Escherichia coli K-12 substr. MG1655 Enzyme: peptidyl-tRNA hydrolase

Gene: pth Accession Numbers: EG10785 (EcoCyc), b1204, ECK1192

Synonyms: rap

Regulation Summary Diagram: ?

Regulation summary diagram for pth

Peptidyl-tRNA hydrolase (Pth) catalyzes the removal of peptides from peptidyl-tRNAs that have been prematurely released from the ribosome. The enzyme is essential for growth in E. coli [Menninger79, Singh04]. lysV, encoding a tRNALys, was found to be a multicopy suppressor of a temperature sensitive pth mutant, indicating that the pth mutant phenotype is due to starvation for tRNALys [HeurgueHamard96, VivancoDomingue06]. In general, Pth relieves growth inhibition by freeing tRNAs from aborted translation products [Tenson99, Dincbas99]. Pth is also required for growth of bacteriophage lambda due to translation of minigene ORFs in the lambda bar region [Henderson76, Ontiveros97, Valadez01, Oviedo04].

The crystal structure of Pth has been solved at 1.2 Å resolution [Schmitt97, Schmitt97a]. Pth is monomeric. Predicted active site residues were confirmed by site-directed mutagenesis [Schmitt97a]. The His20 residue is essential for catalytic activity [Goodall04]. The catalytic center has been mapped by NMR [Giorgi11].

The integrity of ychF, the downstream open reading frame in the pth operon, influences the stability of the transcript. Lower RNase E activity results in overproduction of Pth, and thus it is proposed that RNase E processing within ychF causes mRNA degradation [CruzVera02].

A temperature-sensitive pth mutant was isolated [Atherly72, Menninger73]; the mutant protein is unstable in vivo [CruzVera00]. The mutant allele can revert rapidly by gene duplication [Menez01]. Overexpression of tmRNA can rescue the defect of the pthts allele [Singh04]. The rap mutant of Pth [Henderson76] is highly sensitive to the length of the peptidyl-tRNA [HeurgueHamard00].

Reviews: [Hernandez97, Das06]

Locations: cytosol

Map Position: [1,257,152 <- 1,257,736] (27.1 centisomes, 98°)
Length: 585 bp / 194 aa

Molecular Weight of Polypeptide: 21.082 kD (from nucleotide sequence), 21.0 kD (experimental) [GarciaVillegas91 ]

pI: 10.0 [Dutka93]

Unification Links: ASAP:ABE-0004043 , CGSC:352 , DIP:DIP-35932N , EchoBASE:EB0778 , EcoGene:EG10785 , EcoliWiki:b1204 , Mint:MINT-1225563 , ModBase:P0A7D1 , OU-Microarray:b1204 , PortEco:pth , PR:PRO_000023628 , Pride:P0A7D1 , Protein Model Portal:P0A7D1 , RefSeq:NP_415722 , RegulonDB:EG10785 , SMR:P0A7D1 , String:511145.b1204 , UniProt:P0A7D1

Relationship Links: InterPro:IN-FAMILY:IPR001328 , InterPro:IN-FAMILY:IPR018171 , Panther:IN-FAMILY:PTHR17224 , PDB:Structure:2PTH , PDB:Structure:3VJR , Pfam:IN-FAMILY:PF01195 , Prosite:IN-FAMILY:PS01195 , Prosite:IN-FAMILY:PS01196

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for pth

GO Terms:

Biological Process: GO:0006515 - misfolded or incompletely synthesized protein catabolic process Inferred from experiment [Menninger79, Tenson99, Dincbas99]
GO:0006412 - translation Inferred by computational analysis [GOA06]
Molecular Function: GO:0004045 - aminoacyl-tRNA hydrolase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Schmitt97a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0005829 - cytosol

MultiFun Terms: information transfer protein related translation

Essentiality data for pth knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Last-Curated ? 13-Jul-2011 by Keseler I , SRI International

Enzymatic reaction of: peptidyl-tRNA hydrolase

Synonyms: aminoacyl-tRNA hydrolase, aminoacyl-transfer ribonucleate hydrolase, N-substituted aminoacyl transfer RNA hydrolase, aminoacyl-tRNA aminoacylhydrolase

EC Number:

an N-modified aminoacyl-[tRNA] + H2O <=> an uncharged tRNA + an N-modified amino acid + 2 H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

The enzyme was first purified from E. coli B and E. coli W; e.g. in [Kossel70, De69, Shiloach75].

Cofactors or Prosthetic Groups: Mg2+ [Schmitt97a]

Kinetic Parameters:

Km (μM)
an N-modified aminoacyl-[tRNA]

Sequence Features

Protein sequence of peptidyl-tRNA hydrolase with features indicated

Feature Class Location Citations Comment
Mutagenesis-Variant 101
UniProt: Pth(ts) mutants synthesize thermosensitive PTH and die at 42 degrees Celsius from a defect in protein synthesis.
Mutagenesis-Variant 134
UniProt: Rap mutants do not support vegetative growth of bacteriophage lambda and die upon transcription of lambda DNA bar sites.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


3/2/1998 (pkarp) Merged genes G518/b1204 and EG10785/pth
10/20/97 Gene b1204 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10785; confirmed by SwissProt match.


Atherly72: Atherly AG, Menninger JR (1972). "Mutant E. coli strain with temperature sensitive peptidyl-transfer RNA hydrolase." Nat New Biol 240(103);245-6. PMID: 4566050

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

CruzVera00: Cruz-Vera LR, Toledo I, Hernandez-Sanchez J, Guarneros G (2000). "Molecular basis for the temperature sensitivity of Escherichia coli pth(Ts)." J Bacteriol 182(6);1523-8. PMID: 10692356

CruzVera02: Cruz-Vera LR, Galindo JM, Guarneros G (2002). "Transcriptional analysis of the gene encoding peptidyl-tRNA hydrolase in Escherichia coli." Microbiology 148(Pt 11);3457-66. PMID: 12427937

Das06: Das G, Varshney U (2006). "Peptidyl-tRNA hydrolase and its critical role in protein biosynthesis." Microbiology 152(Pt 8);2191-5. PMID: 16849786

De69: De Groot N, Groner Y, Lapidot Y (1969). "Peptidyl-tRNA. VII. Substrate specificity of peptidyl-tRNA hydrolase." Biochim Biophys Acta 186(2);286-96. PMID: 4898482

Dincbas99: Dincbas V, Heurgue-Hamard V, Buckingham RH, Karimi R, Ehrenberg M (1999). "Shutdown in protein synthesis due to the expression of mini-genes in bacteria." J Mol Biol 291(4);745-59. PMID: 10452886

Dutka93: Dutka S, Meinnel T, Lazennec C, Mechulam Y, Blanquet S (1993). "Role of the 1-72 base pair in tRNAs for the activity of Escherichia coli peptidyl-tRNA hydrolase." Nucleic Acids Res 21(17);4025-30. PMID: 7690473

GarciaVillegas91: Garcia-Villegas MR, De La Vega FM, Galindo JM, Segura M, Buckingham RH, Guarneros G (1991). "Peptidyl-tRNA hydrolase is involved in lambda inhibition of host protein synthesis." EMBO J 10(11);3549-55. PMID: 1833189

Giorgi11: Giorgi L, Plateau P, O'Mahony G, Aubard C, Fromant M, Thureau A, Grotli M, Blanquet S, Bontems F (2011). "NMR-Based Substrate Analog Docking to Escherichia coli Peptidyl-tRNA Hydrolase." J Mol Biol 412(4);619-33. PMID: 21718701

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Goodall04: Goodall JJ, Chen GJ, Page MG (2004). "Essential role of histidine 20 in the catalytic mechanism of Escherichia coli peptidyl-tRNA hydrolase." Biochemistry 43(15);4583-91. PMID: 15078105

Henderson76: Henderson D, Weil J (1976). "A mutant of Escherichia coli that prevents growth of phage lambda and is bypassed by lambda mutants in a nonessential region of the genome." Virology 71(2);546-59. PMID: 779235

Hernandez97: Hernandez J, Ontiveros C, Valadez JG, Buckingham RH, Guarneros G (1997). "Regulation of protein synthesis by minigene expression." Biochimie 79(8);527-31. PMID: 9451455

HeurgueHamard00: Heurgue-Hamard V, Dincbas V, Buckingham RH, Ehrenberg M (2000). "Origins of minigene-dependent growth inhibition in bacterial cells." EMBO J 19(11);2701-9. PMID: 10835367

HeurgueHamard96: Heurgue-Hamard V, Mora L, Guarneros G, Buckingham RH (1996). "The growth defect in Escherichia coli deficient in peptidyl-tRNA hydrolase is due to starvation for Lys-tRNA(Lys)." EMBO J 15(11);2826-33. PMID: 8654380

Kossel70: Kossel H (1970). "Purification and properties of peptidyl-tRNA hydrolase from Escherichia coli." Biochim Biophys Acta 204(1);191-202. PMID: 4908646

Menez01: Menez J, Remy E, Buckingham RH (2001). "Suppression of thermosensitive peptidyl-tRNA hydrolase mutation in Escherichia coli by gene duplication." Microbiology 147(Pt 6);1581-9. PMID: 11390689

Menninger70: Menninger JR, Mulholland MC, Stirewalt WS (1970). "Peptidyl-tRNA hydrolase and protein chain termination." Biochim Biophys Acta 217(2);496-511. PMID: 4919656

Menninger73: Menninger JR, Walker C, Tan PF (1973). "Studies on the metabolic role of peptidyl-tRNA hydrolase. I. Properties of a mutant E. coli with temperature-sensitive peptidyl-tRNA hydrolase." Mol Gen Genet 121(4);307-24. PMID: 4571804

Menninger76: Menninger JR (1976). "Peptidyl transfer RNA dissociates during protein synthesis from ribosomes of Escherichia coli." J Biol Chem 251(11);3392-8. PMID: 776968

Menninger79: Menninger JR (1979). "Accumulation of peptidyl tRNA is lethal to Escherichia coli." J Bacteriol 137(1);694-6. PMID: 368041

Ontiveros97: Ontiveros C, Valadez JG, Hernandez J, Guarneros G (1997). "Inhibition of Escherichia coli protein synthesis by abortive translation of phage lambda minigenes." J Mol Biol 269(2);167-75. PMID: 9191062

Oviedo04: Oviedo de Anda NA, Kameyama L, Galindo JM, Guarneros G, Hernandez-Sanchez J (2004). "Evidence of bar minigene expression and tRNA2Ile sequestration as peptidyl-tRNA2Ile during lambda bacteriophage development." J Bacteriol 186(16);5533-7. PMID: 15292158

Schmitt97: Schmitt E, Fromant M, Plateau P, Mechulam Y, Blanquet S (1997). "Crystallization and preliminary X-ray analysis of Escherichia coli peptidyl-tRNA hydrolase." Proteins 28(1);135-6. PMID: 9144799

Schmitt97a: Schmitt E, Mechulam Y, Fromant M, Plateau P, Blanquet S (1997). "Crystal structure at 1.2 A resolution and active site mapping of Escherichia coli peptidyl-tRNA hydrolase." EMBO J 16(15);4760-9. PMID: 9303320

Shiloach75: Shiloach J, Bauer S, de Groot N, Lapidot Y (1975). "The influence of the peptide chain length on the activity of peptidyl-tRNA hydrolase from E. coli." Nucleic Acids Res 2(10);1941-50. PMID: 1103091

Singh04: Singh NS, Varshney U (2004). "A physiological connection between tmRNA and peptidyl-tRNA hydrolase functions in Escherichia coli." Nucleic Acids Res 32(20);6028-37. PMID: 15547251

Tenson99: Tenson T, Herrera JV, Kloss P, Guarneros G, Mankin AS (1999). "Inhibition of translation and cell growth by minigene expression." J Bacteriol 181(5);1617-22. PMID: 10049395

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Valadez01: Valadez JG, Hernandez-Sanchez J, Magos MA, Ontiveros C, Guarneros G (2001). "Increased bar minigene mRNA stability during cell growth inhibition." Mol Microbiol 39(2);361-9. PMID: 11136457

VivancoDomingue06: Vivanco-Dominguez S, Cruz-Vera LR, Guarneros G (2006). "Excess of charged tRNALys maintains low levels of peptidyl-tRNA hydrolase in pth(Ts) mutants at a non-permissive temperature." Nucleic Acids Res 34(5);1564-70. PMID: 16540595

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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