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The PE-PPE domain in mycobacterium reveals a serine α/β hydrolase fold and function: an in-silico analysis.

Sultana R, Tanneeru K, Guruprasad L - PLoS ONE (2011)

Bottom Line: The structure comprises a lid insertion with a closed structure conformation and has a solvent inaccessible active site.The oxyanion hole that stabilizes the negative charge on the tetrahedral intermediate has been identified.These results provide the directions for the design of experiments to establish the function of PE and PPE proteins.

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry, University of Hyderabad, Hyderabad, India.

ABSTRACT
The PE and PPE proteins first reported in the genome sequence of Mycobacterium tuberculosis strain H37Rv are now identified in all mycobacterial species. The PE-PPE domain (Pfam ID: PF08237) is a 225 amino acid residue conserved region located towards the C-terminus of some PE and PPE proteins and hypothetical proteins. Our in-silico sequence analysis revealed that this domain is present in all Mycobacteria, some Rhodococcus and Nocardia farcinica genomes. This domain comprises a pentapeptide sequence motif GxSxG/S at the N-terminus and conserved amino acid residues Ser, Asp and His that constitute a catalytic triad characteristic of lipase, esterase and cutinase activity. The fold prediction and comparative modeling of the 3-D structure of the PE-PPE domain revealed a "serine α/β hydrolase" structure with a central β-sheet flanked by α-helices on either side. The structure comprises a lid insertion with a closed structure conformation and has a solvent inaccessible active site. The oxyanion hole that stabilizes the negative charge on the tetrahedral intermediate has been identified. Our findings add to the growing list of serine hydrolases in mycobacterium, which are essential for the maintenance of their impermeable cell wall and virulence. These results provide the directions for the design of experiments to establish the function of PE and PPE proteins.

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The overall fold of the serine hydrolases.(A) Rv1430 PE-PPE domain. (B) Rv1800 PE-PPE domain. (C) Rv1184c PE-PPE domain. (D) PDB_ID: 3AJA used as template for homology modeling. The helices are represented in red, strands in blue, the lid insertion in pink. The side chains of the amino acids in the catalytic triad are indicated in ball and stick.
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pone-0016745-g002: The overall fold of the serine hydrolases.(A) Rv1430 PE-PPE domain. (B) Rv1800 PE-PPE domain. (C) Rv1184c PE-PPE domain. (D) PDB_ID: 3AJA used as template for homology modeling. The helices are represented in red, strands in blue, the lid insertion in pink. The side chains of the amino acids in the catalytic triad are indicated in ball and stick.

Mentions: The sequence alignment generated between the H37Rv query proteins and the PDB_ID: 3AJA by the FUGUE method was used for the 3-D structure modeling of the PE-PPE domain using MODELLER. All models exhibited an overall α/β hydrolase fold with central β-sheet, flanked by α-helices on either side of the sheet (Figure 2). The location of the pentapeptide sequence motif and the catalytic amino acid residues Ser, Asp and His are highly conserved in all the structures. A close observation of the region around the active site indicated the presence of the lid insertion region and solvent inaccessible catalytic Ser indicating the closed conformation adopted by these hydrolase structures (Figure 3). Most of the classical lipases (for example PDB_IDs: 2Z8X, 5TGL, 2VEO, 4TGL) possess a lid insertion region over the active site that keeps the active site in a closed conformation. These lids are displaced during interfacial activation allowing the substrate to be activated by opening up and exposing the catalytic triad. Another interesting aspect of the serine hydrolases is the presence of an oxyanion hole that constitutes a part of the active site. The oxyanion hole is formed by the amino acid residues whose main chain nitrogen atoms act as hydrogen donors to the hydrolysed substrate, stabilizing the negative charge on the tetrahedral intermediate arising from the nucleophilic attack of the catalytic Ser during activation [30]. In bacterial lipases, (for example PDB_IDs: 1IVN, 1CRL) the location of an oxyanion hole has been characterized. Based on the homology between these crystal structures and the constructed structure models of PE-PPE domain, we have identified the location of the oxyanion hole in all our modeled structures. For example, in the case of Rv1430, the residues Gln-200 and Thr-121 are responsible for the formation of the oxyanion hole as indicated in Figure 3.


The PE-PPE domain in mycobacterium reveals a serine α/β hydrolase fold and function: an in-silico analysis.

Sultana R, Tanneeru K, Guruprasad L - PLoS ONE (2011)

The overall fold of the serine hydrolases.(A) Rv1430 PE-PPE domain. (B) Rv1800 PE-PPE domain. (C) Rv1184c PE-PPE domain. (D) PDB_ID: 3AJA used as template for homology modeling. The helices are represented in red, strands in blue, the lid insertion in pink. The side chains of the amino acids in the catalytic triad are indicated in ball and stick.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3037379&req=5

pone-0016745-g002: The overall fold of the serine hydrolases.(A) Rv1430 PE-PPE domain. (B) Rv1800 PE-PPE domain. (C) Rv1184c PE-PPE domain. (D) PDB_ID: 3AJA used as template for homology modeling. The helices are represented in red, strands in blue, the lid insertion in pink. The side chains of the amino acids in the catalytic triad are indicated in ball and stick.
Mentions: The sequence alignment generated between the H37Rv query proteins and the PDB_ID: 3AJA by the FUGUE method was used for the 3-D structure modeling of the PE-PPE domain using MODELLER. All models exhibited an overall α/β hydrolase fold with central β-sheet, flanked by α-helices on either side of the sheet (Figure 2). The location of the pentapeptide sequence motif and the catalytic amino acid residues Ser, Asp and His are highly conserved in all the structures. A close observation of the region around the active site indicated the presence of the lid insertion region and solvent inaccessible catalytic Ser indicating the closed conformation adopted by these hydrolase structures (Figure 3). Most of the classical lipases (for example PDB_IDs: 2Z8X, 5TGL, 2VEO, 4TGL) possess a lid insertion region over the active site that keeps the active site in a closed conformation. These lids are displaced during interfacial activation allowing the substrate to be activated by opening up and exposing the catalytic triad. Another interesting aspect of the serine hydrolases is the presence of an oxyanion hole that constitutes a part of the active site. The oxyanion hole is formed by the amino acid residues whose main chain nitrogen atoms act as hydrogen donors to the hydrolysed substrate, stabilizing the negative charge on the tetrahedral intermediate arising from the nucleophilic attack of the catalytic Ser during activation [30]. In bacterial lipases, (for example PDB_IDs: 1IVN, 1CRL) the location of an oxyanion hole has been characterized. Based on the homology between these crystal structures and the constructed structure models of PE-PPE domain, we have identified the location of the oxyanion hole in all our modeled structures. For example, in the case of Rv1430, the residues Gln-200 and Thr-121 are responsible for the formation of the oxyanion hole as indicated in Figure 3.

Bottom Line: The structure comprises a lid insertion with a closed structure conformation and has a solvent inaccessible active site.The oxyanion hole that stabilizes the negative charge on the tetrahedral intermediate has been identified.These results provide the directions for the design of experiments to establish the function of PE and PPE proteins.

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry, University of Hyderabad, Hyderabad, India.

ABSTRACT
The PE and PPE proteins first reported in the genome sequence of Mycobacterium tuberculosis strain H37Rv are now identified in all mycobacterial species. The PE-PPE domain (Pfam ID: PF08237) is a 225 amino acid residue conserved region located towards the C-terminus of some PE and PPE proteins and hypothetical proteins. Our in-silico sequence analysis revealed that this domain is present in all Mycobacteria, some Rhodococcus and Nocardia farcinica genomes. This domain comprises a pentapeptide sequence motif GxSxG/S at the N-terminus and conserved amino acid residues Ser, Asp and His that constitute a catalytic triad characteristic of lipase, esterase and cutinase activity. The fold prediction and comparative modeling of the 3-D structure of the PE-PPE domain revealed a "serine α/β hydrolase" structure with a central β-sheet flanked by α-helices on either side. The structure comprises a lid insertion with a closed structure conformation and has a solvent inaccessible active site. The oxyanion hole that stabilizes the negative charge on the tetrahedral intermediate has been identified. Our findings add to the growing list of serine hydrolases in mycobacterium, which are essential for the maintenance of their impermeable cell wall and virulence. These results provide the directions for the design of experiments to establish the function of PE and PPE proteins.

Show MeSH
Related in: MedlinePlus