Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: sulfur transfer protein complex, TusD subunit



Gene: tusD Accession Numbers: G7714 (EcoCyc), b3345, ECK3332

Synonyms: yheN

Regulation Summary Diagram: ?

Component of: sulfur transfer protein complex (summary available)

Summary:
TusD is labeled by 35S sulfur during 2-thiouridine formation in vitro. The cysteine residue C78 appears to be responsible for accepting the activated sulfur [Ikeuchi06, Numata06].

A tusD deletion mutant lacks the 2-thio modification of mnm5s2U in tRNA and has a severe growth defect [Ikeuchi06].

TusD: "tRNA 2-thiouridine synthesizing protein" [Ikeuchi06]

Locations: cytosol

Map Position: [3,473,354 <- 3,473,740] (74.86 centisomes)
Length: 387 bp / 128 aa

Molecular Weight of Polypeptide: 13.641 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010933 , DIP:DIP-12310N , EchoBASE:EB2735 , EcoGene:EG12898 , EcoliWiki:b3345 , ModBase:P45532 , OU-Microarray:b3345 , PortEco:yheN , PR:PRO_000024146 , Protein Model Portal:P45532 , RefSeq:NP_417804 , RegulonDB:G7714 , SMR:P45532 , String:511145.b3345 , Swiss-Model:P45532 , UniProt:P45532

Relationship Links: InterPro:IN-FAMILY:IPR003787 , InterPro:IN-FAMILY:IPR017463 , InterPro:IN-FAMILY:IPR027396 , PDB:Structure:2D1P , Pfam:IN-FAMILY:PF02635

In Paralogous Gene Group: 262 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006810 - transport Inferred from experiment [Ikeuchi06]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
Molecular Function: GO:0097163 - sulfur carrier activity Inferred from experiment [Ikeuchi06]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016783 - sulfurtransferase activity Inferred by computational analysis [GOA06, GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for tusD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Subunit of: sulfur transfer protein complex

Subunit composition of sulfur transfer protein complex = [TusB]2[TusC]2[TusD]2
         sulfur transfer protein complex, TusB subunit = TusB (summary available)
         sulfur transfer protein complex, TusC subunit = TusC (summary available)
         sulfur transfer protein complex, TusD subunit = TusD (summary available)

Summary:
The TusBDC complex functions as a sulfur mediator during synthesis of 2-thiouridine of the modified wobble base mnm5s2U in tRNA. Activated sulfur appears to be transferred from TusA to a cysteine residue in TusD and subsequently transferred to TusE. TusE stimulates the transfer of sulfur from TusA to TusD. The TusBCD complex does not appear to bind tRNA directly in an in vitro assay, but it does interact with TusE [Ikeuchi06].

A crystal structure of the TusBCD complex has been determined at 2.15 Å resolution. All three subunits show structural similarity to a protein of unknown function, YchN [Numata06].

Molecular Weight: 55 kD (experimental) [Numata06]

Relationship Links: PDB:Structure:2D1P

GO Terms:

Biological Process: GO:0002143 - tRNA wobble position uridine thiolation Inferred from experiment [Ikeuchi06]

Credits:
Created 15-Feb-2006 by Keseler I , SRI International
Last-Curated ? 15-Feb-2006 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 78
[Numata06, Ikeuchi06, UniProt11]
Alternate sequence: C → S; UniProt: Loss of activity.
Active-Site 78
[UniProt10a]
UniProt: Cysteine persulfide intermediate;
Mutagenesis-Variant 122
[Numata06, UniProt11]
Alternate sequence: C → S; UniProt: Reduced activity.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
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.


References

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

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."

Ikeuchi06: Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T (2006). "Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions." Mol Cell 21(1);97-108. PMID: 16387657

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

Numata06: Numata T, Fukai S, Ikeuchi Y, Suzuki T, Nureki O (2006). "Structural Basis for Sulfur Relay to RNA Mediated by Heterohexameric TusBCD Complex." Structure 14(2);357-66. PMID: 16472754

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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 manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


Report Errors or Provide Feedback
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 18.5 on Sun Nov 23, 2014, biocyc14.