Escherichia coli K-12 substr. MG1655 Polypeptide: protein involved in synthesis of threonylcarbamoyladenosine-modified tRNA

Gene: tsaC Accession Numbers: G7698 (EcoCyc), b3282, ECK3269

Synonyms: yrdC, rimN

Regulation Summary Diagram: ?

Regulation summary diagram for tsaC

TsaC is involved in the biosynthesis of the threonylcarbamoyladenosine (t6A) residue at position 37 of ANN-decoding tRNAs. Although TsaC (RimN) was initially thought to function as a ribosome maturation factor [Kaczanowska05], new evidence suggests that TsaC is a component of a heteromultimeric complex with threonylcarbamoyltransferase activity [Harris11]. A mixture of purified TsaD, TsaB, TsaC, and TsaE proteins catalyzes formation of t6A in the presence of a tRNA substrate, ATP, threonine and bicarbonate in vitro [Deutsch12].

It is known that t6A biosynthesis requires ATP [Korner74, Elkins74]; TsaC was shown to bind ATP and ADP, and potential nucleotide-binding residues Arg52 and Lys56 are required for function. tsaC complements the t6A- phenotype of a S. cerevisiae SUA5 mutant strain [El09].

TsaC binds nucleic acids, with a preference for double-stranded RNA [Teplova00]. Specifically, it interacts with both fully and partially modified (lacking t6A37) tRNAThr with high affinity [El09]. It was also shown to bind the unmodified anticodon stem-loop of tRNALys(UUU) with higher affinity than the t6A37-modified form [Harris11].

A crystal structure of TsaC has been determined at 2.0 Å resolution [Teplova00].

tsaC is an essential gene [Baba06, El09]. A probable null mutant allele of tsaCtsaC or rimN141) was identified as a suppressor of the temperature-sensitive growth phenotype of the peptide chain release factor RF1 mutant allele prfA1 [Kaczanowska04, Kaczanowska05]. However, it is not possible to separate the ΔtsaC mutation from the prfA1 allele [Kaczanowska04].

RimN: "ribosome maturation" [Kaczanowska05]

TsaC: "threonylcarbamoyl-6(six)-adenosine" [Deutsch12]

Citations: [Gerdes11]

Locations: cytosol

Map Position: [3,428,865 <- 3,429,437] (73.9 centisomes, 266°)
Length: 573 bp / 190 aa

Molecular Weight of Polypeptide: 20.768 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010766 , DIP:DIP-12916N , EchoBASE:EB2689 , EcoGene:EG12840 , EcoliWiki:b3282 , Mint:MINT-1230775 , ModBase:P45748 , OU-Microarray:b3282 , PortEco:rimN , Pride:P45748 , Protein Model Portal:P45748 , RefSeq:NP_417741 , RegulonDB:G7698 , SMR:P45748 , String:511145.b3282 , UniProt:P45748

Relationship Links: InterPro:IN-FAMILY:IPR006070 , InterPro:IN-FAMILY:IPR017945 , InterPro:IN-FAMILY:IPR023535 , PDB:Structure:1HRU , Pfam:IN-FAMILY:PF01300 , Prosite:IN-FAMILY:PS51163

In Paralogous Gene Group: 268 (3 members)

GO Terms:

Biological Process: GO:0070526 - threonylcarbamoyladenosine biosynthetic process Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Deutsch12, El09]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11a]
GO:0006450 - regulation of translational fidelity Inferred by computational analysis [Gaudet10]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11a]
GO:0042254 - ribosome biogenesis Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0000049 - tRNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, El09, Teplova00]
GO:0003725 - double-stranded RNA binding Inferred from experiment Inferred by computational analysis [GOA01, Teplova00]
GO:0005524 - ATP binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01, El09]
GO:0016779 - nucleotidyltransferase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, Lauhon12]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, Kaczanowska04]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for tsaC 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 No 37 Aerobic 7   No [Baba06, Comment 2]

Last-Curated ? 22-Aug-2012 by Keseler I , SRI International

Sequence Features

Protein sequence of protein involved in synthesis of threonylcarbamoyladenosine-modified tRNA with features indicated

Feature Class Location Citations Comment
Conserved-Region 7 -> 190
UniProt: YrdC-like;
Mutagenesis-Variant 50
[El09, UniProt11]
UniProt: Loss of activity.
Mutagenesis-Variant 52
[El09, UniProt11]
UniProt: Loss of activity.
Mutagenesis-Variant 56
[El09, UniProt11]
UniProt: No change in activity.
Mutagenesis-Variant 110
[El09, UniProt11]
UniProt: No change in activity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Deutsch12: Deutsch C, El Yacoubi B, de Crecy-Lagard V, Iwata-Reuyl D (2012). "Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside." J Biol Chem 287(17);13666-73. PMID: 22378793

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

El09: El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, Crecy-Lagard VD (2009). "The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA." Nucleic Acids Res 37(9):2894-909. PMID: 19287007

Elkins74: Elkins BN, Keller EB (1974). "The enzymatic synthesis of N-(purin-6-ylcarbamoyl)threonine, an anticodon-adjacent base in transfer ribonucleic acid." Biochemistry 13(22);4622-8. PMID: 4609459

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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

Gerdes11: Gerdes S, El Yacoubi B, Bailly M, Blaby IK, Blaby-Haas CE, Jeanguenin L, Lara-Nunez A, Pribat A, Waller JC, Wilke A, Overbeek R, Hanson AD, de Crecy-Lagard V (2011). "Synergistic use of plant-prokaryote comparative genomics for functional annotations." BMC Genomics 12 Suppl 1;S2. PMID: 21810204

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."

Harris11: Harris KA, Jones V, Bilbille Y, Swairjo MA, Agris PF (2011). "YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase." RNA 17(9);1678-87. PMID: 21775474

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Kaczanowska04: Kaczanowska M, Ryden-Aulin M (2004). "Temperature sensitivity caused by mutant release factor 1 is suppressed by mutations that affect 16S rRNA maturation." J Bacteriol 186(10);3046-55. PMID: 15126466

Kaczanowska05: Kaczanowska M, Ryden-Aulin M (2005). "The YrdC protein--a putative ribosome maturation factor." Biochim Biophys Acta 1727(2);87-96. PMID: 15716138

Korner74: Korner A, Soll D (1974). "N-(purin-6-ylcarbamoyl)threonine: biosynthesis in vitro in transfer RNA by an enzyme purified from Escherichia coli." FEBS Lett 39(3);301-6. PMID: 4604806

Lauhon12: Lauhon CT (2012). "Mechanism of N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP." Biochemistry 51(44);8950-63. PMID: 23072323

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

Teplova00: Teplova M, Tereshko V, Sanishvili R, Joachimiak A, Bushueva T, Anderson WF, Egli M (2000). "The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding." Protein Sci 2000;9(12);2557-66. PMID: 11206077

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

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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 Sun Oct 4, 2015, biocyc13.