Annotations: 9VBI

Cryo-EM structure of PLD3 bound to ssDNA (poly(A))

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A], D	PF13918	PLD3/4, PLD-like domain (PLDc_3)	PLD3/4, PLD-like domain	This domain is found in a subset of the phospholipase D family members, including 5'-3' exonuclease PLD3/4 from animals [1,2] and viral phospholipases such as envelope phospholipase F13 (also known as OPG057) and homologues [3]. Human PLD3 is a 5'->3 ...	This domain is found in a subset of the phospholipase D family members, including 5'-3' exonuclease PLD3/4 from animals [1,2] and viral phospholipases such as envelope phospholipase F13 (also known as OPG057) and homologues [3]. Human PLD3 is a 5'->3' DNA exonuclease which digests single-stranded DNA and may regulate inflammatory cytokine responses via the degradation of nucleic acids. PLD3 was initially thought to have phospholipase D activity due to its HKD motifs. The second HKD motif contains Glu instead of the canonical Asp and, therefore, its catalytic phospholipase D activity is still controversial [1,4]. PLD4, its closest homologue, does not posses phospholipase activity. Envelope phospholipase F13 from Vaccinia virus is the major envelope protein that plays a role in the biogenesis of the viral double membrane and in egress of virus from the host cell [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], C [auth B]	DNA (5'-D(APAPAPAP*A)-3')	-	-	-
B [auth A], D	5'-3' exonuclease PLD3	acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity single-stranded DNA 5'-3' DNA exonuclease activity DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity single-stranded DNA 5'-3' DNA exonuclease activity DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds exonuclease activity 5'-3' RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity	immune system process cellular response to stimulus positive regulation of response to biotic stimulus regulation of toll-like receptor 9 signaling pathway regulation of cellular process pattern recognition receptor signaling pathway response to stimulus negative regulation of biological process regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway positive regulation of immune response immune system process cellular response to stimulus positive regulation of response to biotic stimulus regulation of toll-like receptor 9 signaling pathway regulation of cellular process pattern recognition receptor signaling pathway response to stimulus negative regulation of biological process regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway positive regulation of immune response negative regulation of toll-like receptor 9 signaling pathway regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process immune response response to other organism regulation of innate immune response response to external stimulus regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response toll-like receptor 9 signaling pathway activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway signaling negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction positive regulation of biological process regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of cell communication positive regulation of response to stimulus endolysosomal toll-like receptor signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of intracellular signal transduction regulation of response to stress response to stress innate immune response negative regulation of cellular process response to external biotic stimulus regulation of signaling positive regulation of innate immune response defense response negative regulation of response to stimulus biological regulation defense response to symbiont negative regulation of signal transduction negative regulation of immune system process regulation of cell communication cellular process multicellular organismal process regulation of cytokine production involved in inflammatory response cytokine production regulation of cytokine production regulation of multicellular organismal process production of molecular mediator involved in inflammatory response regulation of biosynthetic process regulation of macromolecule metabolic process cytokine production involved in inflammatory response gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process inflammatory response macromolecule metabolic process regulation of metabolic process positive regulation of organelle organization vesicle budding from membrane regulation of localization regulation of cellular component organization positive regulation of cellular component organization transport positive regulation of endosome organization vesicle-mediated transport vesicle organization cellular component organization regulation of endosome organization localization positive regulation of intralumenal vesicle formation endosome organization cellular component organization or biogenesis endomembrane system organization positive regulation of cellular process membrane organization regulation of transport establishment of localization regulation of organelle organization intralumenal vesicle formation organelle organization positive regulation of transport regulation of intralumenal vesicle formation primary metabolic process lipid metabolic process developmental process muscle structure development cellular developmental process cell differentiation anatomical structure development striated muscle cell differentiation muscle cell differentiation myotube differentiation	cellular anatomical structure endomembrane system vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cellular anatomical structure endomembrane system vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm organelle membrane lysosome Golgi membrane Golgi apparatus endosome membrane early endosome endosome intracellular vesicle early endosome membrane cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane vesicle membrane-enclosed lumen vacuolar lumen lysosomal lumen intracellular organelle lumen organelle lumen extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle late endosome membrane late endosome endoplasmic reticulum organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A], D	IPR050874	Diverse function phospholipase D-related protein	Family
B [auth A], D	IPR001736	Phospholipase D/Transphosphatidylase	Domain
B [auth A], D	IPR032803	PLD3/4-like, PLD-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth A], D	: Q8IV08	Alzheimer disease 19 malignant ependymoma neurodegenerative disease otitis media psoriasis astrocytic tumor malignant mesothelioma oligodendroglioma ovarian cancer spinocerebellar ataxia 46 autosomal dominant cerebellar ataxia medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm

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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.

9VBI | pdb_00009vbi

Cryo-EM structure of PLD3 bound to ssDNA (poly(A))

External Resource: Annotation

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Pharos: Disease Associations Pharos Homepage Annotation