4NB4

Pantothenamide-bound Pantothenate kinase from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural characterization of a new N-substituted pantothenamide bound to pantothenate kinases from Klebsiella pneumoniae and Staphylococcus aureus.

Hughes, S.J.Antoshchenko, T.Kim, K.P.Smil, D.Park, H.W.

(2014) Proteins 82: 1542-1548

  • DOI: 10.1002/prot.24524
  • Primary Citation of Related Structures:  
    4NE2, 4NB4

  • PubMed Abstract: 
  • Pantothenate kinase (PanK) is the rate-limiting enzyme in Coenzyme A biosynthesis, catalyzing the ATP-dependent phosphorylation of pantothenate. We solved the co-crystal structures of PanKs from Staphylococcus aureus (SaPanK) and Klebsiella pneumonia ...

    Pantothenate kinase (PanK) is the rate-limiting enzyme in Coenzyme A biosynthesis, catalyzing the ATP-dependent phosphorylation of pantothenate. We solved the co-crystal structures of PanKs from Staphylococcus aureus (SaPanK) and Klebsiella pneumonia (KpPanK) with N-[2-(1,3-benzodioxol-5-yl)ethyl] pantothenamide (N354-Pan). Two different N354-Pan conformers interact with polar/nonpolar mixed residues in SaPanK and aromatic residues in KpPanK. Additionally, phosphorylated N354-Pan is found at the closed active site of SaPanK but not at the open active site of KpPanK, suggesting an exchange of the phosphorylated product with a new N354-Pan only in KpPanK. Together, pantothenamides conformational flexibility and binding pocket are two key considerations for selective compound design.


    Organizational Affiliation

    Department of Pharmacology, University of Toronto, Toronto, Ontario, M5G 1L7.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Type II pantothenate kinaseABCDEFGH285Staphylococcus aureus subsp. aureus MRSA252Mutation(s): 0 
Gene Names: coaAcoaW
EC: 2.7.1.33
Find proteins for Q6G7I0 (Staphylococcus aureus (strain MSSA476))
Explore Q6G7I0 
Go to UniProtKB:  Q6G7I0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SH3
Query on SH3

Download CCD File 
A, C, F, G, H
N-[2-(1,3-benzodioxol-5-yl)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide
C18 H27 N2 O9 P
OQCPPROGRWYIDC-INIZCTEOSA-N
 Ligand Interaction
ADP
Query on ADP

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

Download CCD File 
A, B, C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.01α = 90
b = 70.74β = 90.64
c = 143.115γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-06-25
    Changes: Database references