1vfo: Difference between revisions
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[[Image:1vfo.gif|left|200px]] | [[Image:1vfo.gif|left|200px]] | ||
'''Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/beta-cyclodextrin complex''' | {{Structure | ||
|PDB= 1vfo |SIZE=350|CAPTION= <scene name='initialview01'>1vfo</scene>, resolution 2.81Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene> | |||
|ACTIVITY= [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] | |||
|GENE= | |||
}} | |||
'''Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/beta-cyclodextrin complex''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1VFO is a [ | 1VFO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VFO OCA]. | ||
==Reference== | ==Reference== | ||
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:[http:// | 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:[http://www.ncbi.nlm.nih.gov/pubmed/15138257 15138257] | ||
[[Category: Neopullulanase]] | [[Category: Neopullulanase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: cyclodextrin]] | [[Category: cyclodextrin]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:44:54 2008'' | ||
Revision as of 15:44, 20 March 2008
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| , resolution 2.81Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Activity: | Neopullulanase, with EC number 3.2.1.135 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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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