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Structure of IDP00624

2.05 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (EpiP) from Staphylococcus aureus.

Edit deposit information
CSGID target
IDP00624 
PDB Id
3QFH (NCBI MMDB
Authors
G.Minasov,A.Halavaty,L.Shuvalova,I.Dubrovska,J.Winsor,F.Bagnoli,F.Falugi,M.Bottomley,G.Grandi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Jan 21, 2011 
Release Date
Feb 02, 2011 

Annotation

Description
Epidermin is a 21-amino acid lantibiotic that has antimicrobial activity toward gram-positive bacteria. It is produced and processed through a series of proteins to form the mature epidermin. EpiP is one of the proteins in the cascade to produce this mature lantibiotic. EpiP is intracellularly produced and is then transported across the cell membrane where it is attached to the surface of the cell. It is puzzling as to why Staphylococcus aureus has this protein since it does not produce epidermin and is lacking several of the genes for its production. The EpiP protein from Staphylococcus aureus shows similarity to subtilisin-like serine proteases, and has conserved residues (Asp140, His 187, and Ser393) corresponding to the catalytic triad for serine proteases. In our wild-type structure the polypeptide chain has been cleaved somewhere between residues 95 and 100, indicating that the cleavage may have been autocatalytic. To determine if the protein is acting like a subtilisin-like serine protease, we mutated the hypothesized catalytic serine residue to alanine. The crystal structure of this mutant protein shows that the polypeptide chain is not cleaved and is not interacting with the active site.  
Functional assignment
subtilisin-like serine proteases 

Ligands

Ligand code Name Ligand type
NA Sodium ion crystallization
GOL crystallization
EDO crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 1  
Unit Cell

a=85.50Å, b=94.70Å, c=123.00Å
α=89.98, β=90.37, γ=116.79 
Solvent content
44.69  
Matthews coefficient
2.22  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.69-2.05Å (2.10-2.05Å)  
Rall(%)
17.2 
Rwork(%)
17.0 (24.8) 
Rfree(%)
21.6 (27.2) 
Num. observed reflections
211351 (15468) 
Num. Rfree reflections
10567 (793) 
Completeness(%)
97.8 (96.9) 

Model parameters

Num Atoms
26763  
Num Waters
1511  
Num Hetatoms
1747  
Model mean isotropic B factor
38.610Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.353°  
Filename uploaded
rcsb063578.pdb (uploaded on Feb 15, 2011 5:08 PM)  
Inserted
Feb 15, 2011