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-e 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 (2021-05-27)
A	SCOP2 Family	ThiI-like	8027042	4002568	SCOP2 (2021-05-27)
A	SCOP2 Superfamily	THUMP domain-like	8039422	3001379	SCOP2 (2021-05-27)
A	SCOP2 Superfamily	Adenine nucleotide alpha hydrolases-like	8039421	3001593	SCOP2 (2021-05-27)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF22025	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: PF22025	ECOD (1.6)
A	PF02926	e2c5sA2	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	e2c5sA3	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22025	ThiI ferredoxin-like domain (ThiI_fer)	ThiI ferredoxin-like domain	This entry represents the ferredoxin-like domain found at the N-terminal of ThiI proteins (NFLD) [1-3]. ThiI is responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNA. This domain connect ...	This entry represents the ferredoxin-like domain found at the N-terminal of ThiI proteins (NFLD) [1-3]. ThiI is responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNA. This domain connects the C-terminal catalytic PP-loop pyrophosphatase domain with the THUMP (Pfam:PF02926). NFLD and the THUMP domains jointly form the tRNA-binding surface shaped like a channe which may be of particular importance in ThiI for the correct orientation and distance between residues involved in RNA binding and the active site of the enzyme [2,4].	Domain
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. This domain is found in many tRNA modification enzymes classified into five types, namely 4-thiouridine ...	The THUMP domain is named after after thiouridine synthases, methylases and PSUSs [1]. The THUMP domain consists of about 110 amino acid residues. This domain is found in many tRNA modification enzymes classified into five types, namely 4-thiouridine synthetase, deaminase, methyltransferase, a partner protein of acetyltransferase and pseudouridine synthase [3]. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains [2-3] and was first predicted to function by delivering a variety of RNA modification enzymes to their targets [1]. Studies performed in tRNA 4-thiouridine synthetase, tRNA methyltransferases and tRNA deaminase suggest that the THUMP domain captures the 3'-end of RNA but in some cases this is not applicable due to the modification patterns observed in tRNA [3]. Several THUMP-related proteins are also involved in other RNAs modifications, such as rRNA modification [3].	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 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 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 cellular biosynthetic process organonitrogen compound biosynthetic process thiamine-containing compound metabolic process vitamin 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 sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate 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 RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA 4-thiouridine biosynthesis tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process RNA modification macromolecule modification 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A	IPR020536	Thil, AANH domain	Domain
A	IPR004114	THUMP domain	Domain
A	IPR003720	tRNA sulfurtransferase ThiI	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 R01GM133198.