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Structure of IDP90549

Phosphopantetheine adenylyltransferase from Yersinia pestis complexed with coenzyme A.

Edit deposit information
CSGID target
IDP90549 
PDB Id
3L92 (NCBI MMDB
Authors
J.Osipiuk,N.Maltseva,M.Makowska-Grzyska,K.Kwon,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jan 04, 2010 
Release Date
Jan 19, 2010 

Annotation

Description
Phosphopantetheine adenylyltransferase (PPAT) catalyzes the conversion of ATP and pantetheine 4'-phosphate (PhP) to pyrophosphate (PPi) and 3'-dephospho-CoA (dPCoA). This reaction is known as the penultimate step in the coenzyme A (CoA) biosynthetic pathway and has been shown to be a rate-limiting step in the biosynthesis of CoA. PPAT is part of the nucleotidyltransferase α/β phosphodiesterase superfamily, which includes nicotinate mononucleotide adenylyltransferase (NMAT) and glycerol 3-phosphate cytidylyltransferase. PPAT was identified as an attractive antimicrobial drug target in the CoA biosynthesis pathway due to its broad-spectrum nature and the lack of similarity between bacterial and human enzymes. 
Functional assignment
Transferase  

Ligands

Ligand code Name Ligand type
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological

Structure information

Unit cell parameters

Space Group
H 3 2  
Unit Cell

a=114.82Å, b=114.82Å, c=119.07Å
α=90.00, β=90.00, γ=120.00 
Solvent content
70.77  
Matthews coefficient
4.21  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
38.30-1.89Å (1.94-1.89Å)  
Rall(%)
16.5 
Rwork(%)
16.4 (23.7) 
Rfree(%)
19.2 (28.3) 
Num. observed reflections
24310 (1776) 
Num. Rfree reflections
1239 (89) 
Completeness(%)
100.0 (99.8) 

Model parameters

Num Atoms
1595  
Num Waters
166  
Num Hetatoms
0  
Model mean isotropic B factor
26.900Å2  
RMSD bond length
0.020Å  
RMSD bond angle
1.866°  
Filename uploaded
idp90549_CoA.pdb (uploaded on Jan 18, 2010 2:03 PM)  
Inserted
Jan 18, 2010