6J33

Crystal structure of ligand-free of PulA from Klebsiella pneumoniae


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 

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:  
    6J34, 6J33, 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
pullulanaseA, B1053Klebsiella pneumoniaeMutation(s): 0 
Gene Names: pulABANRA_01860BN49_4178C2U49_24295C3F39_10140DD583_02940F3G17_17450SAMEA3673122_01849
EC: 3.2.1.41
UniProt
Find proteins for W9BQ28 (Klebsiella pneumoniae)
Explore W9BQ28 
Go to UniProtKB:  W9BQ28
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth B] , C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , 
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
 Ligand Interaction
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 = 60.357α = 96.7
b = 80.276β = 102.3
c = 127.741γ = 112.1
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
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