Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 120.92 kDa 
• Atom Count: 8783 
• Modelled Residue Count: 1055 
• Deposited Residue Count: 1102 
• Unique protein chains: 1

5YNA

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

• PDB DOI: 10.2210/pdb5YNA/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Mutation(s): No 


• Deposited: 2017-10-24 Released: 2018-10-24 
• Deposition Author(s): Saka, N., Iwamoto, H., Takahashi, N., Mizutani, K., Mikami, B.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.240 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin

Saka, N., Iwamoto, H., Malle, D., Takahashi, N., Mizutani, K., Mikami, B.

(2018) Acta Crystallogr D Struct Biol 74: 1115-1123

• PubMed: 30387770 
• DOI: 10.1107/S2059798318014523
• Primary Citation of Related Structures:  
  5YN2, 5YN7, 5YNA, 5YNC, 5YND, 5YNE, 5YNH


• 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 _i values of the F746A mutant for β-CD supported the importance of Phe746 in the strong interaction of pullulanase with β-CD.

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Organizational Affiliation: 

Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PulA protein	A	1102	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: pulA, BANRA_01860, BN49_4178, C3F39_10140, DD583_02940, SAMEA3512100_03461 EC: 3.2.1.41
UniProt
Find proteins for W9BQ28 (Klebsiella pneumoniae) Explore W9BQ28  Go to UniProtKB:  W9BQ28

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
Cyclohexakis-(1-4)-(alpha-D-glucopyranose)	B	6		N/A
Glycosylation Resources
GlyTouCan:  G22307HL GlyCosmos:  G22307HL

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	J [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	K [auth A], L [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900015	B	alpha-cyclodextrin	Oligosaccharide / Drug delivery		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.240 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.278	α = 90
b = 89.278	β = 90
c = 299.375	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-10-24 
• Released Date: 2018-10-24 
Deposition Author(s): Saka, N., Iwamoto, H., Takahashi, N., Mizutani, K., Mikami, B.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	16H04909

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2018-11-14
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary