1R3E

Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit

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)
D [auth A]	d1r3ea1	All beta proteins	PUA domain-like	PUA domain-like	PUA domain	Pseudouridine synthase II TruB, C-terminal domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
D [auth A]	d1r3ea2	Alpha and beta proteins (a+b)	Pseudouridine synthase	Pseudouridine synthase	Pseudouridine synthase II TruB	Pseudouridine synthase II TruB	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth A]	SCOP2 Family	PUA domain	8027904	4003536	SCOP2 (2022-06-29)
D [auth A]	SCOP2 Family	Pseudouridine synthase II TruB	8027905	4003455	SCOP2 (2022-06-29)
D [auth A]	SCOP2 Superfamily	PUA domain-like	8040283	3001015	SCOP2 (2022-06-29)
D [auth A]	SCOP2 Superfamily	Pseudouridine synthase	8040284	3001360	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)
D [auth A]	PUA	e1r3eA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PUA	ECOD (1.6)
D [auth A]	TruB_N	e1r3eA2	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)
D [auth A]	3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	CATH (4.3.0)
D [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
D [auth A]	PF16198	tRNA pseudouridylate synthase B C-terminal domain (TruB_C_2)	tRNA pseudouridylate synthase B C-terminal domain	-	Family
D [auth A]	PF01509	TruB family pseudouridylate synthase (N terminal domain) (TruB_N)	TruB family pseudouridylate synthase (N terminal domain)	-	Family
D [auth A]	PF01472	PUA domain (PUA)	PUA domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C]	5'-R(CPUPGPUPGPUP(FHU)PCPGPAPUPCPCPAPCPAP*G)-3'	-	-	-
B [auth D], C [auth E]	5'-R(CPUPGPUPGPUPUPCPGPAPUPCPCPAPCPAP*G)-3'	-	-	-
D [auth A]	tRNA pseudouridine synthase B	isomerase activity pseudouridine synthase activity catalytic activity intramolecular transferase activity RNA binding binding nucleic acid binding tRNA pseudouridine synthase activity catalytic activity, acting on RNA tRNA pseudouridine(55) synthase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA	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 pseudouridine synthesis mRNA modification mRNA metabolic process mRNA pseudouridine synthesis tRNA pseudouridine synthesis	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth A]	IPR015947	PUA-like superfamily	Homologous Superfamily
D [auth A]	IPR020103	Pseudouridine synthase, catalytic domain superfamily	Homologous Superfamily
D [auth A]	IPR002501	Pseudouridine synthase II, N-terminal	Domain
D [auth A]	IPR032819	tRNA pseudouridylate synthase B, C-terminal	Domain
D [auth A]	IPR036974	PUA domain superfamily	Homologous Superfamily
D [auth A]	IPR014780	tRNA pseudouridine synthase II, TruB	Family
D [auth A]	IPR002478	PUA domain	Domain

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.