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PDBsum entry 1od6

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protein ligands links
Transferase PDB id
1od6
Jmol
Contents
Protein chain
155 a.a. *
Ligands
PNS
SO4 ×3
Waters ×162
* Residue conservation analysis
PDB id:
1od6
Name: Transferase
Title: The crystal structure of phosphopantetheine adenylyltransferase from thermus thermophilus in complex with 4'-phosphopantetheine
Structure: Phosphopantetheine adenylyltransferase. Chain: a. Synonym: ppat. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Hexamer (from PDB file)
Resolution:
1.5Å     R-factor:   0.196     R-free:   0.201
Authors: H.Takahashi,E.Inagaki,M.Miyano,T.Tahirov
Key ref:
H.Takahashi et al. (2004). Structure and implications for the thermal stability of phosphopantetheine adenylyltransferase from Thermus thermophilus. Acta Crystallogr D Biol Crystallogr, 60, 97. PubMed id: 14684898 DOI: 10.1107/S0907444903025319
Date:
13-Feb-03     Release date:   13-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5SJS9  (COAD_THET8) -  Phosphopantetheine adenylyltransferase
Seq:
Struc:
160 a.a.
155 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.3  - Pantetheine-phosphate adenylyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Coenzyme A Biosynthesis (late stages)
      Reaction: ATP + pantetheine 4'-phosphate = diphosphate + 3'-dephospho-CoA
ATP
+
pantetheine 4'-phosphate
Bound ligand (Het Group name = PNS)
corresponds exactly
= diphosphate
+ 3'-dephospho-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     biosynthetic process   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444903025319 Acta Crystallogr D Biol Crystallogr 60:97 (2004)
PubMed id: 14684898  
 
 
Structure and implications for the thermal stability of phosphopantetheine adenylyltransferase from Thermus thermophilus.
H.Takahashi, E.Inagaki, Y.Fujimoto, C.Kuroishi, Y.Nodake, Y.Nakamura, F.Arisaka, K.Yutani, S.Kuramitsu, S.Yokoyama, M.Yamamoto, M.Miyano, T.H.Tahirov.
 
  ABSTRACT  
 
Phosphopantetheine adenylyltransferase (PPAT) is an essential enzyme in bacteria that catalyzes the rate-limiting step in coenzyme A (CoA) biosynthesis by transferring an adenylyl group from ATP to 4'-phosphopantetheine (Ppant), yielding 3'-dephospho-CoA (dPCoA). The crystal structure of PPAT from Thermus thermophilus HB8 (Tt PPAT) complexed with Ppant has been determined by the molecular-replacement method at 1.5 A resolution. The overall fold of the enzyme is almost the same as that of Escherichia coli PPAT, a hexamer having point group 32. The asymmetric unit of Tt PPAT contains a monomer and the crystallographic triad and dyad coincide with the threefold and twofold axes of the hexamer, respectively. Most of the important atoms surrounding the active site in E. coli PPAT are conserved in Tt PPAT, indicating similarities in their substrate binding and enzymatic reaction. The notable difference between E. coli PPAT and Tt PPAT is the simultaneous substrate recognition by all six subunits of Tt PPAT compared with substrate recognition by only three subunits in E. coli PPAT. Comparative analysis also revealed that the higher stability of Tt PPAT arises from stabilization of each subunit by hydrophobic effects, hydrogen bonds and entropic effects.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Ribbon diagram of the PPAT protomer. -Helices are depicted by red helical ribbons and -strands by blue arrows. The substrate, Ppant and three sulfate anions are shown in ball-and-stick representation. The colours of the atoms are the same as in Fig. 1-. This figure was produced with MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]).
Figure 5.
Figure 5 Schematic representation of hydrogen bonding between Ppant and Tt PPAT. Ppant is shown in red and residues from a protomer of the PPAT hexamer are shown in black. The residue from the neighbouring subunit related by the triad axis is shown in green. The hydrogen bonds are drawn using dashed lines and the donor-to-acceptor distances (Å) are also indicated.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 97-0) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20656493 M.Fischer, Q.Y.Zhang, R.E.Hubbard, and G.H.Thomas (2010).
Caught in a TRAP: substrate-binding proteins in secondary transport.
  Trends Microbiol, 18, 471-478.  
18811972 S.Frago, M.Martínez-Júlvez, A.Serrano, and M.Medina (2008).
Structural analysis of FAD synthetase from Corynebacterium ammoniagenes.
  BMC Microbiol, 8, 160.  
  17077496 J.Y.Kang, H.H.Lee, H.J.Yoon, H.S.Kim, and S.W.Suh (2006).
Overexpression, crystallization and preliminary X-ray crystallographic analysis of phosphopantetheine adenylyltransferase from Enterococcus faecalis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1131-1133.  
  16511109 E.Inagaki, H.Takahashi, C.Kuroishi, and T.H.Tahirov (2005).
Crystallization and avoiding the problem of hemihedral twinning in crystals of Delta1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 609-611.  
  16508086 T.Kitao, C.Kuroishi, and T.H.Tahirov (2005).
Crystallization and preliminary crystallographic analysis of the nickel-responsive regulator NikR from Pyrococcus horikoshii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 43-45.  
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.