Escherichia coli K-12 substr. MG1655 Enzyme: tRNA pseudouridine 13 synthase

Gene: truD Accession Numbers: G7422 (EcoCyc), b2745, ECK2740

Synonyms: ygbO

Regulation Summary Diagram: ?

Regulation summary diagram for truD

TruD is responsible for biosynthesis of the pseudouridine13 modification of tRNA(Glu) [Kaya03]. The enzyme has been purified, and activity has been observed in vitro [Kaya03].

A truD mutant lacks tRNA(Glu) pseudouridine13 [Kaya03]. A conserved Asp is required for catalysis [Kaya03].

TruD is a member of a family of pseudouridine synthases that is widely conserved, yet unrelated to the families of pseudouridine synthases characterized previously [Kaya03]. The crystal structure showed that the protein consists of two domains, a catalytic domain with a fold similar to other pseudouridine synthases, and an insertion domain with a novel fold [Kaya04, Ericsson04, Ericsson04a, Hoang04a].

Reviews: [Hamma06, Hur06]

Locations: cytosol

Map Position: [2,868,277 <- 2,869,326] (61.82 centisomes, 223°)
Length: 1050 bp / 349 aa

Molecular Weight of Polypeptide: 39.091 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009011 , EchoBASE:EB2912 , EcoGene:EG13109 , EcoliWiki:b2745 , ModBase:Q57261 , OU-Microarray:b2745 , PortEco:truD , PR:PRO_000024128 , Pride:Q57261 , Protein Model Portal:Q57261 , RefSeq:NP_417225 , RegulonDB:G7422 , SMR:Q57261 , String:511145.b2745 , UniProt:Q57261

Relationship Links: InterPro:IN-FAMILY:IPR001656 , InterPro:IN-FAMILY:IPR011760 , InterPro:IN-FAMILY:IPR020103 , InterPro:IN-FAMILY:IPR020119 , Panther:IN-FAMILY:PTHR13326 , PDB:Structure:1SB7 , PDB:Structure:1SI7 , PDB:Structure:1SZW , Pfam:IN-FAMILY:PF01142 , Prosite:IN-FAMILY:PS01268 , Prosite:IN-FAMILY:PS50984

In Paralogous Gene Group: 451 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0001522 - pseudouridine synthesis Inferred from experiment Inferred by computational analysis [GOA01a, Kaya03]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11a]
GO:0031119 - tRNA pseudouridine synthesis Inferred by computational analysis [GOA06]
Molecular Function: GO:0009982 - pseudouridine synthase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Kaya03]
GO:0003723 - RNA binding Inferred by computational analysis [GOA01a]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
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 truD 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 13 synthase)

EC Number:

a uridine13 in tRNA <=> a pseudouridine13 in tRNA

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 13 synthase with features indicated

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 27
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 31
[Chan09a, UniProt11a]
[Chan09a, UniProt11a]
E → D: 3-fold decrease in activity.
E → Q: Loss of activity.
Active-Site 31
UniProt: Proton acceptor; Non-Experimental Qualifier: potential.
Mutagenesis-Variant 79
[Chan09a, UniProt11a]
[Chan09a, UniProt11a]
K → R: 10-fold decrease in activity.
K → L: 20-fold decrease in activity.
Active-Site 80
[Chan09a, UniProt11a]
UniProt: Nucleophile.
Mutagenesis-Variant 80
[Kaya03, UniProt11]
D → N or T: Loss of activity.
Mutagenesis-Variant 87
[Chan09a, UniProt11a]
UniProt: 3-fold decrease in activity.
Mutagenesis-Variant 129
[Chan09a, UniProt11a]
UniProt: Loss of activity.
Amino-Acid-Sites-That-Bind 129
UniProt: Substrate; Non-Experimental Qualifier: probable;
Mutagenesis-Variant 131
[Chan09a, UniProt11a]
UniProt: 1.5-fold decrease in activity.
Conserved-Region 155 -> 303
UniProt: TRUD;
Protein-Segment 180 -> 187
UniProt: RNA binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: probable;
Amino-Acid-Sites-That-Bind 329
UniProt: Substrate; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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

Chan09a: Chan CM, Huang RH (2009). "Enzymatic characterization and mutational studies of TruD--the fifth family of pseudouridine synthases." Arch Biochem Biophys 489(1-2);15-9. PMID: 19664587

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

Ericsson04: Ericsson UB, Andersson ME, Engvall B, Nordlund P, Hallberg BM (2004). "Expression, purification, crystallization and preliminary diffraction studies of the tRNA pseudouridine synthase TruD from Escherichia coli." Acta Crystallogr D Biol Crystallogr 60(Pt 4);775-6. PMID: 15039583

Ericsson04a: Ericsson UB, Nordlund P, Hallberg BM (2004). "X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold." FEBS Lett 565(1-3);59-64. PMID: 15135053

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

GOA01a: 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."

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

Hoang04a: Hoang C, Ferre-D'Amare AR (2004). "Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold." RNA 10(7);1026-33. PMID: 15208439

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

Kaya03: Kaya Y, Ofengand J (2003). "A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya." RNA 9(6);711-21. PMID: 12756329

Kaya04: Kaya Y, Del Campo M, Ofengand J, Malhotra A (2004). "Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold." J Biol Chem 279(18);18107-10. PMID: 14999002

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

UniProt10a: 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.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

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 Thu Oct 8, 2015, biocyc13.