Escherichia coli K-12 substr. MG1655 Enzyme: tRNA pseudouridine 55 synthase

Gene: truB Accession Numbers: EG11177 (EcoCyc), b3166, ECK3155

Synonyms: yhbA

Regulation Summary Diagram: ?

Regulation summary diagram for truB

TruB catalyzes pseudouridylation at position 55 in tRNA [Nurse95]. TruB activity contributes to wild-type thermal stability of tRNA [Urbonavicius02, Kinghorn02]. TruB also has a role distinct from its catalytic activity, perhaps RNA chaperone activity [Gutgsell00].

Crystal structures of TruB have been solved [Hoang01, Pan03, Hoang05].

The substrate specificity of the enzyme has been described and characterization of the reaction has been performed [Nurse95]. The reaction does not appear to use a catalytic cysteine [Ramamurthy99]. The U substrate is "flipped out" into the enzyme during catalysis [Hoang01]. Unlike RluA, TruB activity is not inhibited by RNA containing 5-fluorouridine [Spedaliere04].

A truB mutant exhibits a competitive disadvantage in a mixed culture [Gutgsell00]. The growth phenotypes of a truB mutant are complemented by production of catalytically inactive D48C mutant protein [Gutgsell00]. A truB mutant exhibits pliotropic phenotypes including greater than wild-type sensitivity to heat shock, and this phenotype is not complemented by production of D48C mutant protein [Kinghorn02]. A trmA truB double mutant exhibits more severe sensitivity to heat shock than a truB mutant, whereas a trmH truB double mutant and a truB mutant exhibit similar sensitivity [Kinghorn02]. A trmH trmA truB triple mutant exhibits a growth defect that is enhanced by elevated temperature as well as other defects consistent with destabilization of tRNAs lacking the wild-type modifications [Urbonavicius02].

Reviews: [Hamma06, Hur06]

Citations: [Spedaliere00, Urbonavicius03, Phannachet05]

Gene Citations: [Sands88, Nakamura85]

Locations: cytosol

Map Position: [3,309,855 <- 3,310,799] (71.34 centisomes, 257°)
Length: 945 bp / 314 aa

Molecular Weight of Polypeptide: 35.087 kD (from nucleotide sequence), 39.7 kD (experimental)

Unification Links: ASAP:ABE-0010404 , CGSC:35528 , EchoBASE:EB1164 , EcoGene:EG11177 , EcoliWiki:b3166 , ModBase:P60340 , OU-Microarray:b3166 , PortEco:truB , PR:PRO_000024126 , Pride:P60340 , Protein Model Portal:P60340 , RefSeq:NP_417635 , RegulonDB:EG11177 , SMR:P60340 , String:511145.b3166 , UniProt:P60340

Relationship Links: InterPro:IN-FAMILY:IPR002501 , InterPro:IN-FAMILY:IPR014780 , InterPro:IN-FAMILY:IPR015240 , InterPro:IN-FAMILY:IPR015947 , InterPro:IN-FAMILY:IPR020103 , Panther:IN-FAMILY:PTHR13767 , PDB:Structure:1K8W , PDB:Structure:1R3F , PDB:Structure:1ZL3 , Pfam:IN-FAMILY:PF01509 , Pfam:IN-FAMILY:PF09157

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for truB

GO Terms:

Biological Process: GO:0001522 - pseudouridine synthesis Inferred from experiment Inferred by computational analysis [GOA01, Nurse95]
GO:0006396 - RNA processing Inferred by computational analysis [GOA01]
GO:0006400 - tRNA modification Inferred by computational analysis [Gaudet10]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11]
GO:0031119 - tRNA pseudouridine synthesis Inferred by computational analysis [GOA06]
GO:1990481 - mRNA pseudouridine synthesis Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0009982 - pseudouridine synthase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Gutgsell00]
GO:0003723 - RNA binding Inferred by computational analysis [GOA01]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for truB 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]

Enzymatic reaction of: tRNA pseudouridine synthase (tRNA pseudouridine 55 synthase)

Synonyms: pseudouridylate synthase, uracil hydro-lyase (adding D-ribose 5-phosphate)

EC Number:

a uridine55 in tRNA <=> a tRNA pseudouridine55

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Sequence Features

Protein sequence of tRNA pseudouridine 55 synthase with features indicated

Feature Class Location Citations Comment
Mutagenesis-Variant 19
[Spedaliere00, UniProt11]
K → M or R: Reduced structural stability and decrease in activity.
Mutagenesis-Variant 20
[Spedaliere00, UniProt11]
P → G or L: Reduced structural stability and no change in activity.
Amino-Acid-Sites-That-Bind 43
UniProt: Substrate.
Mutagenesis-Variant 43
[Hamilton05, UniProt11]
[Hamilton05, UniProt11]
[Hamilton05, UniProt11]
[Hamilton05, UniProt11]
[Hamilton05, UniProt11]
H → N: 180-fold decrease in catalytic efficiency.
H → F: 2-fold decrease in catalytic efficiency.
H → G: 250-fold decrease in catalytic efficiency.
H → A: 330-fold decrease in catalytic efficiency.
H → Q: 50-fold decrease in catalytic efficiency.
Active-Site 48
UniProt: Nucleophile.
Mutagenesis-Variant 48
[Gutgsell00, UniProt11]
UniProt: Loss of activity.
Mutagenesis-Variant 58
[Ramamurthy99, UniProt11]
UniProt: Slight increase in activity. Slight increase in activity; when associated with A-174 and A-193.
Amino-Acid-Sites-That-Bind 76
UniProt: Substrate.
Protein-Segment 124 -> 152
UniProt: RNA binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 174
[Ramamurthy99, UniProt11]
UniProt: Slight increase in activity. Slight increase in activity; when associated with A-58 and A-193.
Amino-Acid-Sites-That-Bind 179
UniProt: Substrate; Non-Experimental Qualifier: probable;
Mutagenesis-Variant 193
[Ramamurthy99, UniProt11]
[Ramamurthy99, UniProt11]
C → V: Slight increase in activity.
C → A: Slight increase in activity; when associated with A-58 and A-174.
Amino-Acid-Sites-That-Bind 202
UniProt: Substrate.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3166 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11177; confirmed by SwissProt match.


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

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

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."

Gutgsell00: Gutgsell N, Englund N, Niu L, Kaya Y, Lane BG, Ofengand J (2000). "Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells." RNA 6(12);1870-81. PMID: 11142385

Hamilton05: Hamilton CS, Spedaliere CJ, Ginter JM, Johnston MV, Mueller EG (2005). "The roles of the essential Asp-48 and highly conserved His-43 elucidated by the pH dependence of the pseudouridine synthase TruB." Arch Biochem Biophys 433(1);322-34. PMID: 15581587

Hamma06: Hamma T, Ferre-D'Amare AR (2006). "Pseudouridine synthases." Chem Biol 13(11);1125-35. PMID: 17113994

Hoang01: Hoang C, Ferre-D'Amare AR (2001). "Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme." Cell 107(7);929-39. PMID: 11779468

Hoang05: Hoang C, Hamilton CS, Mueller EG, Ferre-D'Amare AR (2005). "Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain." Protein Sci 14(8);2201-6. PMID: 15987897

Hur06: Hur S, Stroud RM, Finer-Moore J (2006). "Substrate recognition by RNA 5-methyluridine methyltransferases and pseudouridine synthases: a structural perspective." J Biol Chem 281(51);38969-73. PMID: 17085441

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

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

Kinghorn02: Kinghorn SM, O'Byrne CP, Booth IR, Stansfield I (2002). "Physiological analysis of the role of truB in Escherichia coli: a role for tRNA modification in extreme temperature resistance." Microbiology 148(Pt 11);3511-20. PMID: 12427942

Nakamura85: Nakamura Y, Mizusawa S (1985). "In vivo evidence that the nusA and infB genes of E. coli are part of the same multi-gene operon which encodes at least four proteins." EMBO J 1985;4(2);527-32. PMID: 2990900

Nurse95: Nurse K, Wrzesinski J, Bakin A, Lane BG, Ofengand J (1995). "Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli." RNA 1(1);102-12. PMID: 7489483

Pan03: Pan H, Agarwalla S, Moustakas DT, Finer-Moore J, Stroud RM (2003). "Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit." Proc Natl Acad Sci U S A 100(22);12648-53. PMID: 14566049

Phannachet05: Phannachet K, Elias Y, Huang RH (2005). "Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase." Biochemistry 44(47);15488-94. PMID: 16300397

Ramamurthy99: Ramamurthy V, Swann SL, Spedaliere CJ, Mueller EG (1999). "Role of cysteine residues in pseudouridine synthases of different families." Biochemistry 38(40);13106-11. PMID: 10529181

Sands88: Sands JF, Regnier P, Cummings HS, Grunberg-Manago M, Hershey JW (1988). "The existence of two genes between infB and rpsO in the Escherichia coli genome: DNA sequencing and S1 nuclease mapping." Nucleic Acids Res 1988;16(22);10803-16. PMID: 2849753

Spedaliere00: Spedaliere CJ, Hamilton CS, Mueller EG (2000). "Functional importance of motif I of pseudouridine synthases: mutagenesis of aligned lysine and proline residues." Biochemistry 39(31);9459-65. PMID: 10924141

Spedaliere04: Spedaliere CJ, Mueller EG (2004). "Not all pseudouridine synthases are potently inhibited by RNA containing 5-fluorouridine." RNA 10(2);192-9. PMID: 14730018

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

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 manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Urbonavicius02: Urbonavicius J, Durand JM, Bjork GR (2002). "Three modifications in the D and T arms of tRNA influence translation in Escherichia coli and expression of virulence genes in Shigella flexneri." J Bacteriol 184(19);5348-57. PMID: 12218021

Urbonavicius03: Urbonavicius J, Stahl G, Durand JM, Ben Salem SN, Qian Q, Farabaugh PJ, Bjork GR (2003). "Transfer RNA modifications that alter +1 frameshifting in general fail to affect -1 frameshifting." RNA 9(6);760-8. PMID: 12756333

Other References Related to Gene Regulation

Caldara06: Caldara M, Charlier D, Cunin R (2006). "The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation." Microbiology 152(Pt 11);3343-54. PMID: 17074904

Charlier92: Charlier D, Roovers M, Van Vliet F, Boyen A, Cunin R, Nakamura Y, Glansdorff N, Pierard A (1992). "Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression." J Mol Biol 1992;226(2);367-86. PMID: 1640456

Granston90: Granston AE, Thompson DL, Friedman DI (1990). "Identification of a second promoter for the metY-nusA-infB operon of Escherichia coli." J Bacteriol 172(5);2336-42. PMID: 1692017

Ishii84: Ishii S, Kuroki K, Imamoto F (1984). "tRNAMetf2 gene in the leader region of the nusA operon in Escherichia coli." Proc Natl Acad Sci U S A 1984;81(2);409-13. PMID: 6364142

Krin03: Krin E, Laurent-Winter C, Bertin PN, Danchin A, Kolb A (2003). "Transcription regulation coupling of the divergent argG and metY promoters in Escherichia coli K-12." J Bacteriol 185(10);3139-46. PMID: 12730174

Makarova01: Makarova KS, Mironov AA, Gelfand MS (2001). "Conservation of the binding site for the arginine repressor in all bacterial lineages." Genome Biol 2(4);RESEARCH0013. PMID: 11305941

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.

Regnier87: Regnier P, Grunberg-Manago M, Portier C (1987). "Nucleotide sequence of the pnp gene of Escherichia coli encoding polynucleotide phosphorylase. Homology of the primary structure of the protein with the RNA-binding domain of ribosomal protein S1." J Biol Chem 1987;262(1);63-8. PMID: 2432069

Shimada13: Shimada T, Yoshida H, Ishihama A (2013). "Involvement of cyclic AMP receptor protein in regulation of the rmf gene encoding the ribosome modulation factor in Escherichia coli." J Bacteriol 195(10);2212-9. PMID: 23475967

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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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