Structure to function prediction of hypothetical protein KPN_00953 (Ycbk) from Klebsiella pneumoniae MGH 78578 highlights possible role in cell wall metabolism

Abstract

BackgroundKlebsiella pneumoniae plays a major role in causing nosocomial infection in immunocompromised patients. Medical inflictions by the pathogen can range from respiratory and urinary tract infections, septicemia and primarily, pneumonia. As more K. pneumoniae strains are becoming highly resistant to various antibiotics, treatment of this bacterium has been rendered more difficult. This situation, as a consequence, poses a threat to public health. Hence, identification of possible novel drug targets against this opportunistic pathogen need to be undertaken. In the complete genome sequence of K. pneumoniae MGH 78578, approximately one-fourth of the genome encodes for hypothetical proteins (HPs). Due to their low homology and relatedness to other known proteins, HPs may serve as potential, new drug targets.ResultsSequence analysis on the HPs of K. pneumoniae MGH 78578 revealed that a particular HP termed KPN_00953 (YcbK) contains a M15_3 peptidases superfamily conserved domain. Some members of this superfamily are metalloproteases which are involved in cell wall metabolism. BLASTP similarity search on KPN_00953 (YcbK) revealed that majority of the hits were hypothetical proteins although two of the hits suggested that it may be a lipoprotein or related to twin-arginine translocation (Tat) pathway important for transport of proteins to the cell membrane and periplasmic space. As lipoproteins and other components of the cell wall are important pathogenic factors, homology modeling of KPN_00953 was attempted to predict the structure and function of this protein. Three-dimensional model of the protein showed that its secondary structure topology and active site are similar with those found among metalloproteases where two His residues, namely His169 and His209 and an Asp residue, Asp176 in KPN_00953 were found to be Zn-chelating residues. Interestingly, induced expression of the cloned KPN_00953 gene in lipoprotein-deficient E. coli JE5505 resulted in smoother cells with flattened edges. Some cells showed deposits of film-like material under scanning electron microscope.ConclusionsWe postulate that KPN_00953 is a Zn metalloprotease and may play a role in bacterial cell wall metabolism. Structural biology studies to understand its structure, function and mechanism of action pose the possibility of utilizing this protein as a new drug target against K. pneumoniae in the future.

Peptidoglycan hydrolase of an unusual cross-link cleavage specificity contributes to bacterial cell wall synthesis

“…MepK belongs to the M15 family of peptidases that also comprises DdpX, a peptidase that cleaves D-Ala−D-Ala dipeptide in the cytosol of E. coli (14,15). In addition, a mepK homolog of Klebsiella pneumoniae is predicted to be a PG hydrolase (16). Hence, we tested whether increased expression of mepK is able to compensate the loss of MepS and/or MepM, the elongation-specific PG hydrolases (10).…”

“…Based on homology modeling, an earlier study predicted an MepK ortholog of K. pneumoniae to be a metal-binding PG hydrolase (ref. 16, SI Appendix, Fig. S8A).…”

Characterization of hypothetical protein VNG0128C fromHalobacteriumNRC-1 reveals GALE like activity and its involvement in Leloir pathway of galactose metabolism

“…If the protein is unique to the genome, it is labeled as hypothetical protein (Roberts, 2004), and they form around 30-60% of the current repository of genomes (Bork, 2000). With updated knowledge and information, the reassignment of hypothetical proteins to sequences with predicted function can be done with confidence, and these may not only help in uncovering the missing links in critical pathways (Galperin & Koonin, 2004), but also enable these novel proteins to be explored as potential drug targets (Teh et al, 2014). Structural genomics initiatives could also facilitate a thorough investigation toward assigning functions to vital genes and enable delineating the functions of hypothetical proteins which might play key roles in cellular functions.…”

Novel Target Exploration from Hypothetical Proteins of Klebsiella pneumoniae MGH 78578 Reveals a Protein Involved in Host-Pathogen Interaction

“…Out of the available proteome of K. pneumoniae MGH 78578, ∼11% is made up of HPs, which can be potential resources to be studied both functionally and structurally. Although bioinformatics studies on a few hypothetical proteins, such as KPN_00953(YcbK) (Teh et al, 2014), KPN_02809 (a Zinc-Dependent Metalloprotease) (Wong et al, 2012), and KPN_00728, KPN_00729 (Chain C and D of Succinate Dehydrogenase, respectively) (Choi et al, 2009), are available, mining and analysis of all hypothetical proteins to shortlist drug/vaccine targets in this pathogen is yet unexplored. In the present study, a series of in silico analyses of 540 hypothetical proteins encoded by the K. pneumoniae genome were carried out to explore novel drug/vaccine candidates in this organism.…”