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| - | [[Image:2hcv.jpg|left|200px]] | |
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| - | <!-- | + | ==Crystal structure of L-rhamnose isomerase from Pseudomonas stutzeri with metal ion== |
| - | The line below this paragraph, containing "STRUCTURE_2hcv", creates the "Structure Box" on the page.
| + | <StructureSection load='2hcv' size='340' side='right'caption='[[2hcv]], [[Resolution|resolution]] 2.00Å' 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'>[[2hcv]] 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=2HCV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HCV 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]] 2Å</td></tr> |
| - | --> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | {{STRUCTURE_2hcv| PDB=2hcv | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hcv OCA], [https://pdbe.org/2hcv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hcv RCSB], [https://www.ebi.ac.uk/pdbsum/2hcv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hcv 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/hc/2hcv_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=2hcv ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | 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. |
| | | | |
| - | '''Crystal structure of L-rhamnose isomerase from Pseudomonas stutzeri with metal ion'''
| + | 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> |
| - | | + | |
| - | | + | |
| - | ==Overview==
| + | |
| - | 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.
| + | |
| | | | |
| - | ==About this Structure==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | 2HCV is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HCV OCA].
| + | </div> |
| | + | <div class="pdbe-citations 2hcv" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Reference== | + | ==See Also== |
| - | 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://www.ncbi.nlm.nih.gov/pubmed/17141803 17141803]
| + | *[[L-rhamnose isomerase|L-rhamnose isomerase]] |
| - | [[Category: L-rhamnose isomerase]] | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[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: Beta/alpha barrel]]
| + | |
| - | [[Category: Homo-tetramer]]
| + | |
| - | [[Category: Metal-binding protein]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 06:08:01 2008''
| + | |
| Structural highlights
Function
Q75WH8_STUST
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yoshida H, Yamada M, Ohyama Y, Takada G, Izumori K, Kamitori S. The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity. J Mol Biol. 2007 Feb 2;365(5):1505-16. Epub 2006 Nov 6. PMID:17141803 doi:10.1016/j.jmb.2006.11.004
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