Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)

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, Singh04a]. 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 [Singh04a]. 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

Singh04a: 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

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Wed Sep 2, 2015, biocyc12.