4NE2

Pantothenamide-bound Pantothenate Kinase from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb4NE2/pdb

• Classification: TRANSFERASE
• Organism(s): Klebsiella pneumoniae 342
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-10-28 Released: 2014-02-26 
• Deposition Author(s): Hughes, S.J., Antoshchenko, T., Kim, K.P., Smil, D., Park, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.214 
• R-Value Work: 0.154 
• R-Value Observed: 0.157 

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

• PubMed: 24470271 
• DOI: https://doi.org/10.1002/prot.24524
• Primary Citation of Related Structures:  
  4NB4, 4NE2


• 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 (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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78.56 kDa 
• Atom Count: 5,569 
• Modelled Residue Count: 605 
• Deposited Residue Count: 668 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pantothenate kinase	A, B	334	Klebsiella pneumoniae 342	Mutation(s): 0  Gene Names: coaA, KPK_5321, UUU_44690 EC: 2.7.1.33
UniProt
Find proteins for B5XYG3 (Klebsiella pneumoniae (strain 342)) Explore B5XYG3  Go to UniProtKB:  B5XYG3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SH2	D [auth A], G [auth B]	(R)-N-(3-((2-(benzo[d][1,3]dioxol-5-yl)ethyl)amino)-3-oxopropyl)-2,4-dihydroxy-3,3-dimethylbutanamide C18 H26 N2 O6 WTOXXQQUHIAOIP-INIZCTEOSA-N
MG	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.214 
• R-Value Work: 0.154 
• R-Value Observed: 0.157 
• Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.765	α = 90
b = 180.366	β = 90
c = 181.488	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Hughes, S.J., Antoshchenko, T., Kim, K.P., Smil, D., Park, H.W.

Revision History  

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2014-06-25
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description