1SQ5

Crystal Structure of E. coli Pantothenate kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of the pantothenate kinase.ADP.pantothenate ternary complex reveals the relationship between the binding sites for substrate, allosteric regulator, and antimetabolites.

Ivey, R.A.Zhang, Y.-M.Virga, K.G.Hevener, K.Lee, R.E.Rock, C.O.Jackowski, S.Park, H.-W.

(2004) J.Biol.Chem. 279: 35622-35629

  • DOI: 10.1074/jbc.M403152200

  • PubMed Abstract: 
  • Pantothenate kinase catalyzes the first step in the biosynthesis of coenzyme A, the major acyl group carrier in biology. In bacteria, regulation of pantothenate kinase activity is a major factor in controlling intracellular coenzyme A levels, and pan ...

    Pantothenate kinase catalyzes the first step in the biosynthesis of coenzyme A, the major acyl group carrier in biology. In bacteria, regulation of pantothenate kinase activity is a major factor in controlling intracellular coenzyme A levels, and pantothenate analogs are growth-inhibiting antimetabolites. We have extended the structural information on Escherichia coli pantothenate kinase by determining the structure of the enzyme.ADP. pantothenate ternary complex. Pantothenate binding induces a significant conformational change in amino acids 243-263, which form a "lid" that folds over the open pantothenate binding groove. The positioning of the substrates suggests the reaction proceeds by a concerted mechanism that involves a dissociative transition state, although the negative charge neutralization of the gamma-phosphate by Arg-243, Lys-101, and Mg(2+) coupled with hydrogen bonding of the C1 of pantothenate to Asp-127 suggests different interpretations of the phosphoryl transfer mechanism of pantothenate kinase. N-alkylpantothenamides are substrates for pantothenate kinase. Modeling these antimetabolites into the pantothenate active site predicts that they bind in the same orientation as pantothenate with their alkyl chains interacting with the hydrophobic dome over the pantothenate pocket, which is also accessed by the beta-mercaptoethylamine moiety of the allosteric regulator, coenzyme A. These structural/biochemical studies illustrate the intimate relationship between the substrate, allosteric regulator, and antimetabolite binding sites on pantothenate kinase and provide a framework for studies of its catalysis and feedback regulation.


    Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pantothenate kinase
A, B, C, D
308Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: coaA (panK, rts)
EC: 2.7.1.33
Find proteins for P0A6I3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6I3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

Download SDF File 
Download CCD File 
A, B, C, D
PANTOTHENOIC ACID
N-[(2R)-2,4-DIHYDROXY-3,3-DIMETHYLBUTANOYL]-BETA-ALANINE
C9 H17 N O5
GHOKWGTUZJEAQD-ZETCQYMHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 181.203α = 90.00
b = 181.655β = 104.79
c = 47.418γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance