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Structure of IDP00851

Crystal structure of IcaR from Staphylococcus aureus, a member of the tetracycline repressor protein family

Edit deposit information
CSGID target
IDP00851 
PDB Id
3GEU (NCBI MMDB
Authors
S.M.Anderson,J.S.Brunzelle,Z.Wawrzak,T.Skarina,L.Papazisi,W.F.Anderson,A.Savchenko,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Spencer Anderson 
Responsible lab
Northwestern University 
Deposition Date
Feb 26, 2009 
Release Date
Mar 10, 2009 

Annotation

Description
IcaR is a member of the tetracycline repressor (TetR) family, a collection of transcriptional repressors found in a wide variety of bacteria. The TetR family is named after a member that regulates expression of tetracycline resistance genes, but other TetR proteins have been shown to control a great number of pathways, such as antibiotic biosynthesis and response to osmotic stress. IcaR is believed to be involved in the regulation of biofilm production. Biofilms are complex assemblies of single celled organisms that can be formed under a variety of conditions. Bacteria in biofilms demonstrate enhanced antibiotic resistance, which makes them of particular interest. IcaR is an orthogonal bundle of alpha helices that binds to DNA as a homodimer. The DNA binding region is a conserved helix-turn-helix that is rich in aromatic and positively charged residues. Two copies of the homodimer are found in the asymmetric unit and have a nearly identical quaternary arrangement. IcaR has been previously solved in Staphylococcus epidermidis (2ZCN). As expected from 65% sequence identity and 1.2Å RMSD, the structure of IcaR from S. epidermidis and S. aureus are extremely similar. The region distal to the DNA binding motif is better ordered in the current structure and could be completely visualized, although there is no secondary structure present. Other structural examples from the TetR family include proteins from Haloarcula marismortui (3CRJ) and Thermotoga maritime (2ID6). Ramos,J.L., Martinez-Bueno,M., Molina-Henares,A.J., Teran,W., Watanabe,K., Zhang,X., Gallegos,M.T., Brennan,R. and Tobes,R. (2005) The TetR family of transcriptional repressors. Microbiol. Mol. Biol. Rev. 69: 326–356. Jeng, W.Y., Ko, T.P., Liu, C.I., Guo, R.T., Liu, C.L., Shr, H.L., Wang, A.H.J. (2008) Crystal structure of IcaR, a repressor of the TetR family implicated in biofilm formation in Staphylococcus epidermidis Nucleic Acids Res. 36: 1567-1577  
Functional assignment
 

Ligands

Ligand code Name Ligand type
CL
FMT
NA Sodium ion
MSE modified residue

Structure information

Unit cell parameters

Space Group
P 21 21 2  
Unit Cell

a=113.92Å, b=121.14Å, c=61.69Å
α=90.00, β=90.00, γ=90.00 
Solvent content
47.94  
Matthews coefficient
2.36  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
40.42-1.90Å (1.97-1.90Å)  
Rall(%)
18.4 
Rwork(%)
18.2 (25.0) 
Rfree(%)
22.8 (28.7) 
Num. observed reflections
67217 (6284) 
Num. Rfree reflections
3360 (314) 
Completeness(%)
98.8 (93.7) 

Model parameters

Num Atoms
6860  
Num Waters
431  
Num Hetatoms
0  
Model mean isotropic B factor
35.920Å2  
RMSD bond length
0.017Å  
RMSD bond angle
1.501°  
Filename uploaded
zDATA233_refmac7-coot-8.cif (uploaded on Feb 26, 2009 12:36 PM)  
Inserted
Feb 26, 2009