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2i56

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[[Image:2i56.jpg|left|200px]]<br /><applet load="2i56" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2i56, resolution 1.97&Aring;" />
 
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'''Crystal structure of L-Rhamnose Isomerase from Pseudomonas stutzeri with L-Rhamnose'''<br />
 
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==Overview==
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==Crystal structure of L-Rhamnose Isomerase from Pseudomonas stutzeri with L-Rhamnose==
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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.
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<StructureSection load='2i56' size='340' side='right'caption='[[2i56]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</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>
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<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>
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q75WH8_STUST Q75WH8_STUST]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i5/2i56_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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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].
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*[[L-rhamnose isomerase|L-rhamnose isomerase]]
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__TOC__
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==Reference==
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</StructureSection>
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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]
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[[Category: Large Structures]]
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[[Category: L-rhamnose isomerase]]
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[[Category: Pseudomonas stutzeri]]
[[Category: Pseudomonas stutzeri]]
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[[Category: Single protein]]
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[[Category: Izumori K]]
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[[Category: Izumori, K.]]
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[[Category: Kamitori S]]
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[[Category: Kamitori, S.]]
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[[Category: Takada G]]
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[[Category: Takada, G.]]
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[[Category: Yamada M]]
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[[Category: Yamada, M.]]
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[[Category: Yoshida H]]
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[[Category: Yoshida, H.]]
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[[Category: RNS]]
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[[Category: ZN]]
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[[Category: beta/alpha barrel]]
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[[Category: homo-tetramer]]
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[[Category: metal-binding protein]]
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[[Category: tim barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:49:18 2008''
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Current revision

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

PDB ID 2i56

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