3c2u: Difference between revisions

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==Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane==
The line below this paragraph, containing "STRUCTURE_3c2u", creates the "Structure Box" on the page.
<StructureSection load='3c2u' size='340' side='right'caption='[[3c2u]], [[Resolution|resolution]] 1.30&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'>[[3c2u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Selenomonas_ruminantium Selenomonas ruminantium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C2U 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]] 1.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene></td></tr>
{{STRUCTURE_3c2u| PDB=3c2u |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3c2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2u OCA], [https://pdbe.org/3c2u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c2u RCSB], [https://www.ebi.ac.uk/pdbsum/3c2u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c2u ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O52575_SELRU O52575_SELRU]
== 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/c2/3c2u_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=3c2u ConSurf].
<div style="clear:both"></div>


'''Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane'''
==See Also==
 
*[[Xylosidase 3D structures|Xylosidase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
The three-dimensional structure of the catalytically efficient beta-xylosidase from Selenomonas ruminantium in complex with competitive inhibitor 1,3-bis[tris(hydroxymethyl)methylamino]propane (BTP) was determined by using X-ray crystallography (1.3A resolution). Most H bonds between inhibitor and protein occur within subsite -1, including one between the carboxyl group of E186 and an N group of BTP. The other N of BTP occupies subsite +1 near K99. E186 (pK(a) 7.2) serves as catalytic acid. The pH (6-10) profile for 1/K(i)((BTP)) is bell-shaped with pK(a)'s 6.8 and 7.8 on the acidic limb assigned to E186 and inhibitor groups and 9.9 on the basic limb assigned to inhibitor. Mutation K99A eliminates pK(a) 7.8, strongly suggesting that the BTP monocation binds to the dianionic enzyme D14(-)E186(-). A sedimentation equilibrium experiment estimates a K(d) ([dimer](2)/[tetramer]) of 7x10(-9)M. Similar k(cat) and k(cat)/K(m) values were determined when the tetramer/dimer ratio changes from 0.0028 to 26 suggesting that dimers and tetramers are equally active forms.
[[Category: Large Structures]]
 
==About this Structure==
3C2U is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Selenomonas_ruminantium Selenomonas ruminantium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2U OCA].
 
==Reference==
Structure of the two-subsite beta-d-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane., Brunzelle JS, Jordan DB, McCaslin DR, Olczak A, Wawrzak Z, Arch Biochem Biophys. 2008 Mar 14;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18374656 18374656]
[[Category: Selenomonas ruminantium]]
[[Category: Selenomonas ruminantium]]
[[Category: Single protein]]
[[Category: Brunzelle JS]]
[[Category: Brunzelle,J S.]]
[[Category: Jordan DB]]
[[Category: Jordan,D B.]]
[[Category: McCaslin DR]]
[[Category: McCaslin,D R.]]
[[Category: Olczak A]]
[[Category: Olczak,A.]]
[[Category: Wawrzak A]]
[[Category: Wawrzak,A.]]
[[Category: Alpha-l-arabinofuranosidase]]
[[Category: Gh43]]
[[Category: Glycoside hydrolase]]
[[Category: Tetramer]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:51:30 2008''

Latest revision as of 09:32, 21 February 2024

Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane

3c2u, resolution 1.30Å

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