1N3B

Crystal Structure of Dephosphocoenzyme A kinase from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.217 

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This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of a Trimeric Form of Dephosphocoenzyme A Kinase from Escherichia coli

O'Toole, N.Barbosa, J.A.R.G.Li, Y.Hung, L.-W.Matte, A.Cygler, M.

(2003) Protein Sci. 12: 327-336

  • DOI: 10.1110/ps.0227803

  • PubMed Abstract: 
  • Coenzyme A (CoA) is an essential cofactor used in a wide variety of biochemical pathways. The final step in the biosynthesis of CoA is catalyzed by dephosphocoenzyme A kinase (DPCK, E.C. 2.7.1.24). Here we report the crystal structure of DPCK from Es ...

    Coenzyme A (CoA) is an essential cofactor used in a wide variety of biochemical pathways. The final step in the biosynthesis of CoA is catalyzed by dephosphocoenzyme A kinase (DPCK, E.C. 2.7.1.24). Here we report the crystal structure of DPCK from Escherichia coli at 1.8 A resolution. This enzyme forms a tightly packed trimer in its crystal state, in contrast to its observed monomeric structure in solution and to the monomeric, homologous DPCK structure from Haemophilus influenzae. We have confirmed the existence of the trimeric form of the enzyme in solution using gel filtration chromatography measurements. Dephospho-CoA kinase is structurally similar to many nucleoside kinases and other P-loop-containing nucleotide triphosphate hydrolases, despite having negligible sequence similarity to these enzymes. Each monomer consists of five parallel beta-strands flanked by alpha-helices, with an ATP-binding site formed by a P-loop motif. Orthologs of the E. coli DPCK sequence exist in a wide range of organisms, including humans. Multiple alignment of orthologous DPCK sequences reveals a set of highly conserved residues in the vicinity of the nucleotide/CoA binding site.


    Related Citations: 
    • Crystal Structure of Dephospho-coenzyme A Kinase from Haemophilus influenzae
      Oblomova, G.,Teplyakov, A.,Bonander, N.,Eisenstein, E.,Howard, A.,Gilliland, G.
      (2001) J.Struct.Biol. 136: 119
    • The structure of a Trimeric Archael Adenylate Kinase
      Vorhein, C.,Bonisch, H.,Schafer, G.,Schulz, G.E.
      (1998) J.Mol.Biol. 282: 167
    • Identification and Characterization of the Gene Encoding the Human Adenylyltransferase and Dephosphocoenzyme A Kinase Bifunctional Enzyme
      Aghajanian, S.,Worral, D.M.
      (2002) Biochem.J. 365: 13
    • A Bifunctional Enzyme Complex in Coenzyme A Biosynthesis: Purification of Pantetheine Phosphate Adenylyltransferase and Dephospho-CoA Kinase
      Worral, D.M.,Tubbs, P.K.
      (1983) Biochem.J. 215: 153
    • Identification of yace (coaE) as the Structural Gene for Dephosphocoenzyme A Kinase in Escherichia coli K-12
      Mishra, P.K.,Park, P.K.,Drueckhammer, D.G.
      (2001) J.Bacteriol. 183: 2774


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dephospho-CoA kinase
A, B, C
216Escherichia coli (strain K12)Gene Names: coaE (yacE)
EC: 2.7.1.24
Find proteins for P0A6I9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6I9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.500α = 90.00
b = 82.410β = 94.77
c = 76.000γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-28
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-04-16
    Type: Data collection
  • Version 1.4: 2017-02-01
    Type: Structure summary