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Information on EC 4.1.99.17 - phosphomethylpyrimidine synthase and Organism(s) Caulobacter vibrioides and UniProt Accession Q9A6Q5

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EC Tree
     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.99 Other carbon-carbon lyases
                4.1.99.17 phosphomethylpyrimidine synthase
IUBMB Comments
Binds a [4Fe-4S] cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The first stage of catalysis is reduction of the S-adenosyl-L-methionine to produce L-methionine and a 5'-deoxyadenosin-5'-yl radical that is crucial for the conversion of the substrate. Part of the pathway for thiamine biosynthesis.
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Caulobacter vibrioides
UNIPROT: Q9A6Q5
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The taxonomic range for the selected organisms is: Caulobacter vibrioides
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
thi5p, hmp-p synthase, lethic, atthic, phosphomethylpyrimidine synthase, 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase
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thiC
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
5-amino-1-(5-phospho-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + L-methionine + formate + CO
show the reaction diagram
radical reaction mechanism, overview
PATHWAY SOURCE
PATHWAYS
-
-
SYSTEMATIC NAME
IUBMB Comments
5-amino-1-(5-phospho-D-ribosyl)imidazole formate-lyase (decarboxylating, 4-amino-2-methyl-5-phosphomethylpyrimidine-forming)
Binds a [4Fe-4S] cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The first stage of catalysis is reduction of the S-adenosyl-L-methionine to produce L-methionine and a 5'-deoxyadenosin-5'-yl radical that is crucial for the conversion of the substrate. Part of the pathway for thiamine biosynthesis.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
5-amino-1-(5-phospho-D-ribosyl)imidazole + S-adenosyl-L-methionine
4-amino-2-methyl-5-phosphomethylpyrimidine + 5'-deoxyadenosine + L-methionine + formate + CO
show the reaction diagram
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
5-amino-1-(5-phospho-D-ribosyl)imidazole + S-adenosyl-L-methionine
4-amino-2-methyl-5-phosphomethylpyrimidine + 5'-deoxyadenosine + L-methionine + formate + CO
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
S-adenosyl-L-methionine
a S-adenosyl-L-methionine radical enzyme
[4Fe-4S]-center
binds 1 4Fe-4S cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4Fe-4S center
binds 1 4Fe-4S cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine
Fe2+
the enzyme contains a [4Fe-4S] cluster bound by the CXXCXXXXC motif
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
the enzyme is a member of the radical S-adenosylmethionine (AdoMet) superfamily, reactions catalyzed by the radical AdoMet superfamily include mainly glycyl radical generation, sulfur insertion, methylation, methylthiolation, oxidation, isomerization, elimination (fragmentation), overview. ThiC does not contain the canonical CXXXCXXC motif in the N-terminal domain, as do most of the radical AdoMet enzymes, but a CXXCXXXXC motif
metabolism
the enzyme is important in thiamine biosynthesis, an essential compound in all living organisms that participates in several key cellular processes, such as carbohydrate and amino acid metabolism. Thiamine consists of a thiazole and a pyrimidine heterocycle, which are synthesized separately and assembled together by thiamine phosphate synthase
physiological function
the enzyme is involved in the biosynthesis of thiamine diphosphate
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
selenomethionine HMP-P synthase/HMP crystals are grown using the sitting drop vapor diffusion method at 25°C. The crystals are monoclinic, space group P2(1), with unit cell dimension a = 63.3 A, b = 103.4 A, c = 95.4 A and beta = 91.6°
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Chatterjee, A.; Li, Y.; Zhang, Y.; Grove, T.L.; Lee, M.; Krebs, C.; Booker, S.J.; Begley, T.P.; Ealick, S.E.
Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily
Nat. Chem. Biol.
4
758-765
2008
Caulobacter vibrioides (Q9A6Q5)
Manually annotated by BRENDA team
Zhang, Q.; Liu, W.
Complex biotransformations catalyzed by radical S-adenosylmethionine enzymes
J. Biol. Chem.
286
30245-30252
2011
Caulobacter vibrioides (Q9A6Q5), Salmonella enterica (Q9L9I7)
Manually annotated by BRENDA team