2d0f: Difference between revisions
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|PDB= 2d0f |SIZE=350|CAPTION= <scene name='initialview01'>2d0f</scene>, resolution 2.08Å | |PDB= 2d0f |SIZE=350|CAPTION= <scene name='initialview01'>2d0f</scene>, resolution 2.08Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1ji1|1JI1]], [[2d0g|2D0G]], [[2d0h|2D0H]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0f OCA], [http://www.ebi.ac.uk/pdbsum/2d0f PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2d0f RCSB]</span> | |||
}} | }} | ||
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[[Category: Tonozuka, T.]] | [[Category: Tonozuka, T.]] | ||
[[Category: Yoshida, H.]] | [[Category: Yoshida, H.]] | ||
[[Category: alpha-amylase]] | [[Category: alpha-amylase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:28:39 2008'' | ||
Revision as of 02:28, 31 March 2008
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| , resolution 2.08Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | Alpha-amylase, with EC number 3.2.1.1 | ||||||
| Related: | 1JI1, 2D0G, 2D0H
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N complexed with P2, a pullulan model oligosaccharide
OverviewOverview
Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) has unique hydrolyzing activities for pullulan with sequence repeats of alpha-(1,4), alpha-(1,4), and alpha-(1,6) glycosidic linkages, as well as for starch. TVAI mainly hydrolyzes alpha-(1,4) glycosidic linkages to produce a panose, but it also hydrolyzes alpha-(1,6) glycosidic linkages with a lesser efficiency. X-ray structures of three complexes comprising an inactive mutant TVAI (D356N or D356N/E396Q) and a pullulan model oligosaccharide (P2; [Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]2 or P5; [Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]5) were determined. The complex D356N/P2 is a mimic of the enzyme/product complex in the main catalytic reaction of TVAI, and a structural comparison with Aspergillus oryzaealpha-amylase showed that the (-) subsites of TVAI are responsible for recognizing both starch and pullulan. D356N/E396Q/P2 and D356N/E396Q/P5 provided models of the enzyme/substrate complex recognizing the alpha-(1,6) glycosidic linkage at the hydrolyzing site. They showed that only subsites -1 and -2 at the nonreducing end of TVAI are effective in the hydrolysis of alpha-(1,6) glycosidic linkages, leading to weak interactions between substrates and the enzyme. Domain N of TVAI is a starch-binding domain acting as an anchor in the catalytic reaction of the enzyme. In this study, additional substrates were also found to bind to domain N, suggesting that domain N also functions as a pullulan-binding domain.
About this StructureAbout this Structure
2D0F is a Single protein structure of sequence from Thermoactinomyces vulgaris. Full crystallographic information is available from OCA.
ReferenceReference
Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages., Abe A, Yoshida H, Tonozuka T, Sakano Y, Kamitori S, FEBS J. 2005 Dec;272(23):6145-53. PMID:16302977
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