Bioinformatics and structural characterization of a hypothetical protein from Streptococcus mutans: implication of antibiotic resistance.
As an oral bacterial pathogen, Streptococcus mutans has been known as the aetiologic agent of human dental caries. Among a total of 1960 identified proteins within the genome of this organism, there are about 500 without any known functions. One of these proteins, SMU.440, has very few homologs in the current protein databases and it does not fall into any protein functional families. Phylogenetic studies showed that SMU.440 is related to a particular ecological niche and conserved specifically in some oral pathogens, due to lateral gene transfer. The co-occurrence of a MarR protein within the same operon among these oral pathogens suggests that SMU.440 may be associated with antibiotic resistance. The structure determination of SMU.440 revealed that it shares the same fold and a similar pocket as polyketide cyclases, which indicated that it is very likely to bind some polyketide-like molecules. From the interlinking structural and bioinformatics studies, we have concluded that SMU.440 could be involved in polyketide-like antibiotic resistance, providing a better understanding of this hypothetical protein. Besides, the combination of multiple methods in this study can be used as a general approach for functional studies of a protein with unknown function.
National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, People's Republic of China.
Jie
J
Nan
Erik
E
Brostromer
Xiang-Yu
XY
Liu
Ole
O
Kristensen
Xiao-Dong
XD
Su
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray / Q000379:methods; D030562:Databases, Protein; D003731:Dental Caries / Q000382:microbiology; D004352:Drug Resistance, Microbial; D022761:Gene Transfer, Horizontal; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017433:Protein Structure, Secondary; D017386:Sequence Homology, Amino Acid; D013295:Streptococcus mutans / Q000378:metabolism*
D001426:Bacterial Proteins; D008024:Ligands