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PDBsum entry 1n3b

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1n3b
Jmol
Contents
Protein chains
176 a.a. *
206 a.a. *
Ligands
SO4 ×10
Waters ×449
* Residue conservation analysis
PDB id:
1n3b
Name: Transferase
Title: Crystal structure of dephosphocoenzyme a kinase from escheri
Structure: Dephospho-coa kinase. Chain: a, b, c. Synonym: dephosphocoenzyme a kinase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: coae. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.217     R-free:   0.246
Authors: N.O'Toole,J.A.R.G.Barbosa,Y.Li,L-W.Hung,A.Matte,M.Cygler,Mon Kingston Bacterial Structural Genomics Initiative (Bsgi)
Key ref:
N.O'Toole et al. (2003). Crystal structure of a trimeric form of dephosphocoenzyme A kinase from Escherichia coli. Protein Sci, 12, 327-336. PubMed id: 12538896 DOI: 10.1110/ps.0227803
Date:
25-Oct-02     Release date:   28-Jan-03    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A6I9  (COAE_ECOLI) -  Dephospho-CoA kinase
Seq:
Struc:
206 a.a.
176 a.a.
Protein chains
Pfam   ArchSchema ?
P0A6I9  (COAE_ECOLI) -  Dephospho-CoA kinase
Seq:
Struc:
206 a.a.
206 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.2.7.1.24  - Dephospho-CoA kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Coenzyme A Biosynthesis (late stages)
      Reaction: ATP + 3'-dephospho-CoA = ADP + CoA
ATP
+ 3'-dephospho-CoA
= ADP
+ CoA
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     phosphorylation   2 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1110/ps.0227803 Protein Sci 12:327-336 (2003)
PubMed id: 12538896  
 
 
Crystal structure of a trimeric form of dephosphocoenzyme A kinase from Escherichia coli.
N.O'Toole, J.A.Barbosa, Y.Li, L.W.Hung, A.Matte, M.Cygler.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Ribbon diagram depicting the E. coli DPCK monomer structure. The LID domain is red and the CoA-binding domain is blue, whereas the rest of the molecule is green. The nucleotide-binding P-loop motif is marked in pink. Secondary structural elements are marked. Figures 1 Go-, 2 Go-, and 4 Go-were produced with Molscript (Kraulis 1991) and Raster3D (Merrit and Bacon 1997).
Figure 2.
Figure 2. Stereo ribbon diagram of the E. coli DPCK trimer structure, looking down the pseudo-threefold axis. The molecule is colored according to the temperature factors of the C[ ]atoms in each residue, from blue (B = 14 2) to orange (B = 60 2). Sulfate ions in the structure are displayed, as well as the side chains of residues Ser-119, Tyr-121, and Lys-122 from each monomer. Sulfates bound to the P-loop motif are shown as space-filling models in green.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2003, 12, 327-336) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21264299 G.Walia, K.Gajendar, and A.Surolia (2011).
Identification of critical residues of the mycobacterial dephosphocoenzyme a kinase by site-directed mutagenesis.
  PLoS One, 6, e15228.  
17962407 S.Nauli, S.Farr, Y.J.Lee, H.Y.Kim, S.Faham, and J.U.Bowie (2007).
Polymer-driven crystallization.
  Protein Sci, 16, 2542-2551.
PDB codes: 2qar 2qb0 2qb1
15526298 A.Seto, K.Murayama, M.Toyama, A.Ebihara, N.Nakagawa, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2005).
ATP-induced structural change of dephosphocoenzyme A kinase from Thermus thermophilus HB8.
  Proteins, 58, 235-242.
PDB code: 1uf9
15908386 B.Wang, and H.K.Kuramitsu (2005).
Inducible antisense RNA expression in the characterization of gene functions in Streptococcus mutans.
  Infect Immun, 73, 3568-3576.  
12837772 A.Matte, J.Sivaraman, I.Ekiel, K.Gehring, Z.Jia, and M.Cygler (2003).
Contribution of structural genomics to understanding the biology of Escherichia coli.
  J Bacteriol, 185, 3994-4002.  
12906818 N.O'Toole, and M.Cygler (2003).
The final player in the coenzyme A biosynthetic pathway.
  Structure, 11, 899-900.  
12837781 T.Izard (2003).
A novel adenylate binding site confers phosphopantetheine adenylyltransferase interactions with coenzyme A.
  J Bacteriol, 185, 4074-4080.
PDB code: 1h1t
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