PDBsum entry: 1g1y

Hydrolase

PDB id: 1g1y

Contents

Protein chains

585 a.a. *

Ligands

BCD ×2

Waters ×523

* Residue conservation analysis

PDB id:

1g1y

Name:

Hydrolase

Title:

Crystal structure of alpha-amylase ii (tvaii) from thermoactinomyces vulgaris r-47 and beta-cyclodextrin complex

Structure:

Alpha-amylase ii. Chain: a, b. Synonym: neopullulanase, tvaii. Engineered: yes. Mutation: yes

Source:

Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

3.00Å R-factor: 0.191 R-free: 0.260

Authors:

S.Kondo,A.Ohtaki,T.Tonozuka,Y.Sakano,S.Kamitori

Key ref:

S.Kondo et al. (2001). Studies on the hydrolyzing mechanism for cyclodextrins of Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structure of the mutant E354A complexed with beta-cyclodextrin, and kinetic analyses on cyclodextrins. J Biochem (tokyo), 129, 423-428. PubMed id: 11226882

Date:

16-Oct-00 Release date: 14-Mar-01

Protein chains

Q08751  (NEPU2_THEVU) -  Neopullulanase 2

Seq: 585 a.a.

Struc: 585 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.2.1.135 - Neopullulanase.
• Reaction: Hydrolysis of pullulan to panose (6-alpha-D-glucosylmaltose).

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (7 terms)

J Biochem (tokyo) 129:423-428 (2001)

PubMed id: 11226882

Studies on the hydrolyzing mechanism for cyclodextrins of Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structure of the mutant E354A complexed with beta-cyclodextrin, and kinetic analyses on cyclodextrins.

S.Kondo, A.Ohtaki, T.Tonozuka, Y.Sakano, S.Kamitori.

ABSTRACT

Crystals of the mutant E354A of Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII) complexed with beta-cyclodextrin were prepared by a soaking method, and the diffraction data were collected at 100 K, using Synchrotron radiation (SPring-8). The crystals belong to an orthorhombic system with the space group P2(1)2(1)2(1) and cell dimensions a = 111.1 A, b = 117.7 A, c = 113.3 A, which is almost isomorphous with crystals of the wild-type TVAII, and the structure was refined to an R-factor = 0.208 (R(free) = 0.252) using 3.0 A resolution data. The refined structure shows that the interactions between Phe286 and two C6 atoms of beta-cyclodextrin at the hydrolyzing site are important for TVAII to recognize cyclodextrins as substrates. This observation from the X-ray structure was supported by kinetic analyses of cyclodextrins using the wild-type TVAII, the mutant F286A and F286L. These studies also suggested that the TVAII-hydrolyzing mechanism for cyclodextrins is slightly different from that for starch.