View source for 1uh3


==Thermoactinomyces vulgaris R-47 alpha-amylase/acarbose complex==
<StructureSection load='1uh3' size='340' side='right'caption='[[1uh3]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1uh3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UH3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UH3 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]] 2.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACI:6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL'>ACI</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GLD:4,6-DIDEOXYGLUCOSE'>GLD</scene>, <scene name='pdbligand=HSD:(1S,2S,3R,6R)-6-AMINO-4-(HYDROXYMETHYL)CYCLOHEX-4-ENE-1,2,3-TRIOL'>HSD</scene>, <scene name='pdbligand=PRD_900001:alpha-maltose'>PRD_900001</scene>, <scene name='pdbligand=PRD_900010:alpha-maltotetraose'>PRD_900010</scene>, <scene name='pdbligand=PRD_900023:alpha-cellobiose'>PRD_900023</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=1uh3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uh3 OCA], [https://pdbe.org/1uh3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uh3 RCSB], [https://www.ebi.ac.uk/pdbsum/1uh3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uh3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NEPU1_THEVU NEPU1_THEVU] Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Also hydrolyzes cyclodextrins.
== 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/uh/1uh3_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=1uh3 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The X-ray structures of complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) with an inhibitor acarbose and an inactive mutant TVAI with malto-hexaose and malto-tridecaose have been determined at 2.6, 2.0 and 1.8A resolution, and the structures have been refined to R-factors of 0.185 (R(free)=0.225), 0.184 (0.217) and 0.164 (0.200), respectively, with good chemical geometries. Acarbose binds to the catalytic site of TVAI, and interactions between acarbose and the enzyme are very similar to those found in other structure-solved alpha-amylase/acarbose complexes, supporting the proposed catalytic mechanism. Based on the structure of the TVAI/acarbose complex, the binding mode of pullulan containing alpha-(1,6) glucoside linkages could be deduced. Due to the structural difference caused by the replaced amino acid residue (Gln396 for Glu) in the catalytic site, malto-hexaose and malto-tridecaose partially bind to the catalytic site, giving a mimic of the enzyme/product complex. Besides the catalytic site, four sugar-binding sites on the molecular surface are found in these X-ray structures. Two sugar-binding sites in domain N hold the oligosaccharides with a regular helical structure of amylose, which suggests that the domain N is a starch-binding domain acting as an anchor to starch in the catalytic reaction of the enzyme. An assay of hydrolyzing activity for the raw starches confirmed that TVAI can efficiently hydrolyze raw starch.

Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 1 with malto-oligosaccharides demonstrate the role of domain N acting as a starch-binding domain.,Abe A, Tonozuka T, Sakano Y, Kamitori S J Mol Biol. 2004 Jan 16;335(3):811-22. PMID:14687576<ref>PMID:14687576</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1uh3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermoactinomyces vulgaris]]
[[Category: Abe A]]
[[Category: Kamitori S]]
[[Category: Sakano Y]]
[[Category: Tonozuka T]]