3a9t: Difference between revisions

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{{Seed}}
[[Image:3a9t.jpg|left|200px]]


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==X-ray Structure of Bacillus pallidus D-Arabinose Isomerase Complex with L-Fucitol==
The line below this paragraph, containing "STRUCTURE_3a9t", creates the "Structure Box" on the page.
<StructureSection load='3a9t' size='340' side='right'caption='[[3a9t]], [[Resolution|resolution]] 2.61&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3a9t]] 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=3A9T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A9T 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]] 2.61&#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=FOC:FUCITOL'>FOC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
{{STRUCTURE_3a9t|  PDB=3a9t  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3a9t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a9t OCA], [https://pdbe.org/3a9t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a9t RCSB], [https://www.ebi.ac.uk/pdbsum/3a9t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a9t ProSAT]</span></td></tr>
</table>
== Function ==
[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 ==
[[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/a9/3a9t_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=3a9t 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 Structure of Bacillus pallidus D-Arabinose Isomerase Complex with L-Fucitol===
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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(as it appears on PubMed at http://www.pubmed.gov), where 20123133 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_20123133}}
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</StructureSection>
==About this Structure==
[[Category: Aeribacillus pallidus]]
3A9T is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Geobacillus_pallidus Geobacillus pallidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A9T OCA].
[[Category: Large Structures]]
 
[[Category: Izumori K]]
==Reference==
[[Category: Kamitori S]]
<ref group="xtra">PMID:20123133</ref><references group="xtra"/>
[[Category: Takeda K]]
[[Category: Arabinose isomerase]]
[[Category: Yoshida H]]
[[Category: Geobacillus pallidus]]
[[Category: Izumori, k.]]
[[Category: Kamitori, S.]]
[[Category: Takeda, K.]]
[[Category: Yoshida, H.]]
[[Category: Bete barrel]]
[[Category: Carbohydrate metabolism]]
[[Category: Cytoplasm]]
[[Category: Fucose metabolism]]
[[Category: Isomerase]]
[[Category: Manganese]]
[[Category: Metal-binding]]
[[Category: Rossmann fold]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  7 10:34:40 2010''
Retrieved from "https://proteopedia.org/3a9t"