2itm: Difference between revisions

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New page: left|200px<br /><applet load="2itm" size="450" color="white" frame="true" align="right" spinBox="true" caption="2itm, resolution 2.10Å" /> '''Crystal structure of...
 
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[[Image:2itm.gif|left|200px]]<br /><applet load="2itm" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2itm, resolution 2.10&Aring;" />
'''Crystal structure of the E. coli xylulose kinase complexed with xylulose'''<br />


==Overview==
==Crystal structure of the E. coli xylulose kinase complexed with xylulose==
The primary metabolic route for D-xylose, the second most abundant sugar, in nature, is via the pentose phosphate pathway after a two-step or, three-step conversion to xylulose-5-phosphate. Xylulose kinase (XK; EC, 2.7.1.17) phosphorylates D-xylulose, the last step in this conversion. The, apo and D-xylulose-bound crystal structures of Escherichia coli XK have, been determined and show a dimer composed of two domains separated by an, open cleft. XK dimerization was observed directly by a cryo-EM, reconstruction at 36 A resolution. Kinetic studies reveal that XK has a, weak substrate-independent MgATP-hydrolyzing activity, and phosphorylates, several sugars and polyols with low catalytic efficiency. Binding of, pentulose and MgATP to form the reactive ternary complex is strongly, synergistic. Although the steady-state kinetic mechanism of XK is formally, random, a path is preferred in which D-xylulose binds before MgATP., Modelling of MgATP binding to XK and the accompanying conformational, change suggests that sugar binding is accompanied by a dramatic, hinge-bending movement that enhances interactions with MgATP, explaining, the observed synergism. A catalytic mechanism is proposed and supported by, relevant site-directed mutants.
<StructureSection load='2itm' size='340' side='right'caption='[[2itm]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[2itm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ITM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ITM FirstGlance]. <br>
2ITM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with XUL, SO4 and NH4 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Xylulokinase Xylulokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.17 2.7.1.17] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2ITM OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XUL:D-XYLULOSE'>XUL</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2itm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2itm OCA], [https://pdbe.org/2itm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2itm RCSB], [https://www.ebi.ac.uk/pdbsum/2itm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2itm ProSAT]</span></td></tr>
Structural and kinetic studies of induced fit in xylulose kinase from Escherichia coli., Di Luccio E, Petschacher B, Voegtli J, Chou HT, Stahlberg H, Nidetzky B, Wilson DK, J Mol Biol. 2007 Jan 19;365(3):783-98. Epub 2006 Oct 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17123542 17123542]
</table>
== Function ==
[https://www.uniprot.org/uniprot/XYLB_ECOLI XYLB_ECOLI]
== 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/it/2itm_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=2itm ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Xylulokinase]]
[[Category: Voegtli J]]
[[Category: Luccio, E.di.]]
[[Category: Wilson DK]]
[[Category: Voegtli, J.]]
[[Category: Di Luccio E]]
[[Category: Wilson, D.K.]]
[[Category: NH4]]
[[Category: SO4]]
[[Category: XUL]]
[[Category: atpase]]
[[Category: fggy kinase]]
[[Category: kinase]]
[[Category: xylulokinase]]
[[Category: xylulose]]
 
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Retrieved from "https://proteopedia.org/2itm"