4S28 image
Deposition Date 2015-01-19
Release Date 2015-04-08
Last Version Date 2023-09-20
Entry Detail
PDB ID:
4S28
Keywords:
Title:
Crystal structure of Arabidopsis thaliana ThiC with bound aminoimidazole ribonucleotide, S-adenosylhomocysteine, Fe4S4 cluster and Fe
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.25 Å
R-Value Free:
0.13
R-Value Work:
0.11
R-Value Observed:
0.11
Space Group:
P 32 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Phosphomethylpyrimidine synthase, chloroplastic
Gene (Uniprot):THIC
Chain IDs:A
Chain Length:576
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Primary Citation
Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.
Nat Commun 6 6480 6480 (?)
PMID: 25813242 DOI: 10.1038/ncomms7480

Abstact

Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

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