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PDBsum entry 2f9t

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protein Protein-protein interface(s) links
Transferase PDB id
2f9t
Jmol
Contents
Protein chains
241 a.a. *
Waters ×180
* Residue conservation analysis
PDB id:
2f9t
Name: Transferase
Title: Structure of the type iii coaa from pseudomonas aeruginosa
Structure: Pantothenate kinase. Chain: a, b. Engineered: yes
Source: Pseudomonas aeruginosa. Organism_taxid: 208964. Strain: pao1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.227     R-free:   0.268
Authors: R.Leonardi,M.K.Yun,S.Chohnan,S.W.White,C.O.Rock,S.Jackowski
Key ref:
B.S.Hong et al. (2006). Prokaryotic type II and type III pantothenate kinases: The same monomer fold creates dimers with distinct catalytic properties. Structure, 14, 1251-1261. PubMed id: 16905099 DOI: 10.1016/j.str.2006.06.008
Date:
06-Dec-05     Release date:   22-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9HWC1  (COAX_PSEAE) -  Type III pantothenate kinase
Seq:
Struc:
248 a.a.
241 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.1.33  - Pantothenate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Coenzyme A Biosynthesis (late stages)
      Reaction: ATP + (R)-pantothenate = ADP + (R)-4'-phosphopantothenate
ATP
+ (R)-pantothenate
= ADP
+ (R)-4'-phosphopantothenate
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     response to antibiotic   3 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2006.06.008 Structure 14:1251-1261 (2006)
PubMed id: 16905099  
 
 
Prokaryotic type II and type III pantothenate kinases: The same monomer fold creates dimers with distinct catalytic properties.
B.S.Hong, M.K.Yun, Y.M.Zhang, S.Chohnan, C.O.Rock, S.W.White, S.Jackowski, H.W.Park, R.Leonardi.
 
  ABSTRACT  
 
Three distinct isoforms of pantothenate kinase (CoaA) in bacteria catalyze the first step in coenzyme A biosynthesis. The structures of the type II (Staphylococcus aureus, SaCoaA) and type III (Pseudomonas aeruginosa, PaCoaA) enzymes reveal that they assemble nearly identical subunits with actin-like folds into dimers that exhibit distinct biochemical properties. PaCoaA has a fully enclosed pantothenate binding pocket and requires a monovalent cation to weakly bind ATP in an open cavity that does not interact with the adenine nucleotide. Pantothenate binds to an open pocket in SaCoaA that strongly binds ATP by using a classical P loop architecture coupled with specific interactions with the adenine moiety. The PaCoaA*Pan binary complex explains the resistance of bacteria possessing this isoform to the pantothenamide antibiotics, and the similarity between SaCoaA and human pantothenate kinase 2 explains the molecular basis for the development of the neurodegenerative phenotype in three mutations in the human protein.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. The Adenine Binding Sites of SaCoaA and PaCoaA
(A) SaCoaA containing the AMP-PNP•Mg^2+ molecule from the crystal structure (gray carbons in stick representation) is shown; the interactions of the adenine ring with Tyr137 and Leu28/Leu11 are also shown. Gln125 forms a hydrogen bond with the ribose hydroxyl.
(B) PaCoaA is shown with the adenine from the SaCoaA structure modeled into the active site. The adenine projects into a large cavity, created by the twisting of helix α5 relative to SaCoaA, that is lined with arginine residues. The specific hydrophobic interactions with the adenine ring that are common in kinases are not evident in PaCoaA.
Figure 7.
Figure 7. The Pantothenate Binding Pockets in PaCoaA and SaCoaA
(A) A stereoview of the PaCoaA•Pan binary complex showing the major hydrogen bonding and van der Waals interactions described in the text. The pocket lies at the dimer interface, and Pan is shown with cyan carbons in stick representation. Note that the carboxyl terminal end of Pan (top) is fully enclosed by the protein.
(B) Modeling of pantothenate into the SaCoaA structure. The binding pocket is open to solvent, allowing the pantothenamide antimetabolites with extensions on the carboxy terminus of pantothenate to be accommodated.
 
  The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 1251-1261) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19854913 M.Takagi, H.Tamaki, Y.Miyamoto, R.Leonardi, S.Hanada, S.Jackowski, and S.Chohnan (2010).
Pantothenate kinase from the thermoacidophilic archaeon Picrophilus torridus.
  J Bacteriol, 192, 233-241.  
20797618 R.Leonardi, Y.M.Zhang, M.K.Yun, R.Zhou, F.Y.Zeng, W.Lin, J.Cui, T.Chen, C.O.Rock, S.W.White, and S.Jackowski (2010).
Modulation of pantothenate kinase 3 activity by small molecules that interact with the substrate/allosteric regulatory domain.
  Chem Biol, 17, 892-902.
PDB code: 3mk6
19763307 A.S.Rowan, N.I.Nicely, N.Cochrane, W.A.Wlassoff, A.Claiborne, and C.J.Hamilton (2009).
Nucleoside triphosphate mimicry: a sugar triazolyl nucleoside as an ATP-competitive inhibitor of B. anthracis pantothenate kinase.
  Org Biomol Chem, 7, 4029-4036.  
19602483 Z.Wu, C.Li, S.Lv, and B.Zhou (2009).
Pantothenate kinase-associated neurodegeneration: insights from a Drosophila model.
  Hum Mol Genet, 18, 3659-3672.  
18641144 C.Paige, S.D.Reid, P.C.Hanna, and A.Claiborne (2008).
The type III pantothenate kinase encoded by coaX is essential for growth of Bacillus anthracis.
  J Bacteriol, 190, 6271-6275.  
17631502 B.S.Hong, G.Senisterra, W.M.Rabeh, M.Vedadi, R.Leonardi, Y.M.Zhang, C.O.Rock, S.Jackowski, and H.W.Park (2007).
Crystal structures of human pantothenate kinases. Insights into allosteric regulation and mutations linked to a neurodegeneration disorder.
  J Biol Chem, 282, 27984-27993.
PDB codes: 2i7n 2i7p
17323930 N.I.Nicely, D.Parsonage, C.Paige, G.L.Newton, R.C.Fahey, R.Leonardi, S.Jackowski, T.C.Mallett, and A.Claiborne (2007).
Structure of the type III pantothenate kinase from Bacillus anthracis at 2.0 A resolution: implications for coenzyme A-dependent redox biology.
  Biochemistry, 46, 3234-3245.
PDB code: 2h3g
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