TY - JOUR
T1 - High-resolution crystal structure of the eukaryotic HMP-P synthase (THIC) from Arabidopsis thaliana
AU - Coquille, Sandrine
AU - Roux, Céline
AU - Mehta, Angad
AU - Begley, Tadhg P.
AU - Fitzpatrick, Teresa B.
AU - Thore, Stéphane
N1 - Funding Information:
We wish to thank Dr. Markus Kaufmann (University of Geneva) for performing preliminary gel filtration experiments, the SLS (Swiss Light Source) for beam time allocation and the staff of beamline X06DA (PXIII) at SLS for help with data collection. We gratefully acknowledge financial support from the E. Boninchi, the E&L Schmidheiny and the Marc Birkigt Foundations . Furthermore, we specifically thank the University of Geneva and the Swiss National Science Foundation (SNSF) R’equip grant no. 316030-128787 for the development of the crystallographic platform. The work was supported by the SNSF ( PP00A-119186 and SINERGIA project CRSI33_127506 to T.B.F., 31003A-124909 and 31003A-140924 to S.T.) and by the University of Geneva.
PY - 2013/12
Y1 - 2013/12
N2 - Vitamin B1 is an essential compound in all organisms acting as a cofactor in key metabolic reactions. It is formed by the condensation of two independently biosynthesized molecules referred to as the pyrimidine and thiazole moieties. In bacteria and plants, the biosynthesis of the pyrimidine moiety, 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P), requires a single enzyme, THIC (HMP-P synthase). The enzyme uses an iron-sulfur cluster as well as a 5'-deoxyadenosyl radical as cofactors to rearrange the 5-amino-imidazole ribonucleotide (AIR) substrate to the pyrimidine ring. So far, the only structure reported is the one from the bacteria Caulobacter crescentus. In an attempt to structurally characterize an eukaryotic HMP-P synthase, we have determined the high-resolution crystal structure of THIC from Arabidopsis thaliana at 1.6Å. The structure is highly similar to its bacterial counterpart although several loop regions show significant differences with potential implications for the enzymatic properties. Furthermore, we have found a metal ion with octahedral coordination at the same location as a zinc ion in the bacterial enzyme. Our high-resolution atomic model shows a metal ion with multiple coordinated water molecules in the close vicinity of the substrate binding sites and is an important step toward the full characterization of the chemical rearrangement occurring during HMP-P biosynthesis.
AB - Vitamin B1 is an essential compound in all organisms acting as a cofactor in key metabolic reactions. It is formed by the condensation of two independently biosynthesized molecules referred to as the pyrimidine and thiazole moieties. In bacteria and plants, the biosynthesis of the pyrimidine moiety, 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P), requires a single enzyme, THIC (HMP-P synthase). The enzyme uses an iron-sulfur cluster as well as a 5'-deoxyadenosyl radical as cofactors to rearrange the 5-amino-imidazole ribonucleotide (AIR) substrate to the pyrimidine ring. So far, the only structure reported is the one from the bacteria Caulobacter crescentus. In an attempt to structurally characterize an eukaryotic HMP-P synthase, we have determined the high-resolution crystal structure of THIC from Arabidopsis thaliana at 1.6Å. The structure is highly similar to its bacterial counterpart although several loop regions show significant differences with potential implications for the enzymatic properties. Furthermore, we have found a metal ion with octahedral coordination at the same location as a zinc ion in the bacterial enzyme. Our high-resolution atomic model shows a metal ion with multiple coordinated water molecules in the close vicinity of the substrate binding sites and is an important step toward the full characterization of the chemical rearrangement occurring during HMP-P biosynthesis.
KW - HMP-P synthase
KW - Metal binding site
KW - SAM radical dependent enzyme
KW - Thiamin biosynthesis
KW - X-ray structure
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U2 - 10.1016/j.jsb.2013.10.005
DO - 10.1016/j.jsb.2013.10.005
M3 - Article
C2 - 24161603
AN - SCOPUS:84888039165
SN - 1047-8477
VL - 184
SP - 438
EP - 444
JO - Journal of Structural Biology
JF - Journal of Structural Biology
IS - 3
ER -