4S25

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

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ThiC_Rad_SAM	e4s25A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: ThiC_Rad_SAM	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.540	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Radical SAM ThiC family, central domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01964	Radical SAM ThiC family (ThiC_Rad_SAM)	Radical SAM ThiC family	ThiC is found within the thiamine biosynthesis operon. ThiC is involved in pyrimidine biosynthesis [1]. ThiC participates in the formation of 4-Amino-5-hydroxymethyl-2-methylpyrimidine from AIR, an intermediate in the de novo pyrimidine biosynthesis ...	ThiC is found within the thiamine biosynthesis operon. ThiC is involved in pyrimidine biosynthesis [1]. ThiC participates in the formation of 4-Amino-5-hydroxymethyl-2-methylpyrimidine from AIR, an intermediate in the de novo pyrimidine biosynthesis. Thic is a member of the radical SAM superfamily [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Phosphomethylpyrimidine synthase, chloroplastic	protein binding binding protein domain specific binding iron-sulfur cluster binding metal cluster binding small molecule binding lyase activity catalytic activity carbon-carbon lyase activity 4 iron, 4 sulfur cluster binding cation binding ion binding metal ion binding	pyrimidine-containing compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process thiamine-containing compound metabolic process vitamin biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process thiamine diphosphate metabolic process small molecule metabolic process metabolic process pyrimidine-containing compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process thiamine-containing compound metabolic process vitamin biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process thiamine diphosphate metabolic process small molecule metabolic process metabolic process cellular process sulfur compound metabolic process pyrimidine-containing compound biosynthetic process water-soluble vitamin metabolic process phosphorus metabolic process thiamine diphosphate biosynthetic process thiamine-containing compound biosynthetic process response to nutrient levels response to stimulus response to vitamin B1 response to chemical response to alcohol response to nutrient response to oxygen-containing compound response to nitrogen compound response to vitamin response to organic cyclic compound organic hydroxy compound metabolic process alcohol metabolic process thiamine metabolic process thiamine biosynthetic process primary alcohol biosynthetic process organic hydroxy compound biosynthetic process alcohol biosynthetic process primary alcohol metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle plastid stroma chloroplast stroma chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002817	Phosphomethylpyrimidine synthase ThiC/5-hydroxybenzimidazole synthase BzaA/B	Family
A	IPR038521	ThiC/Bza, core domain	Homologous Superfamily
A	IPR037509	Phosphomethylpyrimidine synthase	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.