Escherichia coli K-12 substr. MG1655 tRNA: tRNAserU

Gene: serU Accession Numbers: EG30094 (EcoCyc), b1975, ECK1971

Synonyms: supH, Su-1, ftsM, su1, supD

Superclasses: a tRNAser

Regulation Summary Diagram: ?

Regulation summary diagram for serU

tRNA(serU) is one of five serine tRNAs.

tRNAs are the adapters that allow synthesis of proteins from mRNAs. Each tRNA carries a specific amino acid to the ribosome for protein synthesis. There, the tRNA recognizes an RNA codon with its own three-nucleotide anticodon, thus allowing synthesis of a specific peptide based on an mRNA template.

tRNAs are processed to their active, mature forms by RNA cleavage and by modification of their bases. RNA cleavage consists of removal of both 5' and 3' extensions in a multistep process involving many RNases [Morl01]. RNases taking part in tRNA processing include ribonuclease E, RNase BN, RNase D, ribonuclease II, and RNase T. tRNAs are also subject to a wide variety of base modifications catalyzed by proteins such as tRNA-dihydrouridine synthase A, tRNA(i6A37) synthase, isopentenyl-adenosine A37 tRNA methylthiolase, tRNA-specific 2-thiouridylase, fused 5-methylaminomethyl-2-thiouridine-forming methyltransferase and FAD-dependent demodification enzyme, tRNA-guanine transglycosylase, tRNA m7G46 methyltransferase, tRNA pseudouridine 13 synthase, tRNA pseudouridine 65 synthase, tRNA pseudouridine 55 synthase, tRNA pseudouridine synthase I, tRNA (Gm18) 2'-O-methyltransferase, and tRNA m5U54 methyltransferase.

Mature tRNAs are linked via a 3' CCA sequence to their cognate amino acid in an ATP-dependent fashion by the appropriate amino-acid-tRNA synthetase, as shown in the tRNA charging. Subsequently, these charged tRNAs interact with the ribosome and template mRNA to generate polypeptides. The discovery of the role of tRNA in protein synthesis is reviewed in detail in [Siekevitz81].

Recognition of tRNA(ser) by seryl-tRNA synthetase depends on tertiary rather than primary structure [Asahara94]. This interaction has been evaluated by a 4 Å resolution structure of tRNA(ser) bound to seryl-tRNA synthetase and by footprinting [Price93a, Schatz91]. In addition, kinetic studies show that the extra stem loop structure of tRNA(ser) makes the biggest contribution to kcat and kM of aminoacylation, and that the anticodon stem loop is not involved [Sampson93].

The identity and relative abundance of serine tRNAs that use various serine codons have both been examined [Ishikura71, Fischer85].

The ftsM1 cell-division mutant is actually a serU mutant [Leclerc89].

Map Position: [2,041,492 <- 2,041,581] (44.0 centisomes, 158°)
Length: 90 bp

Anticodon: CGA

Reactions known to consume the compound:

tRNA charging :
a tRNAser + L-serine + ATP + H+ → an L-seryl-[tRNAser] + AMP + diphosphate

Reactions known to produce the compound:

tRNA processing :
a tRNA precursor with a short 3' extension → an uncharged tRNA + n a nucleoside 5'-monophosphate
a tRNA precursor with a short 3' extension + n phosphate → an uncharged tRNA + n a ribonucleoside diphosphate
a tRNA precursor with a 5' extension + H2O → an uncharged tRNA + a single-stranded RNA

Not in pathways:
an N-modified aminoacyl-[tRNA] + H2O → an uncharged tRNA + an N-modified amino acid + 2 H+
a D-aminoacyl-[tRNA] + H2O → a D-amino acid + an uncharged tRNA + 2 H+

Not in pathways:
a tRNA precursor + H2O → a tRNA + a nucleoside 5'-monophosphate

tRNA processing :
a tRNA precursor with a 5' extension and a short 3' extension + H2O → a tRNA precursor with a short 3' extension + a single-stranded RNA
a tRNA precursor with a 5' extension + H2O → an uncharged tRNA + a single-stranded RNA

Not in pathways:
YhaV endonuclease degradation substrate mRNA + H2O → 2 a single-stranded RNA
an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
RNase E degradation substrate mRNA + n H2O → n a single-stranded RNA
YhaV endonuclease degradation substrate rRNA + H2O → 2 a single-stranded RNA
RNase III mRNA processing substrate + 2 H2O → RNase III processing product mRNA + 2 a single-stranded RNA
23S rRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]
an mRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]
RNase G degradation substrate mRNA + H2O → 2 a single-stranded RNA
9S rRNA + 2 H2O → 5S rRNA + 2 a single-stranded RNA
RNase E mRNA processing substrate + n H2O → RNase E processing product mRNA + n a single-stranded RNA

Reactions known to both consume and produce the compound:

Not in pathways:
a single-stranded RNA + phosphate ↔ a single-stranded RNA + a nucleoside diphosphate

In Reactions of unknown directionality:

Not in pathways:
rRNA[periplasmic space] = 2 a single-stranded RNA[periplasmic space]

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Unification Links: ASAP:ABE-0006554 , CGSC:167 , EchoBASE:EB4257 , EcoGene:EG30094 , EcoliWiki:b1975 , OU-Microarray:b1975 , PortEco:serU , RegulonDB:EG30094

GO Terms:

Molecular Function: GO:0030533 - triplet codon-amino acid adaptor activity
Cellular Component: GO:0005737 - cytoplasm
GO:0005829 - cytosol

MultiFun Terms: information transfer RNA related tRNA

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome
7/10/1998 (pkarp) Merged genes G457/ftsM and EG30094/serU
10/20/97 Gene b1975 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG30094.

Last-Curated ? 26-Apr-2006 by Shearer A , SRI International


Asahara94: Asahara H, Himeno H, Tamura K, Nameki N, Hasegawa T, Shimizu M (1994). "Escherichia coli seryl-tRNA synthetase recognizes tRNA(Ser) by its characteristic tertiary structure." J Mol Biol 236(3);738-48. PMID: 8114091

Fischer85: Fischer W, Sprinzl M (1985). "Serine-specific tRNAs in Escherichia coli: relative abundance and sequence." Biochem Int 11(5);661-8. PMID: 3911956

Ishikura71: Ishikura H, Yamada Y, Nishimura S (1971). "Structure of serine tRNA from Escherichia coli. I. Purification of serine tRNA's with different codon responses." Biochim Biophys Acta 228(2);471-81. PMID: 4925825

Leclerc89: Leclerc G, Sirard C, Drapeau GR (1989). "The Escherichia coli cell division mutation ftsM1 is in serU." J Bacteriol 171(4);2090-5. PMID: 2649486

Morl01: Morl M, Marchfelder A (2001). "The final cut. The importance of tRNA 3'-processing." EMBO Rep 2(1);17-20. PMID: 11252717

Price93a: Price S, Cusack S, Borel F, Berthet-Colominas C, Leberman R (1993). "Crystallization of the seryl-tRNA synthetase:tRNAS(ser) complex of Escherichia coli." FEBS Lett 324(2);167-70. PMID: 8508916

Sampson93: Sampson JR, Saks ME (1993). "Contributions of discrete tRNA(Ser) domains to aminoacylation by E.coli seryl-tRNA synthetase: a kinetic analysis using model RNA substrates." Nucleic Acids Res 21(19);4467-75. PMID: 8233780

Schatz91: Schatz D, Leberman R, Eckstein F (1991). "Interaction of Escherichia coli tRNA(Ser) with its cognate aminoacyl-tRNA synthetase as determined by footprinting with phosphorothioate-containing tRNA transcripts." Proc Natl Acad Sci U S A 88(14);6132-6. PMID: 2068094

Siekevitz81: Siekevitz P, Zamecnik PC (1981). "Ribosomes and protein synthesis." J Cell Biol 91(3 Pt 2);53s-65s. PMID: 7033244

Other References Related to Gene Regulation

Neidhardt96: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low Jr KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE "Escherichia coli and Salmonella, Cellular and Molecular Biology, Second Edition." American Society for Microbiology, Washington, D.C., 1996.

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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 Mon May 25, 2015, BIOCYC14A.