PDBsum entry 1jjv

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Transferase PDB id
Protein chain
194 a.a. *
Waters ×207
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Dephospho-coa kinase in complex with atp
Structure: Dephospho-coa kinase. Chain: a. Synonym: dephosphocoenzyme a kinase. Engineered: yes
Source: Haemophilus influenzae. Organism_taxid: 727. Gene: yace. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
2.00Å     R-factor:   0.168     R-free:   0.218
Authors: G.Obmolova,A.Teplyakov,N.Bonander,E.Eisenstein,A.J.Howard, G.L.Gilliland,Structure 2 Function Project (S2f)
Key ref: G.Obmolova et al. (2001). Crystal structure of dephospho-coenzyme A kinase from Haemophilus influenzae. J Struct Biol, 136, 119-125. PubMed id: 11886213 DOI: 10.1006/jsbi.2001.4428
09-Jul-01     Release date:   01-May-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P44920  (COAE_HAEIN) -  Dephospho-CoA kinase
206 a.a.
194 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Dephospho-CoA kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Coenzyme A Biosynthesis (late stages)
      Reaction: ATP + 3'-dephospho-CoA = ADP + CoA
Bound ligand (Het Group name = ATP)
corresponds exactly
+ 3'-dephospho-CoA
+ 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  


DOI no: 10.1006/jsbi.2001.4428 J Struct Biol 136:119-125 (2001)
PubMed id: 11886213  
Crystal structure of dephospho-coenzyme A kinase from Haemophilus influenzae.
G.Obmolova, A.Teplyakov, N.Bonander, E.Eisenstein, A.J.Howard, G.L.Gilliland.
Dephospho-coenzyme A kinase catalyzes the final step in CoA biosynthesis, the phosphorylation of the 3'-hydroxyl group of ribose using ATP as a phosphate donor. The protein from Haemophilus influenzae was cloned and expressed, and its crystal structure was determined at 2.0-A resolution in complex with ATP. The protein molecule consists of three domains: the canonical nucleotide-binding domain with a five-stranded parallel beta-sheet, the substrate-binding alpha-helical domain, and the lid domain formed by a pair of alpha-helices. The overall topology of the protein resembles the structures of nucleotide kinases. ATP binds in the P-loop in a manner observed in other kinases. The CoA-binding site is located at the interface of all three domains. The double-pocket structure of the substrate-binding site is unusual for nucleotide kinases. Amino acid residues implicated in substrate binding and catalysis have been identified. The structure analysis suggests large domain movements during the catalytic cycle.

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.  
18618710 Q.Chang, X.X.Yan, S.Y.Gu, J.F.Liu, and D.C.Liang (2008).
Crystal structure of human phosphomevalonate kinase at 1.8 A resolution.
  Proteins, 73, 254-258.
PDB code: 3ch4
17603993 C.Wadler, and J.E.Cronan (2007).
Dephospho-CoA kinase provides a rapid and sensitive radiochemical assay for coenzyme A and its thioesters.
  Anal Biochem, 368, 17-23.  
17902708 T.J.Herdendorf, and H.M.Miziorko (2007).
Functional evaluation of conserved basic residues in human phosphomevalonate kinase.
  Biochemistry, 46, 11780-11788.  
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
12756245 J.Armengaud, B.Fernandez, V.Chaumont, F.Rollin-Genetet, S.Finet, C.Marchetti, H.Myllykallio, C.Vidaud, J.L.Pellequer, S.Gribaldo, P.Forterre, and P.Gans (2003).
Identification, purification, and characterization of an eukaryotic-like phosphopantetheine adenylyltransferase (coenzyme A biosynthetic pathway) in the hyperthermophilic archaeon Pyrococcus abyssi.
  J Biol Chem, 278, 31078-31087.  
12906824 N.Manoj, E.Strauss, T.P.Begley, and S.E.Ealick (2003).
Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution.
  Structure, 11, 927-936.
PDB code: 1p9o
12538896 N.O'Toole, J.A.Barbosa, Y.Li, L.W.Hung, A.Matte, and M.Cygler (2003).
Crystal structure of a trimeric form of dephosphocoenzyme A kinase from Escherichia coli.
  Protein Sci, 12, 327-336.
PDB code: 1n3b
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
12866051 Y.Y.Kuttner, V.Sobolev, A.Raskind, and M.Edelman (2003).
A consensus-binding structure for adenine at the atomic level permits searching for the ligand site in a wide spectrum of adenine-containing complexes.
  Proteins, 52, 400-411.  
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