1VBK | pdb_00001vbk

Crystal structure of PH1313 from Pyrococcus horikoshii Ot3

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	d1vbka1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	ThiI-like	Hypothetical protein PH1313, C-terminal domain	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
A	d1vbka2	Alpha and beta proteins (a+b)	THUMP domain	THUMP domain-like	THUMP domain	Hypothetical protein PH1313, N-terminal domain	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
B	d1vbkb1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	ThiI-like	Hypothetical protein PH1313, C-terminal domain	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
B	d1vbkb2	Alpha and beta proteins (a+b)	THUMP domain	THUMP domain-like	THUMP domain	Hypothetical protein PH1313, N-terminal domain	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	ThiI-like	8020744	4002568	SCOP2 (2022-06-29)
A	SCOP2 Family	THUMP domain	8020745	4003734	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Adenine nucleotide alpha hydrolases-like	8033124	3001593	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	THUMP domain-like	8033125	3001379	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8033124	3001593	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	THUMP domain-like	8033125	3001379	SCOP2B (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	e1vbkA1	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	e1vbkA2	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	UNK_F_TYPE	e1vbkA3	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: UNK_F_TYPE	ECOD (1.6)
B	THUMP_ThiI	e1vbkB1	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)
B	THUMP	e1vbkB2	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)
B	UNK_F_TYPE	e1vbkB3	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.1510	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	THUMP domain-like	CATH (4.3.0)
A	3.30.2300.10	Alpha Beta	2-Layer Sandwich	THUMP fold	THUMP superfamily	CATH (4.3.0)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	3.30.70.1510	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	THUMP domain-like	CATH (4.3.0)
B	3.30.2300.10	Alpha Beta	2-Layer Sandwich	THUMP fold	THUMP superfamily	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	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, 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. 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, 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	hypothetical protein PH1313	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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 nucleic acid binding	tRNA thio-modification tRNA 4-thiouridine biosynthesis tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA thio-modification tRNA 4-thiouridine biosynthesis tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification metabolic process cellular process macromolecule metabolic process RNA processing sulfur compound biosynthetic process thiazole biosynthetic process oxazole or thiazole metabolic process sulfur compound metabolic process thiazole metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR020536	Thil, AANH domain	Domain
A, B	IPR004114	THUMP domain	Domain
A, B	IPR054173	ThiI, ferredoxin-like domain	Domain
A, B	IPR049962	ThiI, THUMP domain	Domain
A, B	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A, B	IPR050102	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 R01GM157729.