Annotations: 1DJ0

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1dj0a_	Alpha and beta proteins (a+b)	Pseudouridine synthase	Pseudouridine synthase	Pseudouridine synthase I TruA	Pseudouridine synthase I TruA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1dj0b_	Alpha and beta proteins (a+b)	Pseudouridine synthase	Pseudouridine synthase	Pseudouridine synthase I TruA	Pseudouridine synthase I TruA	(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 I TruA	8023154	4001351	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Pseudouridine synthase	8035534	3001360	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Pseudouridine synthase	8035534	3001360	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	PseudoU_synth_1	e1dj0A1	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: PseudoU_synth_1	ECOD (1.6)
B	PseudoU_synth_1	e1dj0B1	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: PseudoU_synth_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.660	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Pseudouridine synthase I, catalytic domain, C-terminal subdomain	CATH (4.3.0)
A	3.30.70.580	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Pseudouridine synthase I, catalytic domain, N-terminal subdomain	CATH (4.3.0)
B	3.30.70.660	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Pseudouridine synthase I, catalytic domain, C-terminal subdomain	CATH (4.3.0)
B	3.30.70.580	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Pseudouridine synthase I, catalytic domain, N-terminal subdomain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01416	tRNA pseudouridine synthase (PseudoU_synth_1)	tRNA pseudouridine synthase	Involved in the formation of pseudouridine at the anticodon stem and loop of transfer-RNAs Pseudouridine is an isomer of uridine (5-(beta-D-ribofuranosyl) uracil, and id the most abundant modified nucleoside found in all cellular RNAs. The TruA-like ...	Involved in the formation of pseudouridine at the anticodon stem and loop of transfer-RNAs Pseudouridine is an isomer of uridine (5-(beta-D-ribofuranosyl) uracil, and id the most abundant modified nucleoside found in all cellular RNAs. The TruA-like proteins also exhibit a conserved sequence with a strictly conserved aspartic acid, likely involved in catalysis.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PSEUDOURIDINE SYNTHASE I	isomerase activity tRNA pseudouridine synthase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid pseudouridine synthase activity catalytic activity, acting on a tRNA catalytic activity tRNA pseudouridine(38-40) synthase activity intramolecular transferase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity isomerase activity tRNA pseudouridine synthase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid pseudouridine synthase activity catalytic activity, acting on a tRNA catalytic activity tRNA pseudouridine(38-40) synthase activity intramolecular transferase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity RNA binding organic cyclic compound binding tRNA binding nucleic acid binding	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing pseudouridine synthesis tRNA pseudouridine synthesis cellular metabolic process tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing pseudouridine synthesis tRNA pseudouridine synthesis cellular metabolic process tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process RNA modification biosynthetic process macromolecule modification metabolic process cellular process macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001406	Pseudouridine synthase I, TruA	Family
A, B	IPR020103	Pseudouridine synthase, catalytic domain superfamily	Homologous Superfamily
A, B	IPR020094	Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal	Homologous Superfamily
A, B	IPR020097	Pseudouridine synthase I, TruA, alpha/beta domain	Domain
A, B	IPR020095	Pseudouridine synthase I, TruA, C-terminal	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	tRNA pseudouridine38-40 synthase M-CSA #493	Pseudouridylate synthase is a member of the pseudouridine synthase family and catalyses the synthesis of pseudourine, the C5-C1' isomer of uridine, in a variety of RNAs. Pseudouridine synthases display varying degrees of specificity for their individual, three dimensionally folded RNA substrates which include tRNA, rRNA and snRNA. Pseudouridine is the most abundant modified nucleoside in the cell and many of the sites targeted for pseudouridine formation, such as those that map to the peptidyl-transfer region of rRNA, are highly conserved in evolution.	Defined by 3 residues: ARG:A-52 [auth A-58]ASP:A-54 [auth A-60]ARG:A-199 [auth A-205] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.2.1.70 (PDB Primary Data) Search M-CSA Motif + EC 4.2.1.70 EC: 5.4.99.12 (UniProt) Search M-CSA Motif + EC 5.4.99.12

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.