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Information on EC 4.1.99.17 - phosphomethylpyrimidine synthase and Organism(s) Arabidopsis thaliana and UniProt Accession O82392

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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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This record set is specific for:
Arabidopsis thaliana
UNIPROT: O82392
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The taxonomic range for the selected organisms is: Arabidopsis thaliana
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
thiC
-
-
-
-
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
iron-sulfur centre
-
S-adenosyl-L-methionine
a S-adenosyl-L-methionine radical enzyme
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
a metal ion with octahedral coordination (two strictly conserved histidine residues (H426 and H490) and four water molecules) at the same location as a zinc ion in the bacterial enzyme, and a metal ion with multiple coordinated water molecules in the close vicinity of the substrate binding sites, binding structures, overview
Fe2+
the enzyme contains a [4Fe-4S] cluster
iron-sulfur centre
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
strong expression
Manually annotated by BRENDA team
strong expression
Manually annotated by BRENDA team
THIC transcript is not detectable two days after germination, but is readily detectable at day five
Manually annotated by BRENDA team
strong expression
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
the enzyme is important in thiamine diphosphate, vitamin B1, biosynthesis, an essential cofactor for key cellular metabolic enzymes in all forms of life
physiological function
additional information
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
THIC_ARATH
644
0
71987
Swiss-Prot
Chloroplast (Reliability: 1)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
130000
recombinant His-tagged DELTAN71-AtTHIC mutant, gel filtration
65451
2 * 65451, recombinant His-tagged DELTAN71-AtTHIC mutant, mass spectrometry and crystal structure
71994
x * 71994, calculated from sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 71994, calculated from sequence
dimer
2 * 65451, recombinant His-tagged DELTAN71-AtTHIC mutant, mass spectrometry and crystal structure
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant His-tagged DELTAN71-AtTHIC mutant, by a proteolysis assay (especially alpha-chymotrypsin) coupled with the sitting drop vapor diffusion technique at 18°C, using 0.01 M cobalt (II) chloride hexahydrate, 0.1 M sodium acetate trihydrate, pH 4.6, 1 M 1,6-hexanediol, X-ray diffraction structure determination and analysis at 1.6 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged N-terminally truncated mutant DELTAN71-AtTHIC from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene thiC, recombinant expression of His-tagged N-terminally truncated mutant DELTAN71-AtTHIC in Escherichia coli strain BL21(DE3)
heterologous expression of AtTHIC can functionally complement the thiC knock-out mutant of Escherichia coli
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
downregulation of AtTHIC expression by T-DNA insertion at its promoter region results in a drastic reduction of thiamine content in plants and the knock-down mutant thic1 shows albino (white leaves) and lethal phenotypes under the normal culture conditions
the THIC gene is negatively regulated by thiamin itself, regulation by conserved regions of mRNA that bind specific metabolites (riboswitches). As the thiamine riboswitch only responds to thiamin diphosphate but not thiamine, the down-regulation of THIC mRNA implies that the externally provided thiamine is converted to thiamine diphosphate inside the cell leading to the conformational change inducing mRNA instability
the transcript level in seedlings grown in 24 h of light is substantially higher than that in seedlings exposed to a single long day cycle (16-h light/8-h dark)
THIC transcript is not detectable two days after germination, but is readily detectable at day five
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kong, D.; Zhu, Y.; Wu, H.; Cheng, X.; Liang, H.; Ling, H.Q.
AtTHIC, a gene involved in thiamine biosynthesis in Arabidopsis thaliana
Cell Res.
18
566-576
2008
Arabidopsis thaliana (O82392), Arabidopsis thaliana
Manually annotated by BRENDA team
Raschke, M.; Brkle, L.; Mller, N.; Nunes-Nesi, A.; Fernie, A.R.; Arigoni, D.; Amrhein, N.; Fitzpatrick, T.B.
Vitamin B1 biosynthesis in plants requires the essential iron sulfur cluster protein, THIC
Proc. Natl. Acad. Sci. USA
104
19637-19642
2007
Arabidopsis thaliana (O82392), Arabidopsis thaliana ecotype Col-0 (O82392)
Manually annotated by BRENDA team
Coquille, S.; Roux, C.; Mehta, A.; Begley, T.P.; Fitzpatrick, T.B.; Thore, S.
High-resolution crystal structure of the eukaryotic HMP-P synthase (THIC) from Arabidopsis thaliana
J. Struct. Biol.
184
438-444
2013
Arabidopsis thaliana (O82392), Arabidopsis thaliana
Manually annotated by BRENDA team