Rhea - reaction knowledgebase

Enzymes

UniProtKB ^help_outline	22,944 proteins
Enzyme class ^help_outline	EC 4.1.99.17 phosphomethylpyrimidine synthase

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Name ^help_outline 5-amino-1-(5-phospho-β-D-ribosyl)imidazole Identifier CHEBI:137981 Charge -1 Formula C8H13N3O7P InChIKey^help_outline PDACUKOKVHBVHJ-XVFCMESISA-M SMILES^help_outline O1[C@@H]([C@H]([C@H]([C@@H]1N2C(=C[NH+]=C2)N)O)O)COP(=O)([O-])[O-] 2D coordinates Mol file for the small molecule Search links Involved in 6 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline S-adenosyl-L-methionine Identifier CHEBI:59789 Charge 1 Formula C15H23N6O5S InChIKey^help_outline MEFKEPWMEQBLKI-AIRLBKTGSA-O SMILES^help_outline C[S+](CC[C@H]([NH3+])C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 2D coordinates Mol file for the small molecule Search links Involved in 924 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine Identifier CHEBI:58354 Charge -2 Formula C6H8N3O4P InChIKey^help_outline PKYFHKIYHBRTPI-UHFFFAOYSA-L SMILES^help_outline Cc1ncc(COP([O-])([O-])=O)c(N)n1 2D coordinates Mol file for the small molecule Search links Involved in 5 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline CO Identifier CHEBI:17245 (Beilstein: 1900508,3587264,3535285; CAS: 630-08-0) ^help_outline Charge 0 Formula CO InChIKey^help_outline UGFAIRIUMAVXCW-UHFFFAOYSA-N SMILES^help_outline [C-]#[O+] 2D coordinates Mol file for the small molecule Search links Involved in 15 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline 5'-deoxyadenosine Identifier CHEBI:17319 (CAS: 4754-39-6) ^help_outline Charge 0 Formula C10H13N5O3 InChIKey^help_outline XGYIMTFOTBMPFP-KQYNXXCUSA-N SMILES^help_outline C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 2D coordinates Mol file for the small molecule Search links Involved in 76 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline formate Identifier CHEBI:15740 (CAS: 71-47-6) ^help_outline Charge -1 Formula CHO2 InChIKey^help_outline BDAGIHXWWSANSR-UHFFFAOYSA-M SMILES^help_outline [H]C([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 99 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline L-methionine Identifier CHEBI:57844 Charge 0 Formula C5H11NO2S InChIKey^help_outline FFEARJCKVFRZRR-BYPYZUCNSA-N SMILES^help_outline CSCC[C@H]([NH3+])C([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 130 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline H⁺ Identifier CHEBI:15378 Charge 1 Formula H InChIKey^help_outline GPRLSGONYQIRFK-UHFFFAOYSA-N SMILES^help_outline [H+] 2D coordinates Mol file for the small molecule Search links Involved in 9,717 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule

Cross-references

	RHEA:24840	RHEA:24841	RHEA:24842	RHEA:24843
Reaction direction	undefined	left-to-right	right-to-left	bidirectional
UniProtKB ^help_outline	22,944 proteins
EC numbers ^help_outline	4.1.99.17
KEGG ^help_outline				R03472
MetaCyc ^help_outline		PYRIMSYN1-RXN
EcoCyc ^help_outline		PYRIMSYN1-RXN

Publications

Biosynthesis of the thiamin pyrimidine: the reconstitution of a remarkable rearrangement reaction.

Lawhorn B.G., Mehl R.A., Begley T.P.

The conversion of 5-aminoimidazole ribonucleotide (AIR) into 4-amino-2-methyl-5-hydroxymethylpyrimidine (HMP) is a fascinating reaction on the thiamin biosynthetic pathway in bacteria and is probably the most complex unresolved rearrangement in primary metabolism. We have successfully reconstitute ... >> More

The conversion of 5-aminoimidazole ribonucleotide (AIR) into 4-amino-2-methyl-5-hydroxymethylpyrimidine (HMP) is a fascinating reaction on the thiamin biosynthetic pathway in bacteria and is probably the most complex unresolved rearrangement in primary metabolism. We have successfully reconstituted this reaction in a cell-free system. The E. coli thiC gene product and an additional unidentified E. coli protein are required for the reaction. In addition, SAM and nicotinamide cofactors are required for full activity. Labeling studies to determine the origin of most of the atoms in the pyrimidine are described. Based on these studies, a new mechanism for HMP formation is proposed. << Less

Org. Biomol. Chem. 2:2538-2546(2004) [PubMed] [EuropePMC]
ThiC is an [Fe-S] cluster protein that requires AdoMet to generate the 4-amino-5-hydroxymethyl-2-methylpyrimidine moiety in thiamin synthesis.

Martinez-Gomez N.C., Downs D.M.

Thiamin pyrophosphate is a required cofactor in all organisms. The biosynthesis of thiamin requires the independently synthesized 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate (HMP-PP) and 5-hydroxyethyl-4-methylthiazole phosphate (THZ-P) moieties. In bacteria, the pyrimidine moiety is ... >> More

Thiamin pyrophosphate is a required cofactor in all organisms. The biosynthesis of thiamin requires the independently synthesized 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate (HMP-PP) and 5-hydroxyethyl-4-methylthiazole phosphate (THZ-P) moieties. In bacteria, the pyrimidine moiety is derived from 5-aminoimidazole ribotide (AIR), and ThiC is the only gene product known to be required for this conversion in vivo. We report here the purification and characterization of the ThiC protein from Salmonella enterica. The data showed this protein generated HMP when AIR, S-adenosylmethionine (AdoMet), and an appropriate reducing agent were present. It is further shown that ThiC carries an oxygen labile [Fe-S] cluster essential for this activity. << Less

Biochemistry 47:9054-9056(2008) [PubMed] [EuropePMC]
Reaction of AdoMet with ThiC generates a backbone free radical.

Martinez-Gomez N.C., Poyner R.R., Mansoorabadi S.O., Reed G.H., Downs D.M.

ThiC is an [4Fe-4S] cluster protein that catalyzes the formation of 4-amino-5-hydroxymethyl-2-methylpyrimidine. EPR spectroscopic studies demonstrate that, upon interaction with AdoMet, active ThiC from Salmonella enterica generates a persistent free radical on the alpha-carbon of an amino acid re ... >> More

ThiC is an [4Fe-4S] cluster protein that catalyzes the formation of 4-amino-5-hydroxymethyl-2-methylpyrimidine. EPR spectroscopic studies demonstrate that, upon interaction with AdoMet, active ThiC from Salmonella enterica generates a persistent free radical on the alpha-carbon of an amino acid residue. The EPR properties of the radical are consistent with any residue other than a Gly or Ala. Exposure to oxygen was accompanied by a fission of the radical-carrying polypeptide chain between the Gly436 and His437 residues in ThiC. Regardless of whether the backbone radical is part of the catalytic machinery, its presence provides evidence that ThiC employs free radical chemistry as expected for radical SAM enzymes. << Less

Biochemistry 48:217-219(2009) [PubMed] [EuropePMC]
A 'radical dance' in thiamin biosynthesis: mechanistic analysis of the bacterial hydroxymethylpyrimidine phosphate synthase.

Chatterjee A., Hazra A.B., Abdelwahed S., Hilmey D.G., Begley T.P.

Angew. Chem. Int. Ed. 49:8653-8656(2010) [PubMed] [EuropePMC]
Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily.

Chatterjee A., Li Y., Zhang Y., Grove T.L., Lee M., Krebs C., Booker S.J., Begley T.P., Ealick S.E.

4-Amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase catalyzes a complex rearrangement of 5-aminoimidazole ribonucleotide (AIR) to form HMP-P, the pyrimidine moiety of thiamine phosphate. We determined the three-dimensional structures of HMP-P synthase and its complexes with the p ... >> More

4-Amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase catalyzes a complex rearrangement of 5-aminoimidazole ribonucleotide (AIR) to form HMP-P, the pyrimidine moiety of thiamine phosphate. We determined the three-dimensional structures of HMP-P synthase and its complexes with the product HMP-P and a substrate analog imidazole ribotide. The structure of HMP-P synthase reveals a homodimer in which each protomer comprises three domains: an N-terminal domain with a novel fold, a central (betaalpha)(8) barrel and a disordered C-terminal domain that contains a conserved CX(2)CX(4)C motif, which is suggestive of a [4Fe-4S] cluster. Biochemical studies have confirmed that HMP-P synthase is iron sulfur cluster-dependent, that it is a new member of the radical SAM superfamily and that HMP-P and 5'-deoxyadenosine are products of the reaction. Mössbauer and EPR spectroscopy confirm the presence of one [4Fe-4S] cluster. Structural comparisons reveal that HMP-P synthase is homologous to a group of adenosylcobalamin radical enzymes. This similarity supports an evolutionary relationship between these two superfamilies. << Less

Nat. Chem. Biol. 4:758-765(2008) [PubMed] [EuropePMC]
A connection between iron-sulfur cluster metabolism and the biosynthesis of 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate in Salmonella enterica.

Dougherty M.J., Downs D.M.

Several cellular pathways have been identified which affect the efficiency of thiamine biosynthesis in Salmonella enterica. Mutants defective in iron-sulfur (Fe-S) cluster metabolism are less efficient at synthesis of the pyrimidine moiety of thiamine. These mutants are compromised for the convers ... >> More

Several cellular pathways have been identified which affect the efficiency of thiamine biosynthesis in Salmonella enterica. Mutants defective in iron-sulfur (Fe-S) cluster metabolism are less efficient at synthesis of the pyrimidine moiety of thiamine. These mutants are compromised for the conversion of aminoimidazole ribotide (AIR) to 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P), not the synthesis of AIR. The gene product ThiC contains potential ligands for an Fe-S cluster that are required for function in vivo. The conversion of AIR to HMP-P is sensitive to oxidative stress, and variants of ThiC have been identified that have increased sensitivity to oxidative growth conditions. The data are consistent with ThiC or an as-yet-unidentified protein involved in HMP-P synthesis containing an Fe-S cluster required for its physiological function. << Less

Microbiology 152:2345-2353(2006) [PubMed] [EuropePMC]

RHEA:24840 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + CO + 5'-deoxyadenosine + formate + L-methionine + 3 H(+)

Enzymes

Reaction participants Show >> << Hide

Cross-references

Publications

Biosynthesis of the thiamin pyrimidine: the reconstitution of a remarkable rearrangement reaction.

ThiC is an [Fe-S] cluster protein that requires AdoMet to generate the 4-amino-5-hydroxymethyl-2-methylpyrimidine moiety in thiamin synthesis.

Reaction of AdoMet with ThiC generates a backbone free radical.

A 'radical dance' in thiamin biosynthesis: mechanistic analysis of the bacterial hydroxymethylpyrimidine phosphate synthase.

Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily.

A connection between iron-sulfur cluster metabolism and the biosynthesis of 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate in Salmonella enterica.