1uh4: Difference between revisions
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|PDB= 1uh4 |SIZE=350|CAPTION= <scene name='initialview01'>1uh4</scene>, resolution 1.80Å | |PDB= 1uh4 |SIZE=350|CAPTION= <scene name='initialview01'>1uh4</scene>, resolution 1.80Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <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]], [[1uh2|1UH2]], [[1uh3|1UH3]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1uh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uh4 OCA], [http://www.ebi.ac.uk/pdbsum/1uh4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1uh4 RCSB]</span> | |||
}} | }} | ||
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[[Category: Sakano, Y.]] | [[Category: Sakano, Y.]] | ||
[[Category: Tonozuka, T.]] | [[Category: Tonozuka, T.]] | ||
[[Category: starch binding domain]] | [[Category: starch binding domain]] | ||
''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 00:10:11 2008'' | ||
Revision as of 21:10, 30 March 2008
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| 1uh4, resolution 1.80Å | |||||||||||||
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| Ligands: | BGC, CA, GLC, MPD | ||||||||||||
| Activity: | Alpha-amylase, with EC number 3.2.1.1 | ||||||||||||
| Related: | 1ji1, 1UH2, 1UH3
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Thermoactinomyces vulgaris R-47 alpha-amylase 1/malto-tridecaose complex
Overview
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.
About this Structure
1UH4 is a Single protein structure of sequence from Thermoactinomyces vulgaris. Full crystallographic information is available from OCA.
Reference
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
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