1JI2

Improved X-ray Structure of Thermoactinomyces vulgaris R-47 alpha-Amylase 2

Summary for 1JI2

• Entry DOI: 10.2210/pdb1ji2/pdb
• Related: 1BVZ 1JI1
• Descriptor: ALPHA-AMYLASE II, CALCIUM ION (3 entities in total)
• Functional Keywords: beta/alpha barrel, hydrolase
• Biological source: Thermoactinomyces vulgaris
• Total number of polymer chains: 2
• Total formula weight: 135188.37

Authors

Kamitori, S.,Abe, A.,Ohtaki, A.,Kaji, A.,Tonozuka, T.,Sakano, Y. (deposition date: 2001-06-28, release date: 2002-06-05, Last modification date: 2024-03-13)

Primary citation

Kamitori, S.,Abe, A.,Ohtaki, A.,Kaji, A.,Tonozuka, T.,Sakano, Y.
Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution.
J.Mol.Biol., 318:443-453, 2002

PubMed Abstract: The X-ray crystal structures of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) and alpha-amylase 2 (TVAII) have been determined at 1.6 A and 2.3 A resolution, respectively. The structures of TVAI and TVAII have been refined, R-factor of 0.182 (R(free)=0.206) and 0.179 (0.224), respectively, with good chemical geometries. Both TVAI and TVAII have four domains, N, A, B and C, and all very similar in structure. However, there are some differences in the structures between them. Domain N of TVAI interacts strongly with domains A and B, giving a spherical shape structure to the enzyme, while domain N of TVAII is isolated from the other domains, which leads to the formation of a dimer. TVAI has three bound Ca ions, whereas TVAII has only one. TVAI has eight extra loops compared to TVAII, while TVAII has two extra loops compared to TVAI. TVAI can hydrolyze substrates more efficiently than TVAII with a high molecular mass such as starch, while TVAII is much more active against cyclodextrins than TVAI and other alpha-amylases. A structural comparison of the active sites has clearly revealed this difference in substrate specificity.

PubMed: 12051850
DOI: 10.1016/S0022-2836(02)00111-0

Experimental method

X-RAY DIFFRACTION (2.3 Å)