1Z2Z

Crystal Structure of the Putative tRNA pseudouridine synthase D (TruD) from Methanosarcina mazei, Northeast Structural Genomics Target MaR1

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	TruD_1st	e1z2zA1	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	e1z2zA2	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	e1z2zB1	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	e1z2zB2	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	3.30.70.3160	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	1.10.1510.30	Mainly Alpha	Orthogonal Bundle	Hypothetical Protein Yqey	Chain: A	CATH (4.3.0)
B	3.30.2350.20	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	TruD, catalytic domain	CATH (4.3.0)
B	3.30.70.3160	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	1.10.1510.30	Mainly Alpha	Orthogonal Bundle	Hypothetical Protein Yqey	Chain: A	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	Probable tRNA pseudouridine synthase D	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(13) synthase activity intramolecular transferase activity RNA binding binding organic cyclic compound 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	IPR020103	Pseudouridine synthase, catalytic domain superfamily	Homologous Superfamily
A, B	IPR042214	Pseudouridine synthase, TruD, catalytic domain	Homologous Superfamily
A, B	IPR001656	Pseudouridine synthase, TruD	Family
A, B	IPR020119	Pseudouridine synthase TruD, conserved site	Conserved Site
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.