1YT3

Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing

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	d1yt3a1	All alpha proteins	SAM domain-like	HRDC-like	RNase D C-terminal domains	Ribonuclease D	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1yt3a3	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Ribonuclease D, catalytic domain	(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)
A	SCOP2 Family	RNase D C-terminal domains-like	8022561	4001385	SCOP2 (2022-06-29)
A	SCOP2 Family	RNase D C-terminal domains-like	8022564	4001385	SCOP2 (2022-06-29)
A	SCOP2 Family	DnaQ-like 3'-5' exonuclease	8022566	4000547	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HRDC-like	8034941	3000132	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HRDC-like	8034944	3000132	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribonuclease H-like	8034946	3000143	SCOP2 (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	HRDC	e1yt3A1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HRDC	ECOD (1.6)
A	PRK10829	e1yt3A2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PRK10829	ECOD (1.6)
A	DNA_pol_A_exo1	e1yt3A3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_A_exo1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	1.10.150.80	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01612	3'-5' exonuclease (DNA_pol_A_exo1)	3'-5' exonuclease	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 ...	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
A	PF00570	HRDC domain (HRDC)	HRDC domain	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 ...	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
A	PF21293	Ribonuclease D, C-terminal HRDC domain (RNAseD_HRDC_C)	Ribonuclease D, C-terminal HRDC domain	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 ...	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

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ribonuclease D	binding organic cyclic compound binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity binding organic cyclic compound binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity catalytic activity ribonuclease D activity	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 tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing 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 tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process RNA 3'-end processing macromolecule metabolic process RNA processing tRNA 3'-end processing	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR010997	HRDC-like superfamily	Homologous Superfamily
A	IPR002121	HRDC domain	Domain
A	IPR051086	Ribonuclease D-like	Family
A	IPR044876	HRDC domain superfamily	Homologous Superfamily
A	IPR006292	Ribonuclease D	Family
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR002562	3'-5' exonuclease domain	Domain
A	IPR048579	Ribonuclease D, C-terminal HRDC domain	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
A	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 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.1.26.3 (PDB Primary Data) Search M-CSA Motif + EC 3.1.26.3 EC: 3.1.13.5 (UniProt) Search M-CSA Motif + EC 3.1.13.5

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.