6J33

Crystal structure of ligand-free of PulA from Klebsiella pneumoniae

• PDB DOI:  https://doi.org/10.2210/pdb6J33/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-01-09 Released: 2019-09-18 
• 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: 1.30 Å
• R-Value Free: 0.154 
• R-Value Work: 0.128 
• R-Value Observed: 0.129 

Literature

Relationship between the induced-fit loop and the activity of Klebsiella pneumoniae pullulanase.

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

(2019) Acta Crystallogr D Struct Biol 75: 792-803

• PubMed: 31478902 
• DOI: https://doi.org/10.1107/S2059798319010660
• Primary Citation of Related Structures:  
  6J33, 6J34, 6J35, 6J4H


• PubMed Abstract: 
  

Klebsiella pneumoniae pullulanase (KPP) belongs to glycoside hydrolase family 13 subfamily 13 (GH13_13) and is the only enzyme that is reported to perform an induced-fit motion of the active-site loop (residues 706-710). Comparison of pullulanase structures indicated that only KPP has Leu680 present behind the loop, in contrast to the glycine found in other GH13_13 members. Analysis of the structure and activity of recombinant pullulanase from K. pneumoniae ATCC 9621 (rKPP) and its mutant (rKPP-G680L) indicated that the side chain of residue 680 is important for the induced-fit motion of the loop 706-710 and alters the binding affinity of the substrate.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 229.97 kDa 
• Atom Count: 20,463 
• Modelled Residue Count: 2,098 
• Deposited Residue Count: 2,106 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pullulanase	A, B	1,053	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: pulA, BN49_4178, SAMEA3512100_03461 EC: 3.2.1.41
UniProt
Find proteins for W9BQ28 (Klebsiella pneumoniae) Explore W9BQ28  Go to UniProtKB:  W9BQ28

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], N [auth A], O [auth A], P [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	BA [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	AA [auth B], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.154 
• R-Value Work: 0.128 
• R-Value Observed: 0.129 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.357	α = 96.7
b = 80.276	β = 102.3
c = 127.741	γ = 112.1

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-18 
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	JP16H04909

Revision History  

• Version 1.0: 2019-09-18
  Type: Initial release