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| | ==X-ray Structures of Bacillus pallidus D-Arabinose IsomeraseComplex with (4R)-2-METHYLPENTANE-2,4-DIOL== | | ==X-ray Structures of Bacillus pallidus D-Arabinose IsomeraseComplex with (4R)-2-METHYLPENTANE-2,4-DIOL== |
| - | <StructureSection load='3a9r' size='340' side='right' caption='[[3a9r]], [[Resolution|resolution]] 1.77Å' scene=''> | + | <StructureSection load='3a9r' size='340' side='right'caption='[[3a9r]], [[Resolution|resolution]] 1.77Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3a9r]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51176 Atcc 51176]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A9R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A9R FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3a9r]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeribacillus_pallidus Aeribacillus pallidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A9R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A9R FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</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]] 1.77Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3a9s|3a9s]], [[3a9t|3a9t]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dai ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33936 ATCC 51176])</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=3a9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a9r OCA], [https://pdbe.org/3a9r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a9r RCSB], [https://www.ebi.ac.uk/pdbsum/3a9r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a9r ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-arabinose_isomerase D-arabinose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.3 5.3.1.3] </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=3a9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a9r OCA], [http://pdbe.org/3a9r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3a9r RCSB], [http://www.ebi.ac.uk/pdbsum/3a9r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3a9r ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/C0SSE7_9BACI C0SSE7_9BACI]] Converts the aldose L-fucose into the corresponding ketose L-fuculose.[HAMAP-Rule:MF_01254] | + | [https://www.uniprot.org/uniprot/C0SSE7_9BACI C0SSE7_9BACI] Converts the aldose L-fucose into the corresponding ketose L-fuculose.[HAMAP-Rule:MF_01254] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 51176]] | + | [[Category: Aeribacillus pallidus]] |
| - | [[Category: D-arabinose isomerase]] | + | [[Category: Large Structures]] |
| - | [[Category: Izumori, K]] | + | [[Category: Izumori K]] |
| - | [[Category: Kamitori, S]] | + | [[Category: Kamitori S]] |
| - | [[Category: Takeda, K]] | + | [[Category: Takeda K]] |
| - | [[Category: Yoshida, H]] | + | [[Category: Yoshida H]] |
| - | [[Category: Beta barrel]]
| + | |
| - | [[Category: Carbohydrate metabolism]]
| + | |
| - | [[Category: Cytoplasm]]
| + | |
| - | [[Category: Fucose metabolism]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Manganese]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| Structural highlights
Function
C0SSE7_9BACI Converts the aldose L-fucose into the corresponding ketose L-fuculose.[HAMAP-Rule:MF_01254]
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
d-Arabinose isomerase (d-AI), also known as l-fucose isomerase (l-FI), catalyzes the aldose-ketose isomerization of d-arabinose to d-ribulose, and l-fucose to l-fuculose. Bacillus pallidus (B. pallidus) d-AI can catalyze isomerization of d-altrose to d-psicose, as well as d-arabinose and l-fucose. Three X-ray structures of B. pallidus d-AI in complexes with 2-methyl-2,4-pentadiol, glycerol and an inhibitor, l-fucitol, were determined at resolutions of 1.77, 1.60 and 2.60 A, respectively. B. pallidus d-AI forms a homo-hexamer, and one subunit has three domains of almost equal size; two Rossmann fold domains and a mimic of the (beta/alpha) barrel fold domain. A catalytic metal ion (Mn(2+)) was found in the active site coordinated by Glu342, Asp366 and His532, and an additional metal ion was found at the channel for the passage of a substrate coordinated by Asp453. The X-ray structures basically supported the ene-diol mechanism for the aldose-ketose isomerization by B. pallidus d-AI, as well as Escherichia coli (E. coli) l-FI, in which Glu342 and Asp366 facing each other at the catalytic metal ion transfer a proton from C2 to C1 and O1 to O2, acting as acid/base catalysts, respectively. However, considering the ionized state of Asp366, the catalytic reaction also possibly occurs through the negatively charged ene-diolate intermediate stabilized by the catalytic metal ion. A structural comparison with E. colil-FI showed that B. pallidus d-AI possibly interconverts between "open" and "closed" forms, and that the additional metal ion found in B. pallidus d-AI may help to stabilize the channel region.
X-ray structures of Bacillus pallidus d-arabinose isomerase and its complex with l-fucitol.,Takeda K, Yoshida H, Izumori K, Kamitori S Biochim Biophys Acta. 2010 Jun;1804(6):1359-68. Epub 2010 Feb 1. PMID:20123133[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Takeda K, Yoshida H, Izumori K, Kamitori S. X-ray structures of Bacillus pallidus d-arabinose isomerase and its complex with l-fucitol. Biochim Biophys Acta. 2010 Jun;1804(6):1359-68. Epub 2010 Feb 1. PMID:20123133 doi:10.1016/j.bbapap.2010.01.018
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