3a9s: Difference between revisions
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[[Image: | ==X-ray Structure of Bacillus pallidus D-Arabinose Isomerase Complex with Glycerol== | ||
<StructureSection load='3a9s' size='340' side='right' caption='[[3a9s]], [[Resolution|resolution]] 1.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3a9s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeribacillus_pallidus Aeribacillus pallidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A9S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A9S FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3a9r|3a9r]], [[3a9t|3a9t]]</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 Aeribacillus pallidus])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arabinose_isomerase 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=3a9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a9s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3a9s RCSB], [http://www.ebi.ac.uk/pdbsum/3a9s PDBsum]</span></td></tr> | |||
</table> | |||
== 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] | |||
== 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/a9/3a9s_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/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:20123133</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
< | |||
[[Category: Aeribacillus pallidus]] | [[Category: Aeribacillus pallidus]] | ||
[[Category: Arabinose isomerase]] | [[Category: Arabinose isomerase]] | ||
[[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: Beta barrel]] | ||
[[Category: Carbohydrate metabolism]] | [[Category: Carbohydrate metabolism]] | ||
