5FIQ | pdb_00005fiq

Exonuclease domain-containing 1 (Exd1) in the native conformation

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e5fiqA1	A: a/b three-layered sandwiches	X: ADP-ribosylation	H: ADP-ribosylation	T: ADP-ribosylation	F:	ECOD (v294.1)
B [auth C]	RE_AlwI	e5fiqC1	A: a/b three-layered sandwiches	X: Caspase-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: RE_AlwI	ECOD (v294.1)
C [auth E]	RE_AlwI	e5fiqE1	A: a/b three-layered sandwiches	X: Caspase-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: RE_AlwI	ECOD (v294.1)
D [auth G]	RE_AlwI	e5fiqG1	A: a/b three-layered sandwiches	X: Caspase-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: RE_AlwI	ECOD (v294.1)
E [auth I]	RE_AlwI	e5fiqI1	A: a/b three-layered sandwiches	X: Caspase-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: RE_AlwI	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth E], D [auth G], E [auth I]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C], C [auth E], D [auth G], E [auth I]	EXD1	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity RNA binding nucleic acid 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 piRNA processing RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process RNA processing primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulatory ncRNA processing sexual reproduction reproductive process meiotic cell cycle cell cycle	intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle pole plasm membraneless organelle cytoplasm supramolecular complex protein-containing complex intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle pole plasm membraneless organelle cytoplasm supramolecular complex protein-containing complex PET complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth E], D [auth G], E [auth I]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B [auth C], C [auth E], D [auth G], E [auth I]	IPR052144	piRNA biogenesis EXD1-related protein	Family
A, B [auth C], C [auth E], D [auth G], E [auth I]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B [auth C], C [auth E], D [auth G], E [auth I]	IPR002562	3'-5' exonuclease domain	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.