› 4s25

X-ray diffraction
1.45Å resolution

Crystal structure of Arabidopsis thaliana ThiC with bound imidazole ribonucleotide, S-adenosylhomocysteine, Fe4S4 cluster and Zn (trigonal crystal form)

Released:
DOI: 10.2210/pdb4s25/pdb
PDB entry 4s25 coloured by chain, front view.
PDB entry 4s25 coloured by chain, side view.
PDB entry 4s25 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.
Fenwick MK, Mehta AP, Zhang Y, Abdelwahed SH, Begley TP, Ealick SE
OpenAccess logo Nat Commun 6 6480 (2015)
PMID: 25813242

Function and Biology Details

Reaction catalysed: 
5-amino-1-(5-phospho-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphomethyl)pyrimidine + 5'-deoxyadenosine + L-methionine + formate + CO
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131366 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphomethylpyrimidine synthase, chloroplastic Chain: A
Molecule details ›
Chain: A
Length: 576 amino acids
Theoretical weight: 64.67 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O82392 (Residues: 72-644; Coverage: 89%)
Gene names: At2g29630, PY, T27A16.27, THIC
Sequence domains: Radical SAM ThiC family

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
5 bound ligands:
Ligand SF4 1 x SF4
Ligand IRN 1 x IRN
Ligand ZN 1 x ZN
Ligand CL 1 x CL
Ligand BU1 2 x BU1
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P3221
Unit cell:
a: 107.477Å b: 107.477Å c: 87.643Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.144 0.142 0.162
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

C-C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products.
Yokoyama et al. (2018)
5 more

2 mentions without citation

Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.
Fenwick et al. (2015)
1 more