1V9F

Crystal structure of catalytic domain of pseudouridine synthase RluD from Escherichia coli

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	d1v9fa_	Alpha and beta proteins (a+b)	Pseudouridine synthase	Pseudouridine synthase	Pseudouridine synthase RsuA/RluD	Ribosomal large subunit pseudouridine synthase D, RluD	(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)
A	SCOP2 Family	Pseudouridine synthase RsuA/RluD	8028845	4002679	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Pseudouridine synthase	8041224	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)
A	PseudoU_synth_2	e1v9fA1	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: PseudoU_synth_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	CATH (4.3.0)
A	6.10.140.230	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00849	RNA pseudouridylate synthase (PseudoU_synth_2)	RNA pseudouridylate synthase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ribosomal large subunit pseudouridine synthase D	isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid pseudouridine synthase activity rRNA pseudouridine synthase activity catalytic activity 23S rRNA pseudouridine(1911/1915/1917) synthase activity intramolecular transferase activity RNA binding binding organic cyclic compound binding nucleic acid binding	ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process rRNA processing enzyme-directed rRNA pseudouridine synthesis 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 ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process rRNA processing enzyme-directed rRNA pseudouridine synthesis 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 cellular metabolic process 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 organelle assembly protein-containing complex organization non-membrane-bounded organelle assembly ribosomal large subunit biogenesis protein-RNA complex assembly cellular component organization organelle organization protein-RNA complex organization cellular component assembly ribosomal large subunit assembly protein-containing complex assembly ribosome assembly	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR020103	Pseudouridine synthase, catalytic domain superfamily	Homologous Superfamily
A	IPR006225	Pseudouridine synthase, RluC/RluD	Family
A	IPR002942	RNA-binding S4 domain	Domain
A	IPR050188	RluA Pseudouridine Synthase	Family
A	IPR036986	RNA-binding S4 domain superfamily	Homologous Superfamily
A	IPR006145	Pseudouridine synthase, RsuA/RluA-like	Domain
A	IPR006224	Pseudouridine synthase, RluA-like, conserved site	Conserved Site

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.