2C5S

Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2c5sa1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	ThiI-like	Thiamine biosynthesis protein ThiI, C-terminal domain	(Bacillus anthracis str. Ames ) [TaxId: 198094 ],	SCOPe (2.08)
A	d2c5sa2	Alpha and beta proteins (a+b)	THUMP domain	THUMP domain-like	THUMP domain	Thiamine biosynthesis protein ThiI, N-terminal domain	(Bacillus anthracis str. Ames ) [TaxId: 198094 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	THUMP domain	8027043	4003734	SCOP2 (2022-06-29)
A	SCOP2 Family	ThiI-like	8027042	4002568	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	THUMP domain-like	8039422	3001379	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Adenine nucleotide alpha hydrolases-like	8039421	3001593	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	THUMP_ThiI	e2c5sA1	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin-like domain in ThiI (From Topology)	T: Ferredoxin-like domain in ThiI	F: THUMP_ThiI	ECOD (1.6)
A	THUMP	e2c5sA2	A: a+b two layers	X: THUMP domain-like (From Topology)	H: THUMP domain-like (From Topology)	T: THUMP domain-like	F: THUMP	ECOD (1.6)
A	tRNA_Me_trans_1st	e2c5sA3	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA_Me_trans_1st	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	PROBABLE THIAMINE BIOSYNTHESIS PROTEIN THII	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 RNA binding tRNA binding nucleic acid binding sulfurtransferase activity transferase activity, transferring sulphur-containing groups tRNA-uracil-4 sulfurtransferase activity	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 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR020536	Thil, AANH domain	Domain
A	IPR004114	THUMP domain	Domain
A	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A	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.