6J33

Crystal structure of ligand-free of PulA from Klebsiella pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.297 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • DOI: 10.1107/S2059798319010660
  • Primary Citation of Related Structures:  

  • 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 str ...

    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.,Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, Gakuen-cho, Fukuyama, Hiroshima 729-0292, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
pullulanase
A, B
1053Klebsiella pneumoniaeMutation(s): 0 
Gene Names: pulA
EC: 3.2.1.41
Find proteins for W9BQ28 (Klebsiella pneumoniae)
Go to UniProtKB:  W9BQ28
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.297 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.128 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 60.357α = 96.70
b = 80.276β = 102.30
c = 127.741γ = 112.10
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data collection
SCALAdata scaling
DENZOdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP16H04909

Revision History 

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