1W0H | pdb_00001w0h

Crystallographic structure of the nuclease domain of 3'hExo, a DEDDh family member, bound to rAMP

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
Pharos: Disease Associations
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	d1w0ha_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Exonuclease ERI1	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DnaQ-like 3'-5' exonuclease	8030825	4000547	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribonuclease H-like	8043204	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	RNase_T	e1w0hA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00929	Exonuclease (RNase_T)	Exonuclease	This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	3'-5' EXONUCLEASE ERI1	hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity pre-mRNA binding RNA binding binding nucleic acid binding histone pre-mRNA stem-loop binding rRNA binding ribonucleoprotein complex binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity pre-mRNA binding RNA binding binding nucleic acid binding histone pre-mRNA stem-loop binding rRNA binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity cation binding ion binding metal ion binding small molecule binding	regulation of biosynthetic process regulation of biological process regulation of cellular process negative regulation of metabolic process biological regulation negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process negative regulation of metabolic process biological regulation negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process negative regulation of macromolecule metabolic process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process cellular component biogenesis nucleic acid biosynthetic process ribosome biogenesis rRNA 3'-end processing RNA 3'-end processing RNA processing cellular component organization or biogenesis rRNA metabolic process exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of 5.8S rRNA maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen histone pre-mRNA 3'end processing complex protein-containing complex nuclear protein-containing complex ribonucleoprotein complex cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR047201	ERI-1-like, DEDDh 3'-5' exonuclease domain	Domain
A	IPR013520	Ribonuclease H-like domain	Domain
A	IPR003034	SAP domain	Domain
A	IPR036361	SAP domain superfamily	Homologous Superfamily
A	IPR051274	3'-5' Exoribonuclease	Family
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q8IV48	atypical teratoid rhabdoid tumor glioblastoma malignant glioma pilocytic astrocytoma subependymal giant cell astrocytoma breast cancer large cell medulloblastoma medulloblastoma primitive neuroectodermal tumor ulcerative colitis chronic obstructive pulmonary disease malignant ependymoma ovarian cancer Sjogren syndrome

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

Chains	Enzyme Name	Description	Catalytic Residues
A	3'-5' exoribonuclease 1 M-CSA #784	3'-5' exoribonuclease (3'hExo) from Homo sapiens is a DEDDh family member. It contains the invariant DEDD working with H sequence of residues. 3'hExo targets human histone mRNAs and degrades them in a 3' to 5' direction in a sequence specific manner.	Defined by 5 residues: ASP:A-16 [auth A-134]GLU:A-18 [auth A-136]ASP:A-116 [auth A-234]HIS:A-175 [auth A-293]ASP:A-180 [auth A-298] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.1 (PDB Primary Data) Search M-CSA Motif + EC 3.1 EC: 3.1.13.1 (UniProt) Search M-CSA Motif + EC 3.1.13.1

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.