3EPN image
Deposition Date 2008-09-29
Release Date 2008-10-28
Last Version Date 2024-02-21
Entry Detail
PDB ID:
3EPN
Title:
Crystal structure of Caulobacter crescentus ThiC complexed with imidazole ribonucleotide
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.11 Å
R-Value Free:
0.24
R-Value Work:
0.16
R-Value Observed:
0.17
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Thiamine biosynthesis protein thiC
Gene (Uniprot):thiC
Chain IDs:A, B
Chain Length:612
Number of Molecules:2
Biological Source:Caulobacter crescentus
Ligand Molecules
Primary Citation
Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily
Nat.Chem.Biol. 4 758 765 (2008)
PMID: 18953358 DOI: 10.1038/nchembio.121

Abstact

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.

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