5YND

Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 1 mM gamma-cyclodextrin

Summary for 5YND

• Entry DOI: 10.2210/pdb5ynd/pdb
• Related PRD ID: PRD_900010
• Descriptor: DUF3372 domain-containing protein, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, CALCIUM ION, ... (6 entities in total)
• Functional Keywords: hydrolase, alpha-amylase, pullulanase, klebsiella pneumoniae, crystal, gamma-cyclodextrin, co-crystallization
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 1
• Total formula weight: 120858.60

Authors

Saka, N.,Iwamoto, H.,Takahashi, N.,Mizutani, K.,Mikami, B. (deposition date: 2017-10-24, release date: 2018-10-24, Last modification date: 2024-10-30)

Primary citation

Saka, N.,Iwamoto, H.,Malle, D.,Takahashi, N.,Mizutani, K.,Mikami, B.
Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin
Acta Crystallogr D Struct Biol, 74:1115-1123, 2018

PubMed Abstract: Crystal structures of Klebsiella pneumoniae pullulanase (KPP) in complex with α-cyclodextrin (α-CD), β-cyclodextrin (β-CD) and γ-cyclodextrin (γ-CD) were refined at around 1.98-2.59 Å resolution from data collected at SPring-8. In the structures of the complexes obtained with 1 mM α-CD or γ-CD, one molecule of CD was found at carbohydrate-binding module 41 only (CBM41). In the structures of the complexes obtained with 1 mM β-CD or with 10 mM α-CD or γ-CD, two molecules of CD were found at CBM41 and in the active-site cleft, where the hydrophobic residue of Phe746 occupies the inside cavity of the CD rings. In contrast to α-CD and γ-CD, one β-CD molecule was found at the active site only in the presence of 0.1 mM β-CD. These results were coincident with the solution experiments, which showed that β-CD inhibits this enzyme more than a thousand times more potently than α-CD and γ-CD. The strong inhibition of β-CD is caused by the optimized interaction between β-CD and the side chain of Phe746. The increased K values of the F746A mutant for β-CD supported the importance of Phe746 in the strong interaction of pullulanase with β-CD.

PubMed: 30387770
DOI: 10.1107/S2059798318014523

Experimental method

X-RAY DIFFRACTION (2.227 Å)