Annotation

Description

In eubacteria as well as in mitochondria and chloroplasts, all nascent polypeptides are synthesized with N-formylmethionine at the N terminus. Peptide deformylase (PDF) is required for the removal of the formyl group at the N terminus in eubacteria. PDF is a metalloenzyme utilizing Fe2+ as catalytic metal whereas the Zn2+ form (presented structure) is nearly inactive. The deletion of the PDF gene was shown to be lethal for Escherichia coli. Formylation/deformylation cycle appears to be a characteristic feature of eubacteria and does not occur in the cytoplasm of eucaryotic cells. Therefore, PDF is an attractive target for the design of new antibiotics. 

Functional assignment

Hydrolase 

Structure information

Unit cell parameters

Space Group

P 41 21 2  

Unit Cell

a=74.30Å, b=74.30Å, c=127.22Å
α=90.00, β=90.00, γ=90.00 

Solvent content

 

Matthews coefficient

 

Refinement

Data for the highest resolution shell is in parentheses.

Resolution range

33.30-1.80Å (1.85-1.80Å)  

R_all(%)

16.9 

R_work(%)

16.7 (19.1) 

R_free(%)

20.4 (23.9) 

Num. observed reflections

33662 (2459) 

Num. R_free reflections

1716 (113) 

Completeness(%)

99.6 (99.8) 

Model parameters

Num Atoms

3103  

Num Waters

306  

Num Hetatoms

0  

Model mean isotropic B factor

22.450Ų  

RMSD bond length

0.018Å  

RMSD bond angle

1.625°  

Filename uploaded

idp01482.pdb (uploaded on Feb 23, 2011 1:33 PM)  

Inserted

Feb 23, 2011