1K8W | pdb_00001k8w

Crystal structure of the E. coli pseudouridine synthase TruB bound to a T stem-loop RNA

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)
B [auth A]	d1k8wa3	All beta proteins	PUA domain-like	PUA domain-like	PUA domain	Pseudouridine synthase II TruB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B [auth A]	d1k8wa5	Alpha and beta proteins (a+b)	Pseudouridine synthase	Pseudouridine synthase	Pseudouridine synthase II TruB	Pseudouridine synthase II TruB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B [auth A]	d1k8wa6	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2 Family	Pseudouridine synthase II TruB	8023218	4003455	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Family	PUA domain	8032030	4003536	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Pseudouridine synthase	8035598	3001360	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	PUA domain-like	8044408	3001015	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)
B [auth A]	TruB-C_2	e1k8wA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: TruB-C_2	ECOD (1.6)
B [auth A]	TruB_N	e1k8wA2	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: TruB_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	CATH (4.3.0)
B [auth A]	2.30.130.10	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF09157	Pseudouridine synthase II TruB, C-terminal (TruB-C_2)	Pseudouridine synthase II TruB, C-terminal	Members of this family adopt a secondary structure consisting of a four-stranded beta sheet and one alpha helix. They are predominantly RNA-binding domains, mostly found in Pseudouridine synthase II TruB [1].	Domain
B [auth A]	PF16198	tRNA pseudouridylate synthase B C-terminal domain (TruB_C_2)	tRNA pseudouridylate synthase B C-terminal domain	-	Family
B [auth A]	PF01509	TruB family pseudouridylate synthase (N terminal domain) (TruB_N)	TruB family pseudouridylate synthase (N terminal domain)	Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in m ...	Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth A]	tRNA Pseudouridine Synthase B	isomerase activity pseudouridine synthase activity catalytic activity intramolecular transferase activity tRNA pseudouridine synthase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA RNA binding binding tRNA binding nucleic acid binding tRNA pseudouridine(55) synthase activity	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 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 RNA folding tRNA folding pseudouridine synthesis mRNA modification mRNA metabolic process mRNA pseudouridine synthesis tRNA pseudouridine synthesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
A [auth B]	5'-R(GPGPCPAPAPCPGPGPUP(FHU)PCPGPAPUPCPCPCPGPUPUPGPC)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR015947	PUA-like superfamily	Homologous Superfamily
B [auth A]	IPR020103	Pseudouridine synthase, catalytic domain superfamily	Homologous Superfamily
B [auth A]	IPR002501	Pseudouridine synthase II, N-terminal	Domain
B [auth A]	IPR032819	tRNA pseudouridylate synthase B, C-terminal	Domain
B [auth A]	IPR036974	PUA domain superfamily	Homologous Superfamily
B [auth A]	IPR015240	tRNA pseudouridine synthase II, TruB, subfamily 1, C-terminal	Domain
B [auth A]	IPR014780	tRNA pseudouridine synthase II, TruB	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.