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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2 FamilyRNase D C-terminal domains-like 8022561 4001385 SCOP2 (2022-06-29)
ASCOP2 FamilyRNase D C-terminal domains-like 8022564 4001385 SCOP2 (2022-06-29)
ASCOP2 FamilyDnaQ-like 3'-5' exonuclease 8022566 4000547 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyHRDC-like 8034941 3000132 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyHRDC-like 8034944 3000132 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyRibonuclease H-like 8034946 3000143 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AHRDCe1yt3A1 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: SAM domain-likeF: HRDCECOD (1.6)
APRK10829e1yt3A2 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: SAM domain-likeF: PRK10829ECOD (1.6)
ADNA_pol_A_exo1e1yt3A3 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: DNA_pol_A_exo1ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.30.420.10 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase domain 5CATH (4.3.0)
A1.10.150.80 Mainly Alpha Orthogonal Bundle DNA polymerase domain 1CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF016123'-5' exonuclease (DNA_pol_A_exo1)3'-5' exonucleaseThis domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the ...This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction [4,5]. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein [3]. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.
Domain
PF00570HRDC domain (HRDC)HRDC domainThe HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains ...The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains [4].
Domain
PF21293Ribonuclease D, C-terminal HRDC domain (RNAseD_HRDC_C)Ribonuclease D, C-terminal HRDC domainRibonuclease D is a bacterial 3'-5' exonuclease that acts on tRNA. It contributes to the 3' maturation of several stable RNAs [1]. It consists of a catalytic domain (Pfam:PF01612) and two alpha- helical domains at the C-terminal that closely resemble ...Ribonuclease D is a bacterial 3'-5' exonuclease that acts on tRNA. It contributes to the 3' maturation of several stable RNAs [1]. It consists of a catalytic domain (Pfam:PF01612) and two alpha- helical domains at the C-terminal that closely resemble the HRDC domain seen in RecQ-family helicases. This is the second HRDC domain from RNAse D. The first one is included in Pfam:PF00570.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Ribonuclease D

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

ChainsEnzyme NameDescriptionCatalytic Residues
ribonuclease D  M-CSA #321

Ribonuclease D is a divalent metal cation dependent exonuclease that acts on tRNA and is involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides.

Defined by 5 residues: ASP:A-28GLU:A-30ASP:A-85TYR:A-151ASP:A-155
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