2NQP

Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA

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]	d2nqpa1	Alpha and beta proteins (a+b)	Pseudouridine synthase	Pseudouridine synthase	Pseudouridine synthase I TruA	Pseudouridine synthase I TruA	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C [auth B]	d2nqpb1	Alpha and beta proteins (a+b)	Pseudouridine synthase	Pseudouridine synthase	Pseudouridine synthase I TruA	Pseudouridine synthase I TruA	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D [auth C]	d2nqpc1	Alpha and beta proteins (a+b)	Pseudouridine synthase	Pseudouridine synthase	Pseudouridine synthase I TruA	Pseudouridine synthase I TruA	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E [auth D]	d2nqpd1	Alpha and beta proteins (a+b)	Pseudouridine synthase	Pseudouridine synthase	Pseudouridine synthase I TruA	Pseudouridine synthase I TruA	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2B Superfamily	Pseudouridine synthase	8035534	3001360	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Pseudouridine synthase	8035534	3001360	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Pseudouridine synthase	8035534	3001360	SCOP2B (2022-06-29)
E [auth D]	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)
B [auth A]	PseudoU_synth_1	e2nqpA1	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: PseudoU_synth_1	ECOD (1.6)
C [auth B]	PseudoU_synth_1	e2nqpB1	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: PseudoU_synth_1	ECOD (1.6)
D [auth C]	PseudoU_synth_1	e2nqpC1	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: PseudoU_synth_1	ECOD (1.6)
E [auth D]	PseudoU_synth_1	e2nqpD1	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)
B [auth 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 [auth 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)
C [auth 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)
C [auth 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)
D [auth C]	3.30.70.580	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Pseudouridine synthase I, catalytic domain, N-terminal subdomain	CATH (4.3.0)
D [auth C]	3.30.70.660	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Pseudouridine synthase I, catalytic domain, C-terminal subdomain	CATH (4.3.0)
E [auth D]	3.30.70.580	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Pseudouridine synthase I, catalytic domain, N-terminal subdomain	CATH (4.3.0)
E [auth D]	3.30.70.660	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Pseudouridine synthase I, catalytic domain, C-terminal subdomain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A], C [auth B], D [auth C], E [auth D]	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 [auth F]	transfer RNA	-	-	-
B [auth A], C [auth B], D [auth C], E [auth D]	tRNA pseudouridine synthase A	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	pseudouridine synthesis tRNA pseudouridine synthesis tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process tRNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process pseudouridine synthesis tRNA pseudouridine synthesis tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process tRNA 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	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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.