Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 73073.59 
• Atom Count: 4597 
• Residue Count: 648 
• Unique protein chains: 1

1N3B

Crystal Structure of Dephosphocoenzyme A kinase from Escherichia coli

• DOI: 10.2210/pdb1N3B/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli


• Deposited: 2002-10-25 Released: 2003-01-28 
• Deposition Author(s): O'Toole, N., Barbosa, J.A.R.G., Li, Y., Hung, L.-W., Matte, A., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

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Experimental Data Snapshot

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

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

• PubMed: 12538896 
• 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 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.

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Related Citations: 

• 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 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
• 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
• 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
• The structure of a Trimeric Archael Adenylate Kinase
  Vorhein, C.,Bonisch, H.,Schafer, G.,Schulz, G.E.
  (1998) J.Mol.Biol. 282: 167




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Dephospho-CoA kinase	A, B, C	216	Escherichia coli (strain K12)	Mutation(s): 0  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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B, C	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 55.500	α = 90.00
b = 82.410	β = 94.77
c = 76.000	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-10-25 
• Released Date: 2003-01-28 
• Deposition Author(s): O'Toole, N., Barbosa, J.A.R.G., Li, Y., Hung, L.-W., Matte, A., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

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