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Escherichia coli K-12 substr. MG1655 Enzyme: tyrosine lyase



Gene: thiH Accession Numbers: EG11590 (EcoCyc), b3990, ECK3981

Synonyms: thiB

Regulation Summary Diagram: ?

Component of:
thiazole synthase (summary available)
thiazole synthase (summary available)

Summary:
ThiH is a tyrosine lyase that cleaves the Cα-Cβ bond of L-tyrosine, generating 4-methylphenol as a by-product, to form 2-iminoacetate. The later acts as one of three substrates for the thiazole cyclization reaction catalyzed by ThiG. [Challand10]

ThiH is a radical S-adenosylmethionine enzyme that utilizes a [4Fe-4S] cluster to reductively cleave AdoMet, forming methionine and a 5'-deoxyadenosyl radical. The radical abstracts a hydrogen radical from a residue in ThiH. Once radicalyzed, the enzyme attach L-tyrosine, forming 2-iminoacetate and 4-methylphenol [Kriek07, Kriek07a].

ThiH and ThiG form a complex. It is possible that 2-iminoacetate remains bound to the enzyme, ensuring that tyrosine cleavage catalyzed by ThiH is synchronized with the incorporation of dehydroglycine by ThiG into the thiazole carboxylate [Kriek07].

Mutagenesis of the thiH gene was performed and residues required for in vivo function were identified. [MartinezGomez04]

Gene Citations: [Vander93, Kelleher98]

Locations: cytosol

Map Position: [4,188,758 <- 4,189,891] (90.28 centisomes)
Length: 1134 bp / 377 aa

Molecular Weight of Polypeptide: 43.32 kD (from nucleotide sequence), 42.0 kD (experimental) [Challand10 ]

pI: 7.0

Unification Links: ASAP:ABE-0013048 , CGSC:34292 , DIP:DIP-6869N , EchoBASE:EB1548 , EcoGene:EG11590 , EcoliWiki:b3990 , ModBase:P30140 , OU-Microarray:b3990 , PortEco:thiH , PR:PRO_000024057 , Pride:P30140 , Protein Model Portal:P30140 , RefSeq:NP_418417 , RegulonDB:EG11590 , SMR:P30140 , String:511145.b3990 , UniProt:P30140

Relationship Links: InterPro:IN-FAMILY:IPR007197 , InterPro:IN-FAMILY:IPR010722 , InterPro:IN-FAMILY:IPR012726 , InterPro:IN-FAMILY:IPR013785 , Pfam:IN-FAMILY:PF04055 , Pfam:IN-FAMILY:PF06968 , Smart:IN-FAMILY:SM00876

In Paralogous Gene Group: 195 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0009228 - thiamine biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Vander93]
GO:0009229 - thiamine diphosphate biosynthetic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Leonardi03]
GO:0016829 - lyase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, Challand10]
GO:0051536 - iron-sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Kriek07a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Kriek07a]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0005506 - iron ion binding Inferred by computational analysis [GOA01]
GO:0036355 - 2-iminoacetate synthase activity Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

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

Essentiality data for thiH 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]
Yes [Feist07, Comment 3]

Credits:
Last-Curated ? 12-Aug-2013 by Kubo A , SRI International


Enzymatic reaction of: tyrosine lyase

EC Number: 4.1.99.19

L-tyrosine + S-adenosyl-L-methionine + NADPH <=> 2-iminoacetate + 4-methylphenol + 5'-deoxyadenosine + L-methionine + NADP+ + H+

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 physiologically favored in the direction shown.

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


Subunit of: thiazole synthase

Subunit composition of thiazole synthase = [ThiG][ThiH]
         tyrosine lyase = ThiH (extended summary available)

Component of: thiazole synthase (summary available)

Summary:
The ThiGH complex catalyzes the conversion of 1-deoxy-D-xylulose 5-phosphate to a thiazole as part of thiamine synthesis.

ThiG and ThiH combine to form a complex containing an iron-sulfuer cluster [Leonardi03]. Together, they are required for the synthesis of 4-methyl-5-(β-hydroxyethyl)thiazole phosphate, which is the rate-limiting step in thiamine synthesis [Vander93, Leonardi04].

Molecular Weight: 440 kD (experimental) [Leonardi03]

Credits:
Created 15-Mar-2006 by Shearer A , SRI International
Last-Curated ? 15-Mar-2006 by Shearer A , SRI International


Subunit of: thiazole synthase

Subunit composition of thiazole synthase = [(ThiG)(ThiH)]6
         thiazole synthase = (ThiG)(ThiH)
                 tyrosine lyase = ThiH (extended summary available)

Summary:
The ThiGH complex catalyzes the conversion of 1-deoxy-D-xylulose 5-phosphate to a thiazole as part of thiamine synthesis.

ThiG and ThiH combine to form a complex containing an iron-sulfuer cluster [Leonardi03]. Together, they are required for the synthesis of 4-methyl-5-(β-hydroxyethyl)thiazole phosphate, which is the rate-limiting step in thiamine synthesis [Vander93, Leonardi04].

Molecular Weight: 440.0 kD (experimental) [Challand10]

Credits:
Created 15-Mar-2010 by Caspi R , SRI International


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 85
[UniProt10a]
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 89
[UniProt10a]
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 92
[UniProt10a]
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3990 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11590; confirmed by SwissProt match.


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

Challand10: Challand MR, Martins FT, Roach PL (2010). "Catalytic activity of the anaerobic tyrosine lyase required for thiamine biosynthesis in Escherichia coli." J Biol Chem 285(8);5240-8. PMID: 19923213

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Kriek07: Kriek M, Martins F, Challand MR, Croft A, Roach PL (2007). "Thiamine biosynthesis in Escherichia coli: identification of the intermediate and by-product derived from tyrosine." Angew Chem Int Ed Engl 46(48);9223-6. PMID: 17969213

Kriek07a: 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

Leonardi03: Leonardi R, Fairhurst SA, Kriek M, Lowe DJ, Roach PL (2003). "Thiamine biosynthesis in Escherichia coli: isolation and initial characterisation of the ThiGH complex." FEBS Lett 539(1-3);95-9. PMID: 12650933

Leonardi04: Leonardi R, Roach PL (2004). "Thiamine biosynthesis in Escherichia coli: in vitro reconstitution of the thiazole synthase activity." J Biol Chem 279(17);17054-62. PMID: 14757766

MartinezGomez04: Martinez-Gomez NC, Robers M, Downs DM (2004). "Mutational analysis of ThiH, a member of the radical S-adenosylmethionine (AdoMet) protein superfamily." J Biol Chem 279(39);40505-10. PMID: 15271986

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: 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

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


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, biocyc13.