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Escherichia coli K-12 substr. MG1655 Enzyme: 2'-5' RNA ligase



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

Synonyms: yadP

Regulation Summary Diagram: ?

Summary:
LigT reversibly ligates RNA to form 2'-5' linkages.

LigT has been shown in vitro to carry out the ligation and cleavage of 2'-5' linkages in RNA [Arn96]. To date, this activity has been demonstrated using tRNA halves, and LigT has some specificity within the limited range of substrates tested [Greer83, Arn96]. The LigT ligation reaction does not require nucleotide triphosphates, as other known ligases do [Greer83].

LigT has been structurally characterized and compared with two other cyclic nucleotide phosphodiesterases from other organisms [Hofmann02]. It appears to exist as a monomer [Hofmann02].

Locations: cytosol

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

Molecular Weight of Polypeptide: 19.934 kD (from nucleotide sequence)

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 , Pfam:IN-FAMILY:PF02834

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0016070 - RNA metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0008664 - 2'-5'-RNA ligase activity Inferred from experiment Inferred by computational analysis [GOA01, Arn96]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for ligT 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]

Credits:
Last-Curated ? 08-Feb-2006 by Shearer A , SRI International


Enzymatic reaction of: 2'-5' RNA ligase

EC Number: 6.5.1.-

a 3' half-tRNA molecule with a hydroxyl on its 5' end + a 3' half-tRNA molecule with a hydroxyl on its 5' end + ATP <=> a ligated tRNA + AMP + diphosphate

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.


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Arn96, UniProt11]
UniProt: Removed.
Chain 2 -> 176
[UniProt09]
UniProt: 2'-5'-RNA ligase;
Sequence-Conflict 174
[Kawamukai91, UniProt10]
Alternate sequence: L → V; UniProt: (in Ref. 4; M60726);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
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.


References

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."

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

Hofmann02: 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

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.

UniProt10: 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."


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 18.5 on Wed Nov 26, 2014, BIOCYC13B.