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Escherichia coli K-12 substr. MG1655 Enzyme: ThiI



Gene: thiI Accession Numbers: G6238 (EcoCyc), b0423, ECK0417

Synonyms: nuvA, nuvC, yajK

Regulation Summary Diagram: ?

Summary:
ThiI is a bifunctional enzyme that is required both for the synthesis of the thiazole moiety of thiamine and for the conversion of uridine to 4-thiouridine at position 8 in tRNA [Ryals82, Mueller98]. The protein contains several domains, and different domains are involved in tRNA modification and thiazole formation. The THUMP and AANH domains are required for tRNA modification, while the only domain necessary for thiozole formation is the C-terminal rhodanese domain (as shown for the enzyme from Salmonella [MartinezGomez11]).

Regarding thiazole biosynthesis, it has been shown that the thiI gene plays an essential role in the formation of a thiocarboxylate on the carboxylic acid group of the carboxyl-terminal glycine of the ThiS protein. ThiS isolated from a thiI-defficient strain does not contain this modification [Taylor98].

Regarding uridine modification, the enzyme adenylates the tRNA uridine and transfers sulfur from a persulfide formed on the protein. It is specific for the U8 residue of tRNA; the substrate specificity appears to be conferred by the secondary and tertiary structure of tRNA [Lauhon04]. The ThiI protein, but not the IscS protein, was shown to interact with tRNA. In vitro studies using radiolabelled sulfur showed transfer of sulfur from IscS to ThiI; if tRNA is included, the sulfur appears to be incorporated into the tRNA in a ThiI- and ATP-dependent manner. Based on these results, a model for mobilization and transfer of sulfur from cysteine via IscS and ThiI to U8 of tRNA has been presented [Kambampati00].

The Cys-456 [Palenchar00] and Cys-344 [Mueller01] residues are critical for the sulfur transfer function of ThiI, and a mechanism for sulfur transfer including the formation of a disulfide bond between Cys-456 and Cys-344 during turnover has been proposed [Mueller01].

The N-domain of ThiI recognizes the acceptor-stem region of tRNA [Tanaka09].

The assignment of thiI to either of the previously identified UV-resistant mutants nuvA or nuvC remains unclear.

Locations: cytosol

Map Position: [440,773 -> 442,221] (9.5 centisomes)
Length: 1449 bp / 482 aa

Molecular Weight of Polypeptide: 54.973 kD (from nucleotide sequence), 57.1 kD (experimental) [Mueller98 ]

Unification Links: ASAP:ABE-0001470 , DIP:DIP-10985N , EchoBASE:EB3058 , EcoGene:EG13273 , EcoliWiki:b0423 , ModBase:P77718 , OU-Microarray:b0423 , PortEco:thiI , PR:PRO_000024058 , Pride:P77718 , Protein Model Portal:P77718 , RefSeq:NP_414957 , RegulonDB:G6238 , SMR:P77718 , String:511145.b0423 , UniProt:P77718

Relationship Links: InterPro:IN-FAMILY:IPR001763 , InterPro:IN-FAMILY:IPR003720 , InterPro:IN-FAMILY:IPR004114 , InterPro:IN-FAMILY:IPR014729 , InterPro:IN-FAMILY:IPR020536 , InterPro:IN-FAMILY:IPR026340 , Pfam:IN-FAMILY:PF02568 , Pfam:IN-FAMILY:PF02926 , Prosite:IN-FAMILY:PS50206 , Prosite:IN-FAMILY:PS51165 , Smart:IN-FAMILY:SM00981

In Paralogous Gene Group: 125 (2 members)

Reactions known to consume the compound:

thiazole biosynthesis I (E. coli) :
an [L-cysteine desulfurase] L-cysteine persulfide + a ThiI sulfur-carrier protein → an [L-cysteine desulfurase]-L-cysteine + an S-sulfanyl-[ThiI sulfur-carrier protein]

Reactions known to produce the compound:

thiazole biosynthesis I (E. coli) :
an S-sulfanyl-[ThiI sulfur-carrier protein] + a carboxy-adenylated-[ThiS sulfur-carrier protein] → a thiocarboxy-adenylated-[ThiS-Protein] + a ThiI sulfur-carrier protein + AMP

In Reactions of unknown directionality:

Not in pathways:
a ThiI sulfur-carrier protein + L-cysteine = an S-sulfanyl-[ThiI sulfur-carrier protein] + L-alanine
a ThiS-ThiI acyl-disulfide + a ThiF protein = a ThiS-ThiF acyl-disulfide + a ThiI sulfur-carrier protein

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0002937 - tRNA 4-thiouridine biosynthesis Inferred from experiment [Ryals82]
GO:0009228 - thiamine biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, Ryals82]
GO:0009229 - thiamine diphosphate biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0034227 - tRNA thio-modification Inferred by computational analysis [GOA06, GOA01]
GO:0052837 - thiazole biosynthetic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0000049 - tRNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, Lauhon04]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0004810 - tRNA adenylyltransferase activity Inferred by computational analysis [GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016783 - sulfurtransferase activity Inferred by computational analysis [GOA06, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]

MultiFun Terms: information transfer RNA related RNA modification
metabolism biosynthesis of building blocks cofactors, small molecule carriers thiamin

Essentiality data for thiI 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]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 13-Aug-2013 by Kubo A , SRI International


Enzymatic reaction of: cysteine sulfur transferase (ThiI)

Synonyms: thiamin biosynthesis protein ThiI

ThiS-COAMP + L-cysteine <=> ThiS-COSH + L-alanine + AMP

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.

Reversibility of this reaction is unspecified.

Summary:
The ThiI and ThiF proteins catalyze the sulfur transfer from cysteine to ThiS during thiazole formation in thiamin biosynthesis. [Taylor98, Begley99, Mueller98, Palenchar00]


Enzymatic reaction of: carboxy-adenylated-[ThiS sulfur-carrier-protein] sulfurtransferase (ThiI)

an S-sulfanyl-[ThiI sulfur-carrier protein] + a carboxy-adenylated-[ThiS sulfur-carrier protein] <=> a thiocarboxy-adenylated-[ThiS-Protein] + a ThiI sulfur-carrier protein + AMP

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 favored in the direction shown.

In Pathways: superpathway of thiamin diphosphate biosynthesis I , thiazole biosynthesis I (E. coli)

Credits:
Imported from MetaCyc 13-Sep-2011 by Caspi R , SRI International


Enzymatic reaction of: tRNA sulfurtransferase (ThiI)

EC Number: 2.8.1.4

'activated' tRNA + L-cysteine <=> L-serine + tRNA containing a thionucleotide

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.

Summary:
ATP hydrolysis is required.

Inhibitors (Irreversible): 5-((2-iodoacetamido)ethyl)-1-aminonapthalene sulfate [Kambampati00]


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 61 -> 165
[UniProt09]
UniProt: THUMP;
Mutagenesis-Variant 108
[Mueller01, UniProt11]
Alternate sequence: C → A; UniProt: No effect.
Nucleotide-Phosphate-Binding-Region 183 -> 184
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 189
[Mueller99a, UniProt11]
Alternate sequence: D → A; UniProt: No activity.
Mutagenesis-Variant 202
[Mueller01, UniProt11]
Alternate sequence: C → A; UniProt: No effect.
Mutagenesis-Variant 207
[Mueller01, UniProt11]
Alternate sequence: C → A; UniProt: Enables partial functional complementation in vivo. Four-fold reduction in activity.
Amino-Acid-Sites-That-Bind 265
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 287
[UniProt10]
UniProt: ATP; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 296
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 321
[Mueller99a, UniProt11]
Alternate sequence: K → R; UniProt: Approximately half of wild-type activity.
Alternate sequence: K → M; UniProt: No activity.
Mutagenesis-Variant 344
[Mueller01, UniProt11]
Alternate sequence: C → A; UniProt: Cannot functionally complement for wild-type enzyme in vivo. 2700-fold reduction in activity.
Disulfide-Bond-Site 456, 344
[Wright06, Mueller01, UniProt11]
UniProt: Redox-active.
Conserved-Region 404 -> 482
[UniProt09]
UniProt: Rhodanese;
Mutagenesis-Variant 456
[Palenchar00, UniProt11]
Alternate sequence: C → A; UniProt: No activity.
Active-Site 456
[UniProt10b]
UniProt: Cysteine persulfide intermediate;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
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

Begley99: Begley TP, Downs DM, Ealick SE, McLafferty FW, Van Loon AP, Taylor S, Campobasso N, Chiu HJ, Kinsland C, Reddick JJ, Xi J (1999). "Thiamin biosynthesis in prokaryotes." Arch Microbiol 1999;171(5);293-300. PMID: 10382260

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

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."

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

Kambampati00: Kambampati R, Lauhon CT (2000). "Evidence for the transfer of sulfane sulfur from IscS to ThiI during the in vitro biosynthesis of 4-thiouridine in Escherichia coli tRNA." J Biol Chem 2000;275(15);10727-30. PMID: 10753862

Lauhon04: Lauhon CT, Erwin WM, Ton GN (2004). "Substrate specificity for 4-thiouridine modification in Escherichia coli." J Biol Chem 279(22);23022-9. PMID: 15037613

MartinezGomez11: Martinez-Gomez NC, Palmer LD, Vivas E, Roach PL, Downs DM (2011). "The Rhodanese Domain of ThiI Is Both Necessary and Sufficient for Synthesis of the Thiazole Moiety of Thiamine in Salmonella enterica." J Bacteriol 193(18);4582-7. PMID: 21724998

Mueller01: Mueller EG, Palenchar PM, Buck CJ (2001). "The role of the cysteine residues of ThiI in the generation of 4-thiouridine in tRNA." J Biol Chem 276(36);33588-95. PMID: 11443125

Mueller98: Mueller EG, Buck CJ, Palenchar PM, Barnhart LE, Paulson JL (1998). "Identification of a gene involved in the generation of 4-thiouridine in tRNA." Nucleic Acids Res 26(11);2606-10. PMID: 9592144

Mueller99a: Mueller EG, Palenchar PM (1999). "Using genomic information to investigate the function of ThiI, an enzyme shared between thiamin and 4-thiouridine biosynthesis." Protein Sci 8(11);2424-7. PMID: 10595545

Palenchar00: Palenchar PM, Buck CJ, Cheng H, Larson TJ, Mueller EG (2000). "Evidence that ThiI, an enzyme shared between thiamin and 4-thiouridine biosynthesis, may be a sulfurtransferase that proceeds through a persulfide intermediate." J Biol Chem 275(12);8283-6. PMID: 10722656

Ryals82: Ryals J, Hsu RY, Lipsett MN, Bremer H (1982). "Isolation of single-site Escherichia coli mutants deficient in thiamine and 4-thiouridine syntheses: identification of a nuvC mutant." J Bacteriol 151(2);899-904. PMID: 6178725

Tanaka09: Tanaka Y, Yamagata S, Kitago Y, Yamada Y, Chimnaronk S, Yao M, Tanaka I (2009). "Deduced RNA binding mechanism of ThiI based on structural and binding analyses of a minimal RNA ligand." RNA 15(8);1498-506. PMID: 19509301

Taylor98: Taylor SV, Kelleher NL, Kinsland C, Chiu HJ, Costello CA, Backstrom AD, McLafferty FW, Begley TP (1998). "Thiamin biosynthesis in Escherichia coli. Identification of this thiocarboxylate as the immediate sulfur donor in the thiazole formation." J Biol Chem 273(26);16555-60. PMID: 9632726

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

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

UniProt10b: 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."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Wright06: Wright CM, Christman GD, Snellinger AM, Johnston MV, Mueller EG (2006). "Direct evidence for enzyme persulfide and disulfide intermediates during 4-thiouridine biosynthesis." Chem Commun (Camb) (29);3104-6. PMID: 16855700

Other References Related to Gene Regulation

Raghavan11: Raghavan R, Groisman EA, Ochman H (2011). "Genome-wide detection of novel regulatory RNAs in E. coli." Genome Res 21(9);1487-97. PMID: 21665928


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 Thu Nov 20, 2014, BIOCYC13B.