View source for 3aki


==Crystal structure of exo-1,5-alpha-L-arabinofuranosidase complexed with alpha-L-arabinofuranosyl azido==
<StructureSection load='3aki' size='340' side='right'caption='[[3aki]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3aki]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avermitilis_MA-4680_=_NBRC_14893 Streptomyces avermitilis MA-4680 = NBRC 14893]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AKI FirstGlance]. <br>
</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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AH8:(2R,3R,4R,5S)-2-AZIDO-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL'>AH8</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=3aki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aki OCA], [https://pdbe.org/3aki PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3aki RCSB], [https://www.ebi.ac.uk/pdbsum/3aki PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3aki ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/IABF_STRAW IABF_STRAW] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes only the cleavage of terminal alpha-(1->5) arabinofuranosyl bonds of arabinan present in the arabinofuranosyl polysaccharides or oligosaccharides. It cannot act on other arabinose-containing polysaccharides and arabinoxylo-oligosaccharides.<ref>PMID:18665359</ref> 
== 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/ak/3aki_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=3aki ConSurf].
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== Publication Abstract from PubMed ==
Exo-1,5-alpha-L-arabinofuranosidases belonging to glycoside hydrolase family 43 have strict substrate specificity. These enzymes hydrolyze only the alpha-1,5-linkages of linear arabinan and arabino-oligosaccharides in an exo-acting manner. The enzyme from Streptomyces avermitilis contains a core catalytic domain belonging to glycoside hydrolase family 43 and a C-terminal arabinan binding module belonging to carbohydrate binding module family 42. We determined the crystal structure of intact exo-1,5-alpha-L-arabinofuranosidase. The catalytic module is composed of a 5-bladed beta-propeller topologically identical to the other family 43 enzymes. The arabinan binding module had three similar subdomains assembled against one another around a pseudo-3-fold axis, forming a beta-trefoil-fold. A sugar complex structure with alpha-1,5-L-arabinofuranotriose revealed three subsites in the catalytic domain, and a sugar complex structure with alpha-L-arabinofuranosyl azide revealed three arabinose-binding sites in the carbohydrate binding module. A mutagenesis study revealed that substrate specificity was regulated by residues Asn-159, Tyr-192, and Leu-289 located at the aglycon side of the substrate-binding pocket. The exo-acting manner of the enzyme was attributed to the strict pocket structure of subsite -1, formed by the flexible loop region Tyr-281-Arg-294 and the side chain of Tyr-40, which occupied the positions corresponding to the catalytic glycon cleft of GH43 endo-acting enzymes.

Crystal structure of an Exo-1,5-{alpha}-L-arabinofuranosidase from Streptomyces avermitilis provides insights into the mechanism of substrate discrimination between exo- and endo-type enzymes in glycoside hydrolase family 43.,Fujimoto Z, Ichinose H, Maehara T, Honda M, Kitaoka M, Kaneko S J Biol Chem. 2010 Oct 29;285(44):34134-43. Epub 2010 Aug 25. PMID:20739278<ref>PMID:20739278</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Streptomyces avermitilis MA-4680 = NBRC 14893]]
[[Category: Fujimoto Z]]
[[Category: Ichinose H]]
[[Category: Kaneko S]]