1JH6

Semi-reduced Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1jh6a_	Alpha and beta proteins (a+b)	LigT-like	LigT-like	tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase	tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d1jh6b_	Alpha and beta proteins (a+b)	LigT-like	LigT-like	tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase	tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase	8024638	4001372	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LigT-like	8037017	3001408	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	LigT-like	8037017	3001408	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	CPDase	e1jh6A1	A: beta barrels	X: LigT-like	H: LigT-related (From Topology)	T: LigT-related	F: CPDase	ECOD (1.6)
B	CPDase	e1jh6B1	A: beta barrels	X: LigT-like	H: LigT-related (From Topology)	T: LigT-related	F: CPDase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.1140.10	Alpha Beta	Alpha-Beta Complex	Cyclic Phosphodiesterase	Chain: A,	CATH (4.3.0)
B	3.90.1140.10	Alpha Beta	Alpha-Beta Complex	Cyclic Phosphodiesterase	Chain: A,	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07823	Cyclic phosphodiesterase-like protein (CPDase)	Cyclic phosphodiesterase-like protein	Cyclic phosphodiesterase (CPDase, Swiss:O04147) is involved in the tRNA splicing pathway. This protein exhibits a bilobal arrangement of two alpha-beta modules. Two antiparallel helices are found on the outer side of each lobe and frame an antiparall ...	Cyclic phosphodiesterase (CPDase, Swiss:O04147) is involved in the tRNA splicing pathway. This protein exhibits a bilobal arrangement of two alpha-beta modules. Two antiparallel helices are found on the outer side of each lobe and frame an antiparallel beta-sheet that is wrapped around an accessible cleft. Moreover, the beta-strands of each lobe interact with the other lobe. The central water-filled cavity houses the enzyme's active site [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	cyclic phosphodiesterase	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity hydrolase activity cyclic-nucleotide phosphodiesterase activity catalytic activity	RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process tRNA metabolic process tRNA splicing, via endonucleolytic cleavage and ligation nucleic acid biosynthetic process biosynthetic process RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process tRNA metabolic process tRNA splicing, via endonucleolytic cleavage and ligation nucleic acid biosynthetic process biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation tRNA processing metabolic process cellular process RNA processing macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR009097	Cyclic phosphodiesterase	Homologous Superfamily
A, B	IPR012386	2',3'-cyclic-nucleotide 3'-phosphodiesterase	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
A	2',3'-cyclic-nucleotide 3'-phosphodiesterase M-CSA #794	During the tRNA splicing reaction in eukaryotes, an ADP ribose cyclic phosphate is formed. Hydrolysis of this to regenerate the monoester ADP ribose-1-phosphate is therefore a necessary part of the overall process. The enzyme cyclic phosphodiesterase is able to catalyse this reaction in the organism Arabidopsis thaliania. It displays a unique fold, but has some sequence identity with the equivalent enzymes in both wheat and zebrafish, specifically in the presence of the sequence motif H-X-T-S-X-H in the active site. Mechanistic and active site features in this family of enzymes are also found to be similar to other RNA processing proteins such as RNAase A.	Defined by 6 residues: HIS:A-42THR:A-44MET:A-117HIS:A-119SER:A-121TYR:A-124 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.1.4 (PDB Primary Data) Search M-CSA Motif + EC 3.1.4 EC: 3.1.4.37 (UniProt) Search M-CSA Motif + EC 3.1.4.37

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.