1SB7 | pdb_00001sb7

Crystal structure of the E.coli 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)
B	d1sb7b1	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	d1sb7b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1sb7a1	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)
A	d1sb7a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
B	SCOP2B Superfamily	Pseudouridine synthase	8041591	3001360	SCOP2B (2022-06-29)
A	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)
B	RNA_pol_Rpb1_2	e1sb7B1	A: a/b three-layered sandwiches	X: Inserted helical domain in fatty acid synthase subunit beta	H: Voltage-gated ion channels	T: Voltage-gated ion channels	F: RNA_pol_Rpb1_2	ECOD (v294.1)
A	RNA_pol_Rpb1_2	e1sb7A1	A: a/b three-layered sandwiches	X: Inserted helical domain in fatty acid synthase subunit beta	H: Voltage-gated ion channels	T: Voltage-gated ion channels	F: RNA_pol_Rpb1_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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 nucleic acid binding	pseudouridine synthesis nucleobase-containing compound metabolic process RNA modification macromolecule modification RNA metabolic process metabolic process cellular process primary metabolic process macromolecule metabolic process nucleic acid metabolic process tRNA pseudouridine synthesis tRNA modification gene expression nucleobase-containing compound biosynthetic process pseudouridine synthesis nucleobase-containing compound metabolic process RNA modification macromolecule modification RNA metabolic process metabolic process cellular process primary metabolic process macromolecule metabolic process nucleic acid metabolic process tRNA pseudouridine synthesis tRNA modification gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process tRNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.