4GI7

Crystal structure of Klebsiella pneumoniae pantothenate kinase in complex with a pantothenate analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of Klebsiella pneumoniae pantothenate kinase in complex with N-substituted pantothenamides.

Li, B.Tempel, W.Smil, D.Bolshan, Y.Schapira, M.Park, H.W.

(2013) Proteins 81: 1466-1472

  • DOI: 10.1002/prot.24290
  • Primary Citation of Related Structures:  4F7W

  • PubMed Abstract: 
  • N-Substituted pantothenamides are derivatives of pantothenate, the precursor in the biosynthesis of the essential metabolic cofactor coenzyme A (CoA). These compounds are substrates of pantothenate kinase (PanK) in the first step of CoA biosynthesis ...

    N-Substituted pantothenamides are derivatives of pantothenate, the precursor in the biosynthesis of the essential metabolic cofactor coenzyme A (CoA). These compounds are substrates of pantothenate kinase (PanK) in the first step of CoA biosynthesis and possess antimicrobial activity against various pathogenic bacteria. Here we solved the crystal structure of the Klebsiella pneumoniae PanK (KpPanK) in complex with N-pentylpantothenamide (N5-Pan) to understand the molecular basis of its antimicrobial activity. The structure reveals a polar pocket interacting with the pantothenate moiety of N5-Pan and an aromatic pocket loosely protecting the pentyl tail, suggesting that the introduction of an aromatic ring to a new pantothenamide may enhance the compound's affinity to KpPanK. To test this idea, we synthesized N-pyridin-3-ylmethylpantothenamide (Np-Pan) and solved its co-crystal structure with KpPanK. The structure reveals two alternat conformations of the aromatic ring of Np-Pan bound at the aromatic pocket, providing the basis for further improvement of pantothenamide binding to KpPanK.


    Organizational Affiliation

    Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pantothenate kinase
A, C, B, D, E, F, G, H
334Klebsiella pneumoniae (strain 342)Gene Names: coaA
EC: 2.7.1.33
Find proteins for B5XYG3 (Klebsiella pneumoniae (strain 342))
Go to UniProtKB:  B5XYG3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
0JR
Query on 0JR

Download SDF File 
Download CCD File 
A, B, C, D, F
(2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(pyridin-3-ylmethyl)amino]propyl}butanamide
C15 H23 N3 O4
VXNNKPMWKMAMDX-ZDUSSCGKSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000903 (0JR)
Query on PRD_000903
A,B,C,D,F(2R)-2,4-DIHYDROXY-3,3-DIMETHYL-N-{3-OXO-3-[(PYRIDIN-3-YLMETHYL)AMINO]PROPYL}BUTANAMIDENon-polymer / Antibiotic, Antimicrobial

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 127.928α = 90.00
b = 130.938β = 90.00
c = 193.022γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-04-17
    Type: Database references
  • Version 1.2: 2013-08-07
    Type: Database references