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1bvz

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(New page: 200px<br /><applet load="1bvz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bvz, resolution 2.6&Aring;" /> '''ALPHA-AMYLASE II (TVA...)
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[[Image:1bvz.gif|left|200px]]<br /><applet load="1bvz" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1bvz, resolution 2.6&Aring;" />
 
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'''ALPHA-AMYLASE II (TVAII) FROM THERMOACTINOMYCES VULGARIS R-47'''<br />
 
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==Overview==
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==ALPHA-AMYLASE II (TVAII) FROM THERMOACTINOMYCES VULGARIS R-47==
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The crystal structure of Thermoactinomyces vulgaris R-47 alpha-Amylase II, (TVAII) has been determined by multiple isomorphous replacement at 2.6 A, resolution. TVAII was crystallized in an orthorhombic system with the, space group P212121 and the cell dimensions a=118.5 A, b=119.5 A, c=114.5, A. There are two molecules in an asymmetric unit, related by the, non-crystallographic 2-fold symmetry. Diffraction data were collected at, 113 K and the cell dimensions reduced to a=114.6 A, b=117.9 A, c=114.2 A, and the model was refined against 7.0-2.6 A resolution data giving an, R-factor of 0.204 (Rfree=0.272). The final model consists of 1170 amino, acid residues (two molecules) and 478 water molecules with good chemical, geometry. TVAII has three domains, A, B, and C, like other alpha-amylases., Domain A with a (beta/alpha)8 barrel structure and domain C with a, beta-sandwich structure are very similar to those found in other, alpha-amylases. Additionally, TVAII has an extra domain N composed of 121, amino acid residues at the N-terminal site, which has a beta-barrel-like, structure consisting of seven antiparallel beta-strands. Domain N is one, of the driving forces in the formation of the dimer structure of TVAII, but its role in the enzyme activity is still not clear. TVAII does not, have the Ca2+ binding site that connects domains A and B in other, alpha-amylases, rather the NZ atom of Lys299 of TVAII serves as the, connector between these domains. TVAII can hydrolyze cyclodextrins and, pullulan as well as starch. Based on a structural comparison with the, complex between a mutant cyclodextrin glucanotransferase and a, beta-cyclodextrin derivative, Phe286 located at domain B is considered the, residue most likely to recognize the hydrophobic cavity of cyclodextrins., The active-site cleft of TVAII is wider and shallower than that of other, alpha-amylases, and seems to be suitable for the binding of pullulan which, is expected not to adopt the helical structure of amylose.
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<StructureSection load='1bvz' size='340' side='right'caption='[[1bvz]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1bvz]] is a 2 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=1BVZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BVZ FirstGlance]. <br>
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</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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvz OCA], [https://pdbe.org/1bvz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bvz RCSB], [https://www.ebi.ac.uk/pdbsum/1bvz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bvz ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NEPU2_THEVU NEPU2_THEVU] Hydrolyzes pullulan efficiently but only a small amount of starch. Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Cleaves also (1-6)-alpha-glucosidic linkages to form maltotriose.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/1bvz_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1bvz ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1BVZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Active as [http://en.wikipedia.org/wiki/Neopullulanase Neopullulanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.135 3.2.1.135] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BVZ OCA].
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*[[Amylase 3D structures|Amylase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution., Kamitori S, Kondo S, Okuyama K, Yokota T, Shimura Y, Tonozuka T, Sakano Y, J Mol Biol. 1999 Apr 16;287(5):907-21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10222200 10222200]
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[[Category: Large Structures]]
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[[Category: Neopullulanase]]
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[[Category: Single protein]]
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[[Category: Thermoactinomyces vulgaris]]
[[Category: Thermoactinomyces vulgaris]]
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[[Category: Kamitori, S.]]
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[[Category: Kamitori S]]
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[[Category: Kondo, S.]]
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[[Category: Kondo S]]
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[[Category: Okuyama, K.]]
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[[Category: Okuyama K]]
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[[Category: Sakano, Y.]]
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[[Category: Sakano Y]]
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[[Category: Shimura, Y.]]
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[[Category: Shimura Y]]
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[[Category: Tonozuka, T.]]
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[[Category: Tonozuka T]]
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[[Category: Yokota, T.]]
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[[Category: Yokota T]]
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[[Category: hydrolase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:57:52 2007''
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Current revision

ALPHA-AMYLASE II (TVAII) FROM THERMOACTINOMYCES VULGARIS R-47

PDB ID 1bvz

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