Crystal structure of peptidyl-tRNA hydrolase from mycobacterium smegmatis reveals novel features related to enzyme dynamics

International Journal of Biochemistry and Molecular Biology

Volumn 3, Issue 1, 2012, Pages 58-69

  Kumar, Ashok ^a   Singh, Nagendra ^b   Yadav, Rahul ^a   Kumar, Ramasamy P ^b   Sharma, Sujata ^b   Arora, Ashish ^a   Singh, T P ^b  

^a CENTRAL DRUG RESEARCH INSTITUTE   (India)

^b ALL INDIA INSTITUTE OF MEDICAL SCIENCES   (India)

Author keywords

C terminus; Cloning; Crystal structure; Mycobacterium smegmatis; Peptidyl tRNA hydrolase; Protein expression

Indexed keywords

ALANINE; ASPARAGINE; ASPARTIC ACID; BACTERIAL PROTEIN; GLYCINE; HISTIDINE; PEPTIDYL TRNA HYDROLASE; UNCLASSIFIED DRUG; VALINE;

ALPHA HELIX; ARTICLE; BETA SHEET; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME KINETICS; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR MODEL; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PROTEIN CONFORMATION; PROTEIN EXPRESSION; PROTEIN INTERACTION; RESIDUE ANALYSIS; SEQUENCE ALIGNMENT; STEREOCHEMISTRY; STRUCTURE ANALYSIS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TUBERCULOSIS;

EID: 84859702544     PISSN: None     EISSN: 21524114     Source Type: Journal    
DOI: None     Document Type: Article

References (29)

1. Das G, Varshney U. Peptidyl-tRNA hydrolase and its critical role in protein biosynthesis. Microbiology 2006; 152: 2191-2195.
2. Singh NS, Varshney U. A physiological connection between tmRNA and peptidyl-tRNA hy- drolase functions in Escherchia coli. Nucleic Acids Res 2004; 32: 6028-6037.
3. Heurgue-Hamard V, Karimi R, Mora L, MacDougall J, Leboeuf C and Grentzmann G. Ribosome release factor RF4 and termination factor RF3 are involved in dissociation of pep- tidyl-tRNA from the ribosome. EMBO J 1998; 17: 808-816.
4. Karimi R, Pavlov MY, Heurgue-Hamard V, Buckingham RH and Ehrenberg M. Initiation factors IF1 and IF2 synergistically remove peptidyl-tRNAs with short polypeptides from the P-site of translating Escherichia coli ri- bosomes. J Mol Biol 1998; 281: 241-252.
5. Guarneros G. The rate of peptidyl-tRNA dissociation from the ribosome during minigene expression depends on the nature of the last decoding interaction. J Biol Chem 2003; 278: 26065-26070.
6. Cuzin F, Kretchmer N, Greenberg RE, Hurwitz R and Chapeville F. Enzymatic hydrolysis of N- substituted aminoacyl tRNA. Proc Natl Acad Sci USA 1967; 58: 2079-2086.
7. Menninger JR. Peptidyl transfer RNA dissociates during protein synthesis from ribosomes of Escherchia coli. J Biol Chem 1976; 251: 3392-3398.
8. Menninger JR. Accumulation of peptidyl tRNA is lethal to Escherichia coli. J Bacteriol 1979; 137: 694-696.
9. Kossel H, Raj Bhandary UL. Studies on polynucleotides LXXXVI. Enzymatic hydrolysis of N- aminoacyl-transfer RNA. J Mol Biol 1968; 273: 389-401.
10. García-Villegas MR, De La Vega FM, Galindo JM, Segura M, Buckingham RH and Guarneros G. Peptidyl-tRNA hydrolase is involved in inhi- bition of host protein synthesis. EMBO J 1991; 10: 3549-3555.
11. Rosas-Sandoval G, Ambrogelly A, Rinehart J, Wei D, Cruz-Vera LR and Graham DE. Orthologs of a novel archaeal and of the bac- terial peptidyl - tRNA hydrolase are nonessen- tial in yeast. Proc Natl Acad Sci USA 2002; 99: 16707-16712.
12. Bonin PD, Choi GH, Trepod CM, Mott JE, Lyle SB, Cialdella JI, Sarver RW, Marshall VP and Erickson LA. Expression, purification and char- acterization of peptidyl-tRNA hydrolase from Staphylococcus aureus. Protein Expr Purif 2002; 24: 123-130.
13. Schmitt E, Mechulam Y, Fromant M, Plateau P and Blanquet S. Crystal structure at 1.2 Ǻ resolution and active site mapping of Es- cherichia coli peptidyl-tRNA hydrolase. EMBO J 1997; 16: 4760-4769.
14. Selvaraj M, Roy S, Singh NS, Sangeetha R, Varshney U and Vijayan M. Structural plasticity and enzyme action: crystal structures of Myco- bacterium tuberculosis peptidyl-tRNA hy- drolase. J Mol Biol 2007; 372: 186-193.
15. Bal NC, Agarwal H, Meher AK and Arora A. Characterization of Peptidyl-tRNA hydrolase encoded by open reading frame Rv1014c of Mycobacterium tuberculosis H37Rv. Biol Chem 2007; 388: 467-479.
16. Fromant M, Schmitt E, Mechulam Y, Lazennec C, Plateau P and Blanquet S. Crystal structure at 1.8 Ǻ resolution and identification of active site residues of Sulfolobus solfataricus pepti- dyl-tRNA hydrolase. Biochemistry 2005; 44: 4294-4301.
17. De Pereda JM, Waas WF, Jan Y, Ruoslahti E, Schimmel P and Pascual J. Crystal structure of a human peptidyl-tRNA hydrolase reveals a new fold and suggests basis for a bifunctional activity. J Biol Chem 2004: 279: 8111-8115.
18. Shimizu C, Kuroishi M, Sugahara and Kunishima N. Structure of peptidyl-tRNA hy- drolase 2 from Pyrococcus horikoshii OT3: insight into the functional role of its dimeric state. Acta Crystallogr 2008; D64: 444-453.
19. Kremer L, Baulard A, Estaquier J, Poulain-Godefroy O and Locht C. Green fluoroscent protein as new expression marker in mycobac- teria. Mol Microl 1995; 17: 913-922.
20. Vagin A, Taplyakov A. MOLREP: an automated program for molecular replacement. J Appl Crystallogr 1997; 30: 1022-1025.
21. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Ric LM, Simonson T and Warren GL. Crystal- lography and NMR System: a new software suite for macromolecular structure determina- tion. Acta Crystallogr 1998; D54: 905-921.
22. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr 2004; D60: 2126-2132.
23. Jones TA, Zou JY, Cowan SW and Kjeldgaard M. Improved methods for building protein models in electron density maps and the loca- tion of errors in these models. Acta Crystallogr 1991; A47: 110-119.
24. Davis IW, Leaver-Fray A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arenddall WB, Snoeyink J, Richardson JS and Richardson DC. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 2007; 35: W375-W383.
25. Laskowski RA, MacArthur MW, Moss DS and Thornton JM. PROCHECK: a program to check stereo chemical quality of protein structures. J Appl Crystallogr 1993; 26: 283-291.
26. Ramachandran GN, Sasisekaran V. Conformation of polypeptides and proteins. Adv Protein Chem 1968; 23: 283-438.
27. Chenna, Ramu, Sugawara, Koike H, Lopez T, Gibson R, Higgins HJ, Desmond G and Thomp- son JD. Multiple sequence alignment with clustal sequence of programs. Nucleic Acids Res 2003; 31: 3497-3500.
28. DeLano WL. The PyMol molecular Graphics System, DeLano Scientific, San Carlos CA. 2002; http://www.pymol.org.
29. Lo KP, Murphy ME, Guillemette JG, Smith M and Brayer GD. Replacements in a conserved leucine cluster in the hydrophobic heme pocket of cytochrome c. Prot Sci 1995; 4: 198-208.