4S28

Crystal structure of Arabidopsis thaliana ThiC with bound aminoimidazole ribonucleotide, S-adenosylhomocysteine, Fe4S4 cluster and Fe

Summary for 4S28

• Entry DOI: 10.2210/pdb4s28/pdb
• Related: 3EPM 3EPN 3EPO 4N7Q 4S25 4S26 4S27 4S29 4S2A
• Descriptor: Phosphomethylpyrimidine synthase, chloroplastic, IRON/SULFUR CLUSTER, 5-AMINOIMIDAZOLE RIBONUCLEOTIDE, ... (8 entities in total)
• Functional Keywords: alpha-beta barrel, radical sam superfamily, iron-sulfur cluster, thiamin, vitamin b1, vitamin b12, domain swapping, adomet and glutamate mutase, lyase
• Biological source: Arabidopsis thaliana (mouse-ear cress,thale-cress)
• Cellular location: Plastid, chloroplast stroma : O82392
• Total number of polymer chains: 1
• Total formula weight: 65972.87

Authors

Fenwick, M.K.,Mehta, A.P.,Zhang, Y.,Abdelwahed, S.,Begley, T.P.,Ealick, S.E. (deposition date: 2015-01-19, release date: 2015-04-08, Last modification date: 2023-09-20)

Primary citation

Fenwick, M.K.,Mehta, A.P.,Zhang, Y.,Abdelwahed, S.H.,Begley, T.P.,Ealick, S.E.
Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.
Nat Commun, 6:6480-6480,

PubMed Abstract: 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.

PubMed: 25813242
DOI: 10.1038/ncomms7480

Experimental method

X-RAY DIFFRACTION (1.25 Å)