Escherichia coli K-12 substr. MG1655 Enzyme: tRNA-dihydrouridine synthase C

Gene: dusC Accession Numbers: EG12022 (EcoCyc), b2140, ECK2133

Synonyms: yohI

Regulation Summary Diagram: ?

Regulation summary diagram for dusC

DusB and DusC together account for about half of the 5,6-dihydrouridine modification observed in wild-type cellular tRNA, and DusA accounts for the other half [Bishop02]. DusC specifically modifies U16 of the D loop in tRNAs. The site selectivity of the enzyme is conveyed by binding the tRNA substrate in a different orientation when compared to an enzyme that modifies U20, on the opposite side of the D loop [Byrne15].

Crystal structures of DusC have been solved, showing an N-terminal catalytic TIM-barrel domain and a C-terminal tRNA binding domain [Chen13a, Byrne15]. Crystal structures of DusC in complex with tRNAs elucidated the basis for modification site specificity of the enzyme [Byrne15].

A dusA dusB dusC triple mutant exhibits a complete lack of 5,6-dihydrouridine modification in cellular tRNA, whereas each single mutant exhibits a partial reduction, compared to wild type [Bishop02].

DusC: "dihydrouridine synthase C"

Locations: cytosol

Map Position: [2,227,460 <- 2,228,407] (48.01 centisomes, 173°)
Length: 948 bp / 315 aa

Molecular Weight of Polypeptide: 35.199 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007074 , DIP:DIP-12808N , EchoBASE:EB1957 , EcoGene:EG12022 , EcoliWiki:b2140 , ModBase:P33371 , OU-Microarray:b2140 , PortEco:dusC , PR:PRO_000022492 , Pride:P33371 , Protein Model Portal:P33371 , RefSeq:NP_416645 , RegulonDB:EG12022 , SMR:P33371 , String:511145.b2140 , UniProt:P33371

Relationship Links: InterPro:IN-FAMILY:IPR001269 , InterPro:IN-FAMILY:IPR013785 , InterPro:IN-FAMILY:IPR018517 , Panther:IN-FAMILY:PTHR11082 , PDB:Structure:3W9Z , PDB:Structure:4BF9 , PDB:Structure:4BFA , Pfam:IN-FAMILY:PF01207 , Prosite:IN-FAMILY:PS01136

In Paralogous Gene Group: 511 (3 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0002943 - tRNA dihydrouridine synthesis Inferred from experiment Inferred by computational analysis [GOA01a, Bishop02]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0017150 - tRNA dihydrouridine synthase activity Inferred from experiment Inferred by computational analysis [GOA01a, Bishop02]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0050660 - flavin adenine dinucleotide binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for dusC 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]

Last-Curated ? 30-Apr-2015 by Keseler I , SRI International

Enzymatic reaction of: tRNA-dihydrouridine synthase

EC Number: 1.1.1.-

a uridine in tRNA + NADPH + H+ <=> a 5,6-dihydrouridine in tRNA + NADP+

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.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b2140 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12022; 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

Bishop02: Bishop AC, Xu J, Johnson RC, Schimmel P, de Crecy-Lagard V (2002). "Identification of the tRNA-dihydrouridine synthase family." J Biol Chem 277(28);25090-5. PMID: 11983710

Byrne15: Byrne RT, Jenkins HT, Peters DT, Whelan F, Stowell J, Aziz N, Kasatsky P, Rodnina MV, Koonin EV, Konevega AL, Antson AA (2015). "Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases." Proc Natl Acad Sci U S A. PMID: 25902496

Chen13a: Chen M, Yu J, Tanaka Y, Tanaka M, Tanaka I, Yao M (2013). "Structure of dihydrouridine synthase C (DusC) from Escherichia coli." Acta Crystallogr Sect F Struct Biol Cryst Commun 69(Pt 8);834-8. PMID: 23908023

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Raghavan11: Raghavan R, Sage A, Ochman H (2011). "Genome-wide identification of transcription start sites yields a novel thermosensing RNA and new cyclic AMP receptor protein-regulated genes in Escherichia coli." J Bacteriol 193(11);2871-4. PMID: 21460078

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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 Fri Oct 9, 2015, biocyc14.