1SZW

Crystal structure of E. coli tRNA pseudouridine synthase TruD

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	d1szwa_	Alpha and beta proteins (a+b)	Pseudouridine synthase	Pseudouridine synthase	tRNA pseudouridine synthase TruD	tRNA pseudouridine synthase TruD	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1szwb_	Alpha and beta proteins (a+b)	Pseudouridine synthase	Pseudouridine synthase	tRNA pseudouridine synthase TruD	tRNA pseudouridine synthase TruD	(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	SCOP2B Superfamily	Pseudouridine synthase	8041591	3001360	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pseudouridine synthase	8041591	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	TruD_1st	e1szwA2	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: TruD_1st	ECOD (1.6)
A	TruD_2nd	e1szwA3	A: a+b two layers	X: tRNA pseudouridine synthase TruD insertion domain (From Topology)	H: tRNA pseudouridine synthase TruD insertion domain (From Topology)	T: tRNA pseudouridine synthase TruD insertion domain	F: TruD_2nd	ECOD (1.6)
B	TruD_1st	e1szwB2	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: TruD_1st	ECOD (1.6)
B	TruD_2nd	e1szwB1	A: a+b two layers	X: tRNA pseudouridine synthase TruD insertion domain (From Topology)	H: tRNA pseudouridine synthase TruD insertion domain (From Topology)	T: tRNA pseudouridine synthase TruD insertion domain	F: TruD_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.2350.20	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	TruD, catalytic domain	CATH (4.3.0)
A	3.30.2340.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	TruD, insertion domain	CATH (4.3.0)
B	3.30.2350.20	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	TruD, catalytic domain	CATH (4.3.0)
B	3.30.2340.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	TruD, insertion domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01142	tRNA pseudouridine synthase D (TruD) (TruD)	tRNA pseudouridine synthase D (TruD)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	tRNA pseudouridine synthase D	isomerase activity pseudouridine synthase activity catalytic activity intramolecular transferase activity tRNA pseudouridine synthase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA tRNA pseudouridine(13) synthase activity RNA binding binding organic cyclic compound binding nucleic acid binding	pseudouridine synthesis nucleobase-containing compound metabolic process RNA modification macromolecule modification RNA metabolic process metabolic process primary metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing pseudouridine synthesis nucleobase-containing compound metabolic process RNA modification macromolecule modification RNA metabolic process metabolic process primary metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA pseudouridine synthesis cellular metabolic process tRNA modification gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process tRNA metabolic process biosynthetic process cellular process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR050170	tRNA pseudouridine synthase D	Family
A, B	IPR020103	Pseudouridine synthase, catalytic domain superfamily	Homologous Superfamily
A, B	IPR001656	Pseudouridine synthase, TruD	Family
A, B	IPR042214	Pseudouridine synthase, TruD, catalytic domain	Homologous Superfamily
A, B	IPR020119	Pseudouridine synthase TruD, conserved site	Conserved Site
A, B	IPR043165	Pseudouridine synthase, TruD, insertion domain superfamily	Homologous Superfamily
A, B	IPR011760	Pseudouridine synthase, TruD, insertion 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 R01GM133198.