3EPM

Crystal structure of Caulobacter crescentus ThiC

Summary for 3EPM

• Entry DOI: 10.2210/pdb3epm/pdb
• Related: 3EPN 3EPO
• Descriptor: Thiamine biosynthesis protein thiC, ZINC ION, 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE, ... (5 entities in total)
• Functional Keywords: alpha-beta barrel, sam superfamily, thiamine biosynthesis, biosynthetic protein
• Biological source: Caulobacter crescentus
• Total number of polymer chains: 2
• Total formula weight: 138072.79

Authors

Li, S.,Chatterjee, A.,Zhang, Y.,Grove, T.L.,Lee, M.,Krebs, C.,Booker, S.J.,Begley, T.P.,Ealick, S.E. (deposition date: 2008-09-29, release date: 2008-10-28, Last modification date: 2024-10-30)

Primary citation

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

PubMed Abstract: 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.

PubMed: 18953358
DOI: 10.1038/nchembio.121

Experimental method

X-RAY DIFFRACTION (2.793 Å)