Escherichia coli K-12 substr. MG1655 Enzyme: ThiS adenylyltransferase

Gene: thiF Accession Numbers: EG11587 (EcoCyc), b3992, ECK3984

Synonyms: thiA, thiamin (thiazole moiety) biosynthesis protein

Regulation Summary Diagram: ?

Regulation summary diagram for thiF

ThiF is involved in the synthesis of the thiazole moiety of thiamin. ThiF catalyzes the posttranslational modification of ThiS by the conversion of the carboxylic acid group of the carboxyl-terminal glycine into a thiocarboxylate [Taylor98]. More specifically, ThiF catalyzes the adenylation of the carboxyl-terminal glycine of ThiS by ATP [Begley99, Taylor98].

ThiS and ThiF form a covalently linked protein-protein conjugate as an essential intermediate of this reaction [Xi01]. The crystal structure of the ThiS-ThiF protein complex was determined at 2.0 Å resolution and shows that the ThiS-ThiF complex is a heterotetramer consisting of a dimer of heterodimers. ThiF was determined to be a zinc containing protein. [Lehmann06]

Crystal structures of ThiF alone and in complex with ATP have been solved and provide insight into the preference of ATP during adenylation of ThiS. Mutational anaysis has highlighted the importance of an ordered crossover loop in ThiF. [Duda05]

Gene Citations: [Vander93, Kelleher98]

Locations: cytosol

Map Position: [4,190,844 <- 4,191,599] (90.33 centisomes, 325°)
Length: 756 bp / 251 aa

Molecular Weight of Polypeptide: 26.97 kD (from nucleotide sequence), 27.0 kD (experimental) [Kriek07 ]

pI: 5.0

Unification Links: ASAP:ABE-0013053 , CGSC:34298 , EchoBASE:EB1546 , EcoGene:EG11587 , EcoliWiki:b3992 , ModBase:P30138 , OU-Microarray:b3992 , PortEco:thiF , PR:PRO_000024055 , Pride:P30138 , Protein Model Portal:P30138 , RefSeq:NP_418420 , RegulonDB:EG11587 , SMR:P30138 , String:511145.b3992 , UniProt:P30138

Relationship Links: InterPro:IN-FAMILY:IPR000594 , InterPro:IN-FAMILY:IPR007901 , InterPro:IN-FAMILY:IPR009036 , InterPro:IN-FAMILY:IPR012731 , InterPro:IN-FAMILY:IPR016040 , PDB:Structure:1ZFN , PDB:Structure:1ZKM , PDB:Structure:1ZUD , Pfam:IN-FAMILY:PF00899 , Pfam:IN-FAMILY:PF05237

In Paralogous Gene Group: 207 (3 members)

In Reactions of unknown directionality:

Not in pathways:
a ThiS-ThiI acyl-disulfide + a ThiF protein = a ThiS-ThiF acyl-disulfide + a ThiI sulfur-carrier protein

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for thiF

GO Terms:

Biological Process: GO:0006464 - cellular protein modification process Inferred by computational analysis [Gaudet10]
GO:0009228 - thiamine biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0009229 - thiamine diphosphate biosynthetic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Taylor98]
GO:0005515 - protein binding Inferred from experiment [Lehmann06]
GO:0005524 - ATP binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Duda05]
GO:0008270 - zinc ion binding Inferred from experiment [Lehmann06]
GO:0016779 - nucleotidyltransferase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Taylor98]
GO:0046872 - metal ion binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Lehmann06]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0008641 - small protein activating enzyme activity Inferred by computational analysis [GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [Gaudet10, DiazMejia09, Ishihama08]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers thiamin

Essentiality data for thiF 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]

Last-Curated ? 09-Aug-2013 by Kubo A , SRI International

Enzymatic reaction of: sulfur transferase (ThiS adenylyltransferase)

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.

The ThiF and ThiI proteins catalyze the transfer of sulfur from cysteine to the ThiS protein. [Begley99, Taylor98]

Enzymatic reaction of: ThiS adenylyltransferase

ThiS protein + ATP <=> ThiS-COAMP + diphosphate

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.

Cofactors or Prosthetic Groups: Mg2+ [Taylor98]

Enzymatic reaction of: adenylate:persulfide transferase (ThiS adenylyltransferase)

EC Number: 2.8.1.-

an S-sulfanyl-[ThiI sulfur-carrier protein] + a carboxy-adenylated-[ThiS sulfur-carrier protein] + 2 a reduced ferredoxin <=> a thiocarboxy-[ThiS-Protein] + a ThiI sulfur-carrier protein + AMP + 2 an oxidized ferredoxin

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)

Enzymatic reaction of: ThiS adenylyltransferase

EC Number:

a ThiS sulfur-carrier protein + ATP + H+ <=> a carboxy-adenylated-[ThiS sulfur-carrier protein] + diphosphate

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

The reaction is favored in the direction shown.

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

Sequence Features

Protein sequence of ThiS adenylyltransferase with features indicated

Feature Class Location Attached Group Citations Comment
Amino-Acid-Sites-That-Bind 11  
UniProt: ATP.
Amino-Acid-Sites-That-Bind 38  
UniProt: ATP; via amide nitrogen.
Amino-Acid-Sites-That-Bind 59  
UniProt: ATP.
Protein-Segment 59 -> 62  
UniProt: Poly-Asp; Sequence Annotation Type: compositionally biased region;
Amino-Acid-Sites-That-Bind 70  
UniProt: ATP.
Amino-Acid-Sites-That-Bind 83  
UniProt: ATP.
Amino-Acid-Sites-That-Bind 107  
UniProt: ATP; via amide nitrogen.
Nucleotide-Phosphate-Binding-Region 127 -> 131 ATP
UniProt: ATP.
Metal-Binding-Site 169  
[Lehmann06, UniProt15]
UniProt: Zinc.
Metal-Binding-Site 172  
[Lehmann06, UniProt15]
UniProt: Zinc.
Mutagenesis-Variant 174  
[Duda05, UniProt11]
UniProt: No adenylation of ThiS.
Active-Site 184  
UniProt: Glycyl persulfide ester intermediate.
Mutagenesis-Variant 184  
[Xi01, UniProt11]
UniProt: No cross-link formed with ThiS. No effect on ThiS thiocarboxylate formation in vitro. Does not support growth.
Interchain-Disulfide-Bond 184  
The C184 residue of ThiF forms an acyldisulfide bond with ThiS [Xi01].
Sequence-Conflict 229 -> 230  
[Vander93, UniProt10a]
UniProt: (in Ref. 1; AAB95618);
Metal-Binding-Site 240  
[Lehmann06, UniProt15]
UniProt: Zinc.
Metal-Binding-Site 243  
[Lehmann06, UniProt15]
UniProt: Zinc.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b3992 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11587; 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

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

Duda05: Duda DM, Walden H, Sfondouris J, Schulman BA (2005). "Structural analysis of Escherichia coli ThiF." J Mol Biol 349(4);774-86. PMID: 15896804

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

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

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

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

Kelleher98: Kelleher NL, Taylor SV, Grannis D, Kinsland C, Chiu HJ, Begley TP, McLafferty FW (1998). "Efficient sequence analysis of the six gene products (7-74 kDa) from the Escherichia coli thiamin biosynthetic operon by tandem high-resolution mass spectrometry." Protein Sci 7(8);1796-801. PMID: 10082377

Kriek07: Kriek M, Martins F, Leonardi R, Fairhurst SA, Lowe DJ, Roach PL (2007). "Thiazole synthase from Escherichia coli: an investigation of the substrates and purified proteins required for activity in vitro." J Biol Chem 282(24);17413-23. PMID: 17403671

Lehmann06: Lehmann C, Begley TP, Ealick SE (2006). "Structure of the Escherichia coli ThiS-ThiF complex, a key component of the sulfur transfer system in thiamin biosynthesis." Biochemistry 45(1);11-9. PMID: 16388576

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

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

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.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

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

Vander93: Vander Horn PB, Backstrom AD, Stewart V, Begley TP (1993). "Structural genes for thiamine biosynthetic enzymes (thiCEFGH) in Escherichia coli K-12." J Bacteriol 1993;175(4);982-92. PMID: 8432721

Xi01: Xi J, Ge Y, Kinsland C, McLafferty FW, Begley TP (2001). "Biosynthesis of the thiazole moiety of thiamin in Escherichia coli: identification of an acyldisulfide-linked protein--protein conjugate that is functionally analogous to the ubiquitin/E1 complex." Proc Natl Acad Sci U S A 98(15);8513-8. PMID: 11438688

Other References Related to Gene Regulation

Winkler02: Winkler W, Nahvi A, Breaker RR (2002). "Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression." Nature 419(6910);952-6. PMID: 12410317

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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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