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

Teh BA, Choi SB, Musa N, Ling FL, Cun ST, Salleh AB, Najimudin N, Wahab HA, Normi YM - BMC Struct. Biol. (2014)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Enzyme and Microbial Technology Research Center (EMTECH), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia. habibahw@usm.my.

ABSTRACT

Background: Klebsiella 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.

Results: Sequence 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.

Conclusions: We 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.

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Phylogenetic analysis of KPN_00953 with other protein structures from 8 other organisms including 1LBU (selected template). The proteins were selected using SCOP hierarchy search. All the proteins contained the conserved Peptidase_M15_3 superfamily domain.
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Figure 2: Phylogenetic analysis of KPN_00953 with other protein structures from 8 other organisms including 1LBU (selected template). The proteins were selected using SCOP hierarchy search. All the proteins contained the conserved Peptidase_M15_3 superfamily domain.

Mentions: Phylogenetics analysis via SCOP search [28] was performed between KPN_00953 with other members of Peptidase_M15_3 superfamily to determine their degree of evolutionary relatedness. The analysis revealed that 1LBU was at a further clad from KPN_00953 (Klebsiella sp) in the cladrogram as compared to other organisms (Figure 2). Although the sequence identity of 1LBU compared with KPN_00953 is only 23%, it is evolutionary closer to Klebsiella sp based on its phylogenetic relationship. Moreover, the length of 1LBU is similar to KPN_00953 (Figure 1). Thus, 1LBU was selected as the template for homology modeling.


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

Teh BA, Choi SB, Musa N, Ling FL, Cun ST, Salleh AB, Najimudin N, Wahab HA, Normi YM - BMC Struct. Biol. (2014)

Phylogenetic analysis of KPN_00953 with other protein structures from 8 other organisms including 1LBU (selected template). The proteins were selected using SCOP hierarchy search. All the proteins contained the conserved Peptidase_M15_3 superfamily domain.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3927764&req=5

Figure 2: Phylogenetic analysis of KPN_00953 with other protein structures from 8 other organisms including 1LBU (selected template). The proteins were selected using SCOP hierarchy search. All the proteins contained the conserved Peptidase_M15_3 superfamily domain.
Mentions: Phylogenetics analysis via SCOP search [28] was performed between KPN_00953 with other members of Peptidase_M15_3 superfamily to determine their degree of evolutionary relatedness. The analysis revealed that 1LBU was at a further clad from KPN_00953 (Klebsiella sp) in the cladrogram as compared to other organisms (Figure 2). Although the sequence identity of 1LBU compared with KPN_00953 is only 23%, it is evolutionary closer to Klebsiella sp based on its phylogenetic relationship. Moreover, the length of 1LBU is similar to KPN_00953 (Figure 1). Thus, 1LBU was selected as the template for homology modeling.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Enzyme and Microbial Technology Research Center (EMTECH), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia. habibahw@usm.my.

ABSTRACT

Background: Klebsiella 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.

Results: Sequence 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.

Conclusions: We 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.

Show MeSH
Related in: MedlinePlus