Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2 FamilytRNA splicing product Appr>p cyclic nucleotide phosphodiesterase 8024638 4001372 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyLigT-like 8037017 3001408 SCOP2 (2022-06-29)
BSCOP2B SuperfamilyLigT-like 8037017 3001408 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ACPDasee1jh6A1 A: beta barrelsX: LigT-likeH: LigT-related (From Topology)T: LigT-relatedF: CPDaseECOD (1.6)
BCPDasee1jh6B1 A: beta barrelsX: LigT-likeH: LigT-related (From Topology)T: LigT-relatedF: CPDaseECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.90.1140.10 Alpha Beta Alpha-Beta Complex Cyclic Phosphodiesterase Chain: A,CATH (4.3.0)
B3.90.1140.10 Alpha Beta Alpha-Beta Complex Cyclic Phosphodiesterase Chain: A,CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B
PF07823Cyclic phosphodiesterase-like protein (CPDase)Cyclic phosphodiesterase-like proteinCyclic 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

InterPro: Protein Family Classification InterPro Database Homepage

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

ChainsEnzyme NameDescriptionCatalytic Residues
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
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Explore in 3DM-CSA Motif Definition
EC: 3.1.4 (PDB Primary Data)