3HJY | pdb_00003hjy

Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nop10-like SnoRNP Znf-like	8040332	3000486	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Pseudouridine synthase	8040330	3001360	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PUA domain-like	8040329	3001015	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)
B	Nop10p	e3hjyB1	A: few secondary structure elements	X: Rubredoxin-like	H: Nucleolar RNA-binding protein Nop10-like (From Topology)	T: Nucleolar RNA-binding protein Nop10-like	F: Nop10p	ECOD (1.6)
A	PUA	e3hjyA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PUA	ECOD (1.6)
A	TruB_N	e3hjyA2	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	2.20.28.40	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	H/ACA ribonucleoprotein complex, subunit Nop10	CATH (4.3.0)
A	2.30.130.10	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (4.3.0)
A	3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF04135	Nucleolar RNA-binding protein, Nop10p family (Nop10p)	Nucleolar RNA-binding protein, Nop10p family	-	Family
A	PF08068	DKCLD (NUC011) domain (DKCLD)	DKCLD (NUC011) domain	This is a TruB_N/PUA domain associated N-terminal domain of Dyskerin-like proteins [1].	Domain
A	PF16198	tRNA pseudouridylate synthase B C-terminal domain (TruB_C_2)	tRNA pseudouridylate synthase B C-terminal domain	-	Family
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
A	PF01472	PUA domain (PUA)	PUA domain	The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modificatio ...	The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes [1]. It is predicted that the PUA domain is an RNA binding domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	RNA (25-MER)	-	-	-
E	5'-R(GPGPAPGPCPGPUPGPCPGPGPUPUPU)-3'	-	-	-
C	5'-R(GPGPGPCPUPCPCPGPGPAPAPAPCPCPGPCPGPGPCPGP*C)-3'	-	-	-
B	Ribosome biogenesis protein Nop10	RNA binding binding snoRNA binding nucleic acid binding	ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process pseudouridine synthesis RNA modification macromolecule modification	protein-containing complex ribonucleoprotein complex
A	pseudouridine synthase CBf5	RNA binding binding nucleic acid binding isomerase activity tRNA pseudouridine synthase activity catalytic activity, acting on RNA tRNA pseudouridine(55) synthase activity catalytic activity, acting on a nucleic acid pseudouridine synthase activity catalytic activity, acting on a tRNA catalytic activity intramolecular transferase activity	ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process pseudouridine synthesis rRNA pseudouridine synthesis ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process pseudouridine synthesis rRNA pseudouridine synthesis primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA modification biosynthetic process macromolecule modification metabolic process cellular process macromolecule metabolic process snRNA modification snRNA pseudouridine synthesis snRNA metabolic process snRNA processing mRNA modification mRNA metabolic process mRNA pseudouridine synthesis box H/ACA sno(s)RNA 3'-end processing sno(s)RNA processing sno(s)RNA 3'-end processing box H/ACA sno(s)RNA processing box H/ACA sno(s)RNA metabolic process sno(s)RNA metabolic process RNA 3'-end processing tRNA pseudouridine synthesis tRNA modification tRNA metabolic process tRNA processing	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR023532	H/ACA ribonucleoprotein complex subunit Nop10 , archaeal-type	Family
B	IPR007264	H/ACA ribonucleoprotein complex, subunit Nop10	Family
B	IPR036756	H/ACA ribonucleoprotein complex, subunit Nop10 superfamily	Homologous Superfamily
A	IPR015947	PUA-like superfamily	Homologous Superfamily
A	IPR020103	Pseudouridine synthase, catalytic domain superfamily	Homologous Superfamily
A	IPR004521	Uncharacterised domain CHP00451	Domain
A	IPR002501	Pseudouridine synthase II, N-terminal	Domain
A	IPR026326	Probable tRNA pseudouridine synthase B, archaeal	Family
A	IPR032819	tRNA pseudouridylate synthase B, C-terminal	Domain
A	IPR036974	PUA domain superfamily	Homologous Superfamily
A	IPR012960	Dyskerin-like	Domain
A	IPR002478	PUA domain	Domain
A	IPR004802	tRNA pseudouridine synthase B family	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.