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PDBsum entry 1tfu

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protein links
Transferase PDB id
1tfu
Jmol
Contents
Protein chain
157 a.a. *
Waters ×132
* Residue conservation analysis
PDB id:
1tfu
Name: Transferase
Title: Phosphopantetheine adenylyltransferase from mycobacterium tu
Structure: Phosphopantetheine adenylyltransferase. Chain: a. Synonym: pantetheine- phosphate adenylyltransferase, ppat, coa pyrophosphorylase. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: coad, kdtb, rv2965c, mt3043, mtcy349.22, u0002e, mb29 expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21 (de3).
Biol. unit: Hexamer (from PDB file)
Resolution:
1.99Å     R-factor:   0.229     R-free:   0.258
Authors: V.K.Morris,T.Izard,Tb Structural Genomics Consortium (Tbsgc)
Key ref:
V.K.Morris and T.Izard (2004). Substrate-induced asymmetry and channel closure revealed by the apoenzyme structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase. Protein Sci, 13, 2547-2552. PubMed id: 15322293 DOI: 10.1110/ps.04816904
Date:
27-May-04     Release date:   14-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam  
P9WPA5  (COAD_MYCTU) -  Phosphopantetheine adenylyltransferase
Seq:
Struc:
161 a.a.
157 a.a.
Key:    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
= 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: 10.1110/ps.04816904 Protein Sci 13:2547-2552 (2004)
PubMed id: 15322293  
 
 
Substrate-induced asymmetry and channel closure revealed by the apoenzyme structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase.
V.K.Morris, T.Izard.
 
  ABSTRACT  
 
Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in prokaryotic coenzyme A (CoA) biosynthesis, directing the transfer of an adenylyl group from ATP to 4'-phosphopantetheine (Ppant) to yield dephospho-CoA (dPCoA). The crystal structures of Escherichia coli PPAT bound to its substrates, product, and inhibitor revealed an allosteric hexameric enzyme with half-of-sites reactivity, and established an in-line displacement catalytic mechanism. To provide insight into the mechanism of ligand binding we solved the apoenzyme (Apo) crystal structure of PPAT from Mycobacterium tuberculosis. In its Apo form, PPAT is a symmetric hexamer with an open solvent channel. However, ligand binding provokes asymmetry and alters the structure of the solvent channel, so that ligand binding becomes restricted to one trimer.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo superposition of the E. coli PPAT structure bound to dPCoA onto the M. tuberculosis PPAT apo-structure. Residues involved in binding to dPCoA or pyrophosphate, as seen in the E. coli PPAT:dPCoA structure, are shown in red and the equivalent residues found in the M. tuberculosis are shown in blue. The product (dPCoA) is shown in ball-and-stick representation. Movements of the catalytic lysine are indicated.
Figure 3.
Figure 3. C trace superposition of the of E. coli PPAT (three shades of gray) hexamer as seen in the PPAT:dPCoA structure onto the apo-form of M. tuberculosis PPAT (three shades of red). The N and C termini are indicated. For clarity, the hexamer is depicted in two halves of trimers. (A) The 195 C positions of residues forming strands or helices of the unliganded E. coli PPAT trimer can be superimposed onto the equivalent C positions of the apo-from of M. tuberculosis PPAT with RMSD of 0.9 .
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2004, 13, 2547-2552) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21527250 C.S.Cheng, C.H.Chen, Y.C.Luo, W.T.Chen, S.Y.Chang, P.C.Lyu, M.C.Kao, and H.S.Yin (2011).
Crystal structure and biophysical characterisation of Helicobacter pylori phosphopantetheine adenylyltransferase.
  Biochem Biophys Res Commun, 408, 356-361.  
19500588 T.D.Gruber, M.J.Borrok, W.M.Westler, K.T.Forest, and L.L.Kiessling (2009).
Ligand binding and substrate discrimination by UDP-galactopyranose mutase.
  J Mol Biol, 391, 327-340.
PDB code: 3gf4
17873050 J.R.Miller, J.Ohren, R.W.Sarver, W.T.Mueller, P.de Dreu, H.Case, and V.Thanabal (2007).
Phosphopantetheine adenylyltransferase from Escherichia coli: investigation of the kinetic mechanism and role in regulation of coenzyme A biosynthesis.
  J Bacteriol, 189, 8196-8205.  
  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.  
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