pdr-1 E3 ubiquitin-protein ligase parkin;RBR-type E3 ubiquitin transferase;Ubiquitin-like domain-containing protein [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: pdr-1
Official Full Name: E3 ubiquitin-protein ligase parkin;RBR-type E3 ubiquitin transferase;Ubiquitin-like domain-containing protein
Primary source: WormBase:WBGene00003967
Locus tag: CELE_K08E3.7
See related: AllianceGenome:WB:WBGene00003967
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Enables ubiquitin conjugating enzyme binding activity. Contributes to ubiquitin-protein transferase activity. Involved in several processes, including determination of adult lifespan; negative regulation of engulfment of apoptotic cell; and protein autoubiquitination. Located in mitochondrial outer membrane and neuronal cell body. Part of ubiquitin ligase complex. Is expressed in muscle cell and neurons. Used to study Parkinson's disease. Human ortholog(s) of this gene implicated in Parkinson's disease; Parkinson's disease 2; lung cancer; and ovarian cancer. Orthologous to human PRKN (parkin RBR E3 ubiquitin protein ligase). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See pdr-1 in Genome Data Viewer

Location:: chromosome: III

Exon count:: 7

Sequence:: Chromosome: III; NC_003281.10 (13771513..13773345)

Chromosome III - NC_003281.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003281.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PINK1 and parkin shape the organism-wide distribution of a deleterious mitochondrial genome.
Title: PINK1 and parkin shape the organism-wide distribution of a deleterious mitochondrial genome.
While no change in mRNA expression of the major Mn importer proteins (smf-1-3) was found in pdr-1 mutants, significant downregulation in mRNA levels of the putative Mn exporter ferroportin (fpn-1.1) was observed.
Title: Loss of pdr-1/parkin influences Mn homeostasis through altered ferroportin expression in C. elegans.
These data show that mutation in the Caenorhabditis elegans orthologue of Parkin (pdr-1) modulates the level of a large heteroplasmic mtDNA truncation.
Title: Parkin modulates heteroplasmy of truncated mtDNA in Caenorhabditis elegans.
The pdr1 and djr1.1 mutants showed enhanced Mn accumulation and oxidative stress that was reduced by alpha-synuclein.
Title: The effects of pdr1, djr1.1 and pink1 loss in manganese-induced toxicity and the role of α-synuclein in C. elegans.
PDR-1 inhibits apoptotic cell engulfment and distal tip cell migration by ubiquitylating CED-10 for degradation.
Title: PDR-1/hParkin negatively regulates the phagocytosis of apoptotic cell corpses in Caenorhabditis elegans.
In contrast to pdr-1 loss-of-function mutants, an in-frame parkin homolog pdr-1 deletion variant with altered solubility and intracellular localization properties is hypersensitive toward different proteotoxic stress conditions.
Title: A Caenorhabditis elegans Parkin mutant with altered solubility couples alpha-synuclein aggregation to proteotoxic stress.
PD-related genetic modifications of alpha-synuclein, parkin, and DJ-1 disrupt the mitochondrial function in C. elegans [K08E3.7 is parkin]
Title: Similar patterns of mitochondrial vulnerability and rescue induced by genetic modification of alpha-synuclein, parkin, and DJ-1 in Caenorhabditis elegans.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

K08E3.6 (e-PCR)
- UniSTS:312689

K08E3.7 (e-PCR)
- UniSTS:313237

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin conjugating enzyme binding	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin conjugating enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
contributes_to ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin-protein transferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in autophagy	IEA Inferred from Electronic Annotation more info
involved_in determination of adult lifespan	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell migration	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of engulfment of apoptotic cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of metabolic process	IEA Inferred from Electronic Annotation more info
involved_in protein autoubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein ubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of apoptotic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cellular response to oxidative stress	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of mitochondrion organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to toxic substance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrial outer membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
part_of ubiquitin ligase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of ubiquitin ligase complex	IEA Inferred from Electronic Annotation more info
part_of ubiquitin ligase complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: E3 ubiquitin-protein ligase parkin;RBR-type E3 ubiquitin transferase;Ubiquitin-like domain-containing protein

NP_001293603.1

Confirmed by transcript evidence

NP_001360308.1

Partially confirmed by transcript evidence

NP_001370029.1

Confirmed by transcript evidence

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_003281.10 Reference assembly

Range

13771513..13773345

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001372678.3 → NP_001360308.1 Ubiquitin-like domain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

V6CLJ6

Conserved Domains (2) summary

cd17039
Location:13 → 77

Ubl_ubiquitin_like; ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins

cd21382
Location:104 → 182

RING0_parkin; RING finger-like zinc-binding domain 0 of parkin
NM_001383028.2 → NP_001370029.1 E3 ubiquitin-protein ligase parkin [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

Q9XUS3

Conserved Domains (5) summary

cd17039
Location:13 → 77

Ubl_ubiquitin_like; ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins

pfam01485
Location:336 → 375

IBR; IBR domain, a half RING-finger domain

pfam17978
Location:182 → 268

zf-RING_14; RING/Ubox like zinc-binding domain

cd21382
Location:104 → 182

RING0_parkin; RING finger-like zinc-binding domain 0 of parkin

cl19760
Location:266 → 317

IBR; IBR domain, a half RING-finger domain
NM_001306674.3 → NP_001293603.1 RBR-type E3 ubiquitin transferase [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001293603.1

Status: REVIEWED

UniProtKB/TrEMBL

V6CLF7

Conserved Domains (3) summary

cl39406
Location:42 → 120

RING0_parkin; RING finger-like zinc-binding domain 0 of parkin

pfam17978
Location:120 → 206

zf-RING_14; RING/Ubox like zinc-binding domain

cl45895
Location:271 → 323

BRcat_Rcat_RBR; BRcat (benign-catalytic) and Rcat (required-for-catalysis) domains, part of the RBR (RING1-BRcat-Rcat) domain