Int J Biochem Mol Biol 2012;3(1):58-69
Original Article
Crystal structure of peptidyl-tRNA hydrolase from mycobacterium smegmatis reveals
novel features related to enzyme dyanamics
Ashok Kumar, Nagendra Singh, Rahul Yadav, Ramasamy P Kumar, Sujata Sharma, Ashish Arora, TP Singh
Molecular and Structural Biology Division, Central Drug Research Institute, Lucknow, India; Department of Biophysics, All India Institute of
Medical Sciences, New Delhi, India. Current address: Gautum Budha University, NOIDA, India
Received January 15, 2012; accepted February 8, 2012; Epub February 15, 2012; Published March 15, 2012
Abstract: Peptidyl- tRNA hydrolase from Mycobacterium smegmatis is a single domain 21 kDa protein involved in the hydrolysis of prematurely
produced peptidyl-tRNAs to ensure the viability of cells in bacteria, thus making it a potentially important drug target. In order to aid the
development of potent drugs for controlling bacterial infections, the three-dimensional structure of peptidyl-tRNA hydrolase from Mycobacterium
smegmatis has been determined. The protein adopts a compact α/β globular fold with a twisted β-sheet surrounded by α-helices. The
functionally important C-terminal stretch has been unambiguously modeled for the first time in the unliganded structure of peptidyl-tRNA
hydrolase. The segment, Gly138 - Val150 is mobile because it lacks significant interactions with the rest of the protein molecule. This
conformational flexibility is reflected through different values of distances between a reference atom Ala147 Cα of the segment Gly138 - Val150
to Gly114 Cα from another segment from opposite side of the substrate binding channel in Mycobacterium smegmatis (7.8 Ǻ), Mycobacterium
tuberculosis (9.5 Ǻ) and Escherichia coli (11.8 Ǻ). Similarly, the conformation of loop Gly109 - Gly117 with respect to another loop Asp95 -
Asp100 also shows variability of the substrate binding cleft as the distance between Asp98 Oδ2 to Gly113 Cα in Mycobacterium smegmatis is
4.5 Ǻ while the corresponding distances in Mycobacterium tuberculosis and Escherichia coli are 3.1 Ǻ and 6.7 Ǻ respectively. The hydrogen
bonded interactions between Asn116, His22 and Asp95 indicate a stereochemically favorable arrangement of these residues for catalytic
action. (IJBMB1201005).
Keywords: Peptidyl-tRNA hydrolase, cloning, crystal structure, mycobacterium smegmatis, c-terminus, protein expression
Address all correspondence to:
Dr. Singh TP
Department of Biophysics
All India Institute of Medical Sciences
Ansari Nagar, New Delhi - 110 029, India.
Tel: +91-11-2658-8931; Fax: +91-11-2658-8663
E-mail: tpsingh.aiims@gmail.com
Original Article
Crystal structure of peptidyl-tRNA hydrolase from mycobacterium smegmatis reveals
novel features related to enzyme dyanamics
Ashok Kumar, Nagendra Singh, Rahul Yadav, Ramasamy P Kumar, Sujata Sharma, Ashish Arora, TP Singh
Molecular and Structural Biology Division, Central Drug Research Institute, Lucknow, India; Department of Biophysics, All India Institute of
Medical Sciences, New Delhi, India. Current address: Gautum Budha University, NOIDA, India
Received January 15, 2012; accepted February 8, 2012; Epub February 15, 2012; Published March 15, 2012
Abstract: Peptidyl- tRNA hydrolase from Mycobacterium smegmatis is a single domain 21 kDa protein involved in the hydrolysis of prematurely
produced peptidyl-tRNAs to ensure the viability of cells in bacteria, thus making it a potentially important drug target. In order to aid the
development of potent drugs for controlling bacterial infections, the three-dimensional structure of peptidyl-tRNA hydrolase from Mycobacterium
smegmatis has been determined. The protein adopts a compact α/β globular fold with a twisted β-sheet surrounded by α-helices. The
functionally important C-terminal stretch has been unambiguously modeled for the first time in the unliganded structure of peptidyl-tRNA
hydrolase. The segment, Gly138 - Val150 is mobile because it lacks significant interactions with the rest of the protein molecule. This
conformational flexibility is reflected through different values of distances between a reference atom Ala147 Cα of the segment Gly138 - Val150
to Gly114 Cα from another segment from opposite side of the substrate binding channel in Mycobacterium smegmatis (7.8 Ǻ), Mycobacterium
tuberculosis (9.5 Ǻ) and Escherichia coli (11.8 Ǻ). Similarly, the conformation of loop Gly109 - Gly117 with respect to another loop Asp95 -
Asp100 also shows variability of the substrate binding cleft as the distance between Asp98 Oδ2 to Gly113 Cα in Mycobacterium smegmatis is
4.5 Ǻ while the corresponding distances in Mycobacterium tuberculosis and Escherichia coli are 3.1 Ǻ and 6.7 Ǻ respectively. The hydrogen
bonded interactions between Asn116, His22 and Asp95 indicate a stereochemically favorable arrangement of these residues for catalytic
action. (IJBMB1201005).
Keywords: Peptidyl-tRNA hydrolase, cloning, crystal structure, mycobacterium smegmatis, c-terminus, protein expression
Address all correspondence to:
Dr. Singh TP
Department of Biophysics
All India Institute of Medical Sciences
Ansari Nagar, New Delhi - 110 029, India.
Tel: +91-11-2658-8931; Fax: +91-11-2658-8663
E-mail: tpsingh.aiims@gmail.com
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