Crystal Structure of maltotriose-complex of PulA-G680L mutant from Klebsiella pneumoniae

Experimental Data Snapshot

  • Resolution: 1.64 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report

This is version 2.0 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pullulanase1,053Klebsiella pneumoniaeMutation(s): 1 
Gene Names: pulA
Find proteins for W9BQ28 (Klebsiella pneumoniae)
Explore W9BQ28 
Go to UniProtKB:  W9BQ28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW9BQ28
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
B, C
Glycosylation Resources
GlyTouCan:  G96370VA
GlyCosmos:  G96370VA
GlyGen:  G96370VA
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 1.64 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.943α = 90
b = 60.103β = 114.66
c = 133.962γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
HKL-2000data collection

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP16H04909

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary