Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction. 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + CO + formate + 3 H(+) + L-methionine Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; thiamine diphosphate biosynthesis. Homodimer. Strongly expressed in cotyledons, leaves, flowers and siliques, and, to a lower extent, in roots (PubMed:18048325, PubMed:25014715). Expressed in all green tissues, but not in roots, seeds, and petals (PubMed:23341335). First detected in five-days seedlings. In seedlings, mostly present at the root tips and in the jointed section between the hypocotyl and root. In two-leaves seedlings, expressed in leaves, cotyledons and vascular bundles of hypocotyls, and very weakly, in the roots. In flowers, detected in sepals, filaments and pistil tips, but not in petals. Later accumulates in the jointed region between the silique and silique stem, and in the tips of siliques. Decreasing expression during seed development (PubMed:25014715). Circadian-regulation (PubMed:23341335). Down-regulated by extrinsic thiamine, via a vitamin B1 derivative thiamine pyrophosphate (TPP)-sensing riboswitch regulation. Detected in both dark and light grown seedlings; increased progressively after transfer of etiolated seedlings to light. Up-regulated by salt, osmotic stress and abscisic acid (PubMed:22214485). Albino (white leaves) and lethal under normal culture conditions, probably due to an impairment in thiamine biosynthesis. Belongs to the ThiC family.