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PDBsum entry 1jjv

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protein ligands metals links
Transferase PDB id
1jjv
Jmol
Contents
Protein chain
194 a.a. *
Ligands
SO4
ATP
Metals
_HG
Waters ×207
* Residue conservation analysis
PDB id:
1jjv
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.
Resolution:
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
Date:
09-Jul-01     Release date:   01-May-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: 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
Bound ligand (Het Group name = ATP)
corresponds exactly
+ 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: 10.1006/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.
 
  ABSTRACT  
 
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.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.