1k9d: Difference between revisions

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[[Image:1k9d.gif|left|200px]]


{{Structure
==The 1.7 A crystal structure of alpha-D-glucuronidase, a family-67 glycoside hydrolase from Bacillus stearothermophilus T-1==
|PDB= 1k9d |SIZE=350|CAPTION= <scene name='initialview01'>1k9d</scene>, resolution 1.70&Aring;
<StructureSection load='1k9d' size='340' side='right'caption='[[1k9d]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
<table><tr><td colspan='2'>[[1k9d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K9D FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Alpha-glucuronidase Alpha-glucuronidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.139 3.2.1.139]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
|GENE= AGUA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=1k9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k9d OCA], [https://pdbe.org/1k9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k9d RCSB], [https://www.ebi.ac.uk/pdbsum/1k9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k9d ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q8VVD2_GEOSE Q8VVD2_GEOSE]  
== 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/k9/1k9d_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1k9d ConSurf].
<div style="clear:both"></div>


'''The 1.7 A crystal structure of alpha-D-glucuronidase, a family-67 glycoside hydrolase from Bacillus stearothermophilus T-1'''
==See Also==
 
*[[Glucuronisidase 3D structures|Glucuronisidase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
Alpha-glucuronidases cleave the alpha-1,2-glycosidic bond between 4-O-methyl-d-glucuronic acid and short xylooligomers as part of the hemicellulose degradation system. To date, all of the alpha-glucuronidases are classified as family 67 glycosidases, which catalyze the hydrolysis via the investing mechanism. Here we describe several high resolution crystal structures of the alpha-glucuronidase (AguA) from Geobacillus stearothermophilus, in complex with its substrate and products. In the complex of AguA with the intact substrate, the 4-O-methyl-d-glucuronic acid sugar ring is distorted into a half-chair conformation, which is closer to the planar conformation required for the oxocarbenium ion-like transition state structure. In the active site, a water molecule is coordinated between two carboxylic acids, in an appropriate position to act as a nucleophile. From the structural data it is likely that two carboxylic acids, Asp(364) and Glu(392), activate together the nucleophilic water molecule. The loop carrying the catalytic general acid Glu(285) cannot be resolved in some of the structures but could be visualized in its "open" and "closed" (catalytic) conformations in other structures. The protonated state of Glu(285) is presumably stabilized by its proximity to the negative charge of the substrate, representing a new variation of substrate-assisted catalysis mechanism.
 
==About this Structure==
1K9D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K9D OCA].
 
==Reference==
Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications., Golan G, Shallom D, Teplitsky A, Zaide G, Shulami S, Baasov T, Stojanoff V, Thompson A, Shoham Y, Shoham G, J Biol Chem. 2004 Jan 23;279(4):3014-24. Epub 2003 Oct 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14573597 14573597]
[[Category: Alpha-glucuronidase]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Baasov, T.]]
[[Category: Baasov T]]
[[Category: Golan, G.]]
[[Category: Golan G]]
[[Category: Shallom, D.]]
[[Category: Shallom D]]
[[Category: Shoham, G.]]
[[Category: Shoham G]]
[[Category: Shoham, Y.]]
[[Category: Shoham Y]]
[[Category: Shulami, S.]]
[[Category: Shulami S]]
[[Category: Stojanoff, V.]]
[[Category: Stojanoff V]]
[[Category: Teplitsky, A.]]
[[Category: Teplitsky A]]
[[Category: Thompson, A.]]
[[Category: Thompson A]]
[[Category: Zaide, G.]]
[[Category: Zaide G]]
[[Category: GOL]]
[[Category: hydrolase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:14:17 2008''

Latest revision as of 07:45, 7 February 2024

The 1.7 A crystal structure of alpha-D-glucuronidase, a family-67 glycoside hydrolase from Bacillus stearothermophilus T-1

1k9d, resolution 1.70Å

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