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New page: left|200px<br /><applet load="2i56" size="350" color="white" frame="true" align="right" spinBox="true" caption="2i56, resolution 1.97Å" /> '''Crystal structure of...
 
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[[Image:2i56.jpg|left|200px]]<br /><applet load="2i56" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2i56, resolution 1.97&Aring;" />
'''Crystal structure of L-Rhamnose Isomerase from Pseudomonas stutzeri with L-Rhamnose'''<br />


==Overview==
==Crystal structure of L-Rhamnose Isomerase from Pseudomonas stutzeri with L-Rhamnose==
Pseudomonas stutzeri L-rhamnose isomerase (P. stutzeri L-RhI) can, efficiently catalyze the isomerization between various aldoses and, ketoses, showing a broad substrate specificity compared to L-RhI from, Escherichia coli (E. coli L-RhI). To understand the relationship between, structure and substrate specificity, the crystal structures of P. stutzeri, L-RhI alone and in complexes with L-rhamnose and D-allose which has, different configurations of C4 and C5 from L-rhamnose, were determined at, a resolution of 2.0 A, 1.97 A, and 1.97 A, respectively. P. stutzeri L-RhI, has a large domain with a (beta/alpha)(8) barrel fold and an additional, small domain composed of seven alpha-helices, forming a homo tetramer, as, found in E. coli L-RhI and D-xylose isomerases (D-XIs) from various, microorganisms. The beta1-alpha1 loop (Gly60-Arg76) of P. stutzeri L-RhI, is involved in the substrate binding of a neighbouring molecule, as found, in D-XIs, while in E. coli L-RhI, the corresponding beta1-alpha1 loop is, extended (Asp52-Arg78) and covers the substrate-binding site of the same, molecule. The complex structures of P. stutzeri L-RhI with L-rhamnose and, D-allose show that both substrates are nicely fitted to the, substrate-binding site. The part of the substrate-binding site interacting, with the substrate at the 1, 2, and 3 positions is equivalent to E. coli, L-RhI, and the other part interacting with the 4, 5, and 6 positions is, similar to D-XI. In E. coli L-RhI, the beta1-alpha1 loop creates an unique, hydrophobic pocket at the the 4, 5, and 6 positions, leading to the, strictly recognition of L-rhamnose as the most suitable substrate, while, in P. stutzeri L-RhI, there is no corresponding hydrophobic pocket where, Phe66 from a neighbouring molecule merely forms hydrophobic interactions, with the substrate, leading to the loose substrate recognition at the 4, 5, and 6 positions.
<StructureSection load='2i56' size='340' side='right'caption='[[2i56]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2i56]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I56 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.97&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RNS:L-RHAMNOSE'>RNS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2i56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i56 OCA], [https://pdbe.org/2i56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i56 RCSB], [https://www.ebi.ac.uk/pdbsum/2i56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i56 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q75WH8_STUST Q75WH8_STUST]
== 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/i5/2i56_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=2i56 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2I56 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri] with <scene name='pdbligand=RNS:'>RNS</scene> and <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/L-rhamnose_isomerase L-rhamnose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.14 5.3.1.14] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I56 OCA].
*[[L-rhamnose isomerase|L-rhamnose isomerase]]
 
__TOC__
==Reference==
</StructureSection>
The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity., Yoshida H, Yamada M, Ohyama Y, Takada G, Izumori K, Kamitori S, J Mol Biol. 2007 Feb 2;365(5):1505-16. Epub 2006 Nov 6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17141803 17141803]
[[Category: Large Structures]]
[[Category: L-rhamnose isomerase]]
[[Category: Pseudomonas stutzeri]]
[[Category: Pseudomonas stutzeri]]
[[Category: Single protein]]
[[Category: Izumori K]]
[[Category: Izumori, K.]]
[[Category: Kamitori S]]
[[Category: Kamitori, S.]]
[[Category: Takada G]]
[[Category: Takada, G.]]
[[Category: Yamada M]]
[[Category: Yamada, M.]]
[[Category: Yoshida H]]
[[Category: Yoshida, H.]]
[[Category: RNS]]
[[Category: ZN]]
[[Category: beta/alpha barrel]]
[[Category: homo-tetramer]]
[[Category: metal-binding protein]]
[[Category: tim barrel]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 20:35:05 2008''

Latest revision as of 06:28, 3 April 2024

Crystal structure of L-Rhamnose Isomerase from Pseudomonas stutzeri with L-Rhamnose

2i56, resolution 1.97Å

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