4KR9

Crystal structure of a 4-thiouridine synthetase - RNA complex at 3.5 Angstrom resolution

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	PF22025	e4kr9A1	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin-like domain in ThiI (From Topology)	T: Ferredoxin-like domain in ThiI	F: PF22025	ECOD (1.6)
A	PF02926	e4kr9A3	A: a+b two layers	X: THUMP domain-like (From Topology)	H: THUMP domain-like (From Topology)	T: THUMP domain-like	F: PF02926	ECOD (1.6)
A	PF02568	e4kr9A2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: PF02568	ECOD (1.6)
B	PF22025	e4kr9B1	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin-like domain in ThiI (From Topology)	T: Ferredoxin-like domain in ThiI	F: PF22025	ECOD (1.6)
B	PF02926	e4kr9B3	A: a+b two layers	X: THUMP domain-like (From Topology)	H: THUMP domain-like (From Topology)	T: THUMP domain-like	F: PF02926	ECOD (1.6)
B	PF02568	e4kr9B2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: PF02568	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.2130.30	Alpha Beta	2-Layer Sandwich	VC0802-like		CATH (4.3.0)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	3.30.2130.30	Alpha Beta	2-Layer Sandwich	VC0802-like		CATH (4.3.0)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02926	THUMP domain (THUMP)	THUMP domain	The THUMP domain is named after after thiouridine synthases, methylases and PSUSs [1]. The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-bi ...	The THUMP domain is named after after thiouridine synthases, methylases and PSUSs [1]. The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains [2]. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets [1].	Domain
A, B	PF02568	Thiamine biosynthesis protein (ThiI) (ThiI)	Thiamine biosynthesis protein (ThiI)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Probable tRNA sulfurtransferase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cytidylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity nucleotidyltransferase activity catalytic activity CCA tRNA nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups sulfurtransferase activity transferase activity, transferring sulphur-containing groups tRNA-uracil-4 sulfurtransferase activity RNA binding tRNA binding nucleic acid binding	cellular biosynthetic process organonitrogen compound biosynthetic process thiamine-containing compound metabolic process vitamin biosynthetic process organic substance metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process thiamine diphosphate metabolic process small molecule metabolic process sulfur compound metabolic process pyrimidine-containing compound biosynthetic process water-soluble vitamin metabolic process phosphorus metabolic process pyrimidine-containing compound metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process thiamine-containing compound metabolic process vitamin biosynthetic process organic substance metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process thiamine diphosphate metabolic process small molecule metabolic process sulfur compound metabolic process pyrimidine-containing compound biosynthetic process water-soluble vitamin metabolic process phosphorus metabolic process pyrimidine-containing compound metabolic process organonitrogen compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process cellular metabolic process vitamin metabolic process organic cyclic compound metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process thiamine diphosphate biosynthetic process thiamine-containing compound biosynthetic process tRNA thio-modification RNA metabolic process nucleobase-containing compound metabolic process tRNA processing RNA processing tRNA 4-thiouridine biosynthesis tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process RNA modification ncRNA metabolic process macromolecule modification nucleic acid catabolic process macromolecule metabolic process thiazole metabolic process oxazole or thiazole biosynthetic process thiazole biosynthetic process oxazole or thiazole metabolic process 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol
C [auth M], D [auth X]	RNA (39-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A, B	IPR020536	Thil, AANH domain	Domain
A, B	IPR004114	THUMP domain	Domain
A, B	IPR003720	tRNA sulfurtransferase ThiI	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.