category: Sethi, R.]]
+
[[Category: Yue WW]]
-
[[Category: Weigelt, J.]]
+
[[Category: Von Delft F]]
-
[[Category: Yue, W W.]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Sgc]]
+
-
[[Category: Structural genomic]]
+
-
[[Category: Structural genomics consortium]]
+
-
[[Category: Thiohemiacetal intermediate]]
+

Current revision

Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate

PDB ID 3khu

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/3khu"
Personal tools