Escherichia coli K-12 substr. MG1655 Enzyme: RNA 2',3'-cyclic phosphodiesterase

Gene: thpR Accession Numbers: EG12330 (EcoCyc), b0147, ECK0146

Synonyms: yadP, ligT

Regulation Summary Diagram: ?

Regulation summary diagram for thpR

ThpR belongs to the family of two-histidine (2H) phosphoesterase enzymes and has been shown to be an "end healing" cyclic phosphodiesterase (CPDase) that hydrolyzes RNA 2',3'-cyclic phosphodiesters [Remus14].

Biophysical characterization of ThpR and comparison to two other cyclic nucleotide phosphodiesterases from yeast and Arabidopsis has been reported. ThpR appears to exist as a monomer in solution [Hofmann02a]. A crystal structure of ThpR in complex with 2'-AMP has been solved at 2 Å resolution, implicating His43 as a general acid catalyst and His125 as a general base catalyst. Arg130 may have a role in stabilizing the transition state. Site-directed mutagenesis of these amino acids confirmed their importance for catalytic activity [Remus14].

ThpR was initially identified as a "2'-5' RNA ligase" that catalyzes the ligation and cleavage of 2'-5' linkages in RNA, a reversible transesterification reaction, in vitro. This activity was demonstrated using tRNA halves prepared with yeast pre-tRNA and splicing enzymes; the reaction does not require nucleotide triphosphates, as other known ligases do [Greer83, Arn96]. This reaction is probably not physiologically relevant [Remus14].

Overproduction of ThpR leads to reduced growth rate and the inability to grow at 43°C; deletion of thpR has no effect on growth under laboratory conditions [Arn96].

ThpR: "two-histidine 2',3'-cyclic phosphodiesterase acting on RNA" [Remus14]

Locations: cytosol

Map Position: [161,501 <- 162,031] (3.48 centisomes, 13°)
Length: 531 bp / 176 aa

Molecular Weight of Polypeptide: 19.934 kD (from nucleotide sequence), 20.0 kD (experimental) [Arn96 ]

Unification Links: ASAP:ABE-0000505 , EchoBASE:EB2234 , EcoGene:EG12330 , EcoliWiki:b0147 , ModBase:P37025 , OU-Microarray:b0147 , PortEco:ligT , PR:PRO_000023091 , Protein Model Portal:P37025 , RefSeq:NP_414689 , RegulonDB:EG12330 , SMR:P37025 , String:511145.b0147 , UniProt:P37025

Relationship Links: InterPro:IN-FAMILY:IPR004175 , InterPro:IN-FAMILY:IPR009097 , InterPro:IN-FAMILY:IPR014051 , PDB:Structure:4QAK , Pfam:IN-FAMILY:PF02834

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0016070 - RNA metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0004113 - 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity Inferred from experiment [Remus14]
GO:0008664 - 2'-5'-RNA ligase activity Inferred from experiment Inferred by computational analysis [GOA01, Arn96]
GO:0008081 - phosphoric diester hydrolase activity Inferred by computational analysis [GOA06]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related

Essentiality data for thpR knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Curated 08-Feb-2006 by Shearer A , SRI International
Last-Curated ? 10-Oct-2014 by Keseler I , SRI International

Enzymatic reaction of: RNA 2',3'-cyclic phosphodiesterase

an RNA terminal-2',3'-cyclic-phosphate + H2O <=> an RNA 2'-terminal-phosphate

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.

Reversibility of this reaction is unspecified.

Alternative Substrates for an RNA terminal-2',3'-cyclic-phosphate: adenosine 2',3'-cyclic monophosphate [Remus14 ]

Enzymatic reaction of: 2'-5' RNA ligase (RNA 2',3'-cyclic phosphodiesterase)

EC Number: 6.5.1.-

a 5' half-tRNA molecule with a 2',3' cyclic phosphate on its 3' end + a 3' half-tRNA molecule with a hydroxyl on its 5' end <=> a ligated tRNA with a 2'-5' linkage

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.

This reaction is reversible. [Arn96]

Note: The enzyme may catalyze this reaction in vitro, but this reaction is not considered to be physiologically relevant.

The reaction is reversible, favoring cleavage of the 2'-5' bond [Arn96].

Sequence Features

Protein sequence of RNA 2',3'-cyclic phosphodiesterase with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Arn96, UniProt11]
UniProt: Removed.
Chain 2 -> 176
UniProt: 2'-5'-RNA ligase;
Sequence-Conflict 174
[Kawamukai91, UniProt10a]
UniProt: (in Ref. 4; M60726);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b0147 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12330; confirmed by SwissProt match.


Arn96: Arn EA, Abelson JN (1996). "The 2'-5' RNA ligase of Escherichia coli. Purification, cloning, and genomic disruption." J Biol Chem 271(49);31145-53. PMID: 8940112

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

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: 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."

Greer83: Greer CL, Javor B, Abelson J (1983). "RNA ligase in bacteria: formation of a 2',5' linkage by an E. coli extract." Cell 33(3);899-906. PMID: 6347395

Hofmann02a: Hofmann A, Tarasov S, Grella M, Ruvinov S, Nasr F, Filipowicz W, Wlodawer A (2002). "Biophysical characterization of cyclic nucleotide phosphodiesterases." Biochem Biophys Res Commun 291(4);875-83. PMID: 11866446

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kawamukai91: Kawamukai M, Utsumi R, Takeda K, Higashi A, Matsuda H, Choi YL, Komano T (1991). "Nucleotide sequence and characterization of the sfs1 gene: sfs1 is involved in CRP*-dependent mal gene expression in Escherichia coli." J Bacteriol 173(8);2644-8. PMID: 2013578

Remus14: Remus BS, Jacewicz A, Shuman S (2014). "Structure and mechanism of E. coli RNA 2',3'-cyclic phosphodiesterase." RNA 20(11);1697-705. PMID: 25239919

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

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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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