1vfo: Difference between revisions
New page: left|200px<br /><applet load="1vfo" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vfo, resolution 2.81Å" /> '''Crystal structure of... |
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[[Image:1vfo.gif|left|200px]]<br /><applet load="1vfo" size=" | [[Image:1vfo.gif|left|200px]]<br /><applet load="1vfo" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1vfo, resolution 2.81Å" /> | caption="1vfo, resolution 2.81Å" /> | ||
'''Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/beta-cyclodextrin complex'''<br /> | '''Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/beta-cyclodextrin complex'''<br /> | ||
==Overview== | ==Overview== | ||
Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII) has the unique | Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII) has the unique ability to hydrolyze cyclodextrins (CDs), with various sized cavities, as well as starch. To understand the relationship between structure and substrate specificity, x-ray structures of a TVAII-acarbose complex and inactive mutant TVAII (D325N/D421N)/alpha-, beta- and gamma-CDs complexes were determined at resolutions of 2.9, 2.9, 2.8, and 3.1 A, respectively. In all complexes, the interactions between ligands and enzymes at subsites -1, -2, and -3 were almost the same, but striking differences in the catalytic site structure were found at subsites +1 and +2, where Trp(356) and Tyr(374) changed the conformation of the side chain depending on the structure and size of the ligands. Trp(356) and Tyr(374) are thought to be responsible for the multiple substrate-recognition mechanism of TVAII, providing the unique substrate specificity. In the beta-CD complex, the beta-CD maintains a regular conical structure, making it difficult for Glu(354) to protonate the O-4 atom at the hydrolyzing site as a previously proposed hydrolyzing mechanism of alpha-amylase. From the x-ray structures, it is suggested that the protonation of the O-4 atom is possibly carried out via a hydrogen atom of the inter-glucose hydrogen bond at the hydrolyzing site. | ||
==About this Structure== | ==About this Structure== | ||
1VFO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. 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:// | 1VFO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1VFO OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: cyclodextrin]] | [[Category: cyclodextrin]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:34:47 2008'' | ||
Revision as of 16:34, 21 February 2008
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Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/beta-cyclodextrin complex
OverviewOverview
Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII) has the unique ability to hydrolyze cyclodextrins (CDs), with various sized cavities, as well as starch. To understand the relationship between structure and substrate specificity, x-ray structures of a TVAII-acarbose complex and inactive mutant TVAII (D325N/D421N)/alpha-, beta- and gamma-CDs complexes were determined at resolutions of 2.9, 2.9, 2.8, and 3.1 A, respectively. In all complexes, the interactions between ligands and enzymes at subsites -1, -2, and -3 were almost the same, but striking differences in the catalytic site structure were found at subsites +1 and +2, where Trp(356) and Tyr(374) changed the conformation of the side chain depending on the structure and size of the ligands. Trp(356) and Tyr(374) are thought to be responsible for the multiple substrate-recognition mechanism of TVAII, providing the unique substrate specificity. In the beta-CD complex, the beta-CD maintains a regular conical structure, making it difficult for Glu(354) to protonate the O-4 atom at the hydrolyzing site as a previously proposed hydrolyzing mechanism of alpha-amylase. From the x-ray structures, it is suggested that the protonation of the O-4 atom is possibly carried out via a hydrogen atom of the inter-glucose hydrogen bond at the hydrolyzing site.
About this StructureAbout this Structure
1VFO is a Single protein structure of sequence from Thermoactinomyces vulgaris with as ligand. Active as Neopullulanase, with EC number 3.2.1.135 Full crystallographic information is available from OCA.
ReferenceReference
Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with acarbose and cyclodextrins demonstrate the multiple substrate recognition mechanism., Ohtaki A, Mizuno M, Tonozuka T, Sakano Y, Kamitori S, J Biol Chem. 2004 Jul 23;279(30):31033-40. Epub 2004 May 11. PMID:15138257
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