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| ==Crystal structure of L-Rhamnose Isomerase from Pseudomonas stutzeri with L-Rhamnose== | | ==Crystal structure of L-Rhamnose Isomerase from Pseudomonas stutzeri with L-Rhamnose== |
| <StructureSection load='2i56' size='340' side='right' caption='[[2i56]], [[Resolution|resolution]] 1.97Å' scene=''> | | <StructureSection load='2i56' size='340' side='right'caption='[[2i56]], [[Resolution|resolution]] 1.97Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[2i56]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_sewerinii"_bergey_et_al._1923 "achromobacter sewerinii" bergey et al. 1923]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I56 FirstGlance]. <br> | | <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RNS:L-RHAMNOSE'>RNS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.97Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2hcv|2hcv]], [[2i57|2i57]]</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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> |
| <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2i56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i56 OCA], [http://pdbe.org/2i56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i56 RCSB], [http://www.ebi.ac.uk/pdbsum/2i56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2i56 ProSAT]</span></td></tr> | |
| </table> | | </table> |
| | == Function == |
| | [https://www.uniprot.org/uniprot/Q75WH8_STUST Q75WH8_STUST] |
| == Evolutionary Conservation == | | == Evolutionary Conservation == |
| [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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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]. | | </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> | | <div style="clear:both"></div> |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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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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| 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:17141803<ref>PMID:17141803</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 2i56" style="background-color:#fffaf0;"></div>
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| ==See Also== | | ==See Also== |
| *[[L-rhamnose isomerase|L-rhamnose isomerase]] | | *[[L-rhamnose isomerase|L-rhamnose isomerase]] |
| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Achromobacter sewerinii bergey et al. 1923]] | | [[Category: Large Structures]] |
| [[Category: L-rhamnose isomerase]] | | [[Category: Pseudomonas stutzeri]] |
| [[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: Beta/alpha barrel]]
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| [[Category: Homo-tetramer]]
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| [[Category: Isomerase]]
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| [[Category: Metal-binding protein]]
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| [[Category: Tim barrel]]
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