DDI1 Ddi1p [Saccharomyces cerevisiae S288C] - Gene

Summary

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Gene symbol: DDI1
Gene description: Ddi1p
Primary source: FungiDB:YER143W
Locus tag: YER143W
See related: SGD:S000000945; AllianceGenome:SGD:S000000945; VEuPathDB:YER143W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: VSM1
Summary: Enables several functions, including aspartic-type endopeptidase activity; proteasome regulatory particle binding activity; and ubiquitin binding activity. Involved in positive regulation of DNA replication; protein transport; and response to hydroxyurea. Located in plasma membrane. Orthologous to human DDI1 (DNA damage inducible 1 homolog 1) and DDI2 (DNA damage inducible 1 homolog 2). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See DDI1 in Genome Data Viewer

Location:: chromosome: V

Exon count:: 1

Sequence:: Chromosome: V; NC_001137.3 (456319..457605)

Chromosome V - NC_001137.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001137.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Domains in Action: Understanding Ddi1's Diverse Functions in the Ubiquitin-Proteasome System.
Title: Domains in Action: Understanding Ddi1's Diverse Functions in the Ubiquitin-Proteasome System.
New insights into the regulation of DNA-Protein Crosslink Repair by the Aspartic Protease Ddi1 in yeast.
Title: New insights into the regulation of DNA-Protein Crosslink Repair by the Aspartic Protease Ddi1 in yeast.
unlike other shuttling factors, Ddi1 and its homologs contain a conserved helical domain (helical domain of Ddi1, HDD) and a retroviral-like protease (RVP) domain. The RVP domain is probably responsible for cleavage of the precursor of the transcription factor Nrf1 in higher eukaryotes, which results in the up-regulation of proteasomal subunit genes.
Title: Ddi1 is a ubiquitin-dependent protease.
The Ddi1 protease contributes to DNA-protein crosslinks proteolysis.
Title: The Aspartic Protease Ddi1 Contributes to DNA-Protein Crosslink Repair in Yeast.
The yeast proteases Ddi1 and Wss1 are both involved in the DNA replication stress response. Double-deleted Deltaddi1, Deltawss1 yeast strain is hypersensitive to the replication drug hydroxyurea and this phenotype can be complemented only by catalytically competent Ddi1 protease. Key involvement of the helical domain preceding the Ddi1 protease domain is also shown.
Title: The yeast proteases Ddi1 and Wss1 are both involved in the DNA replication stress response.
Data show that DNA-damage inducible protein 1 (Ddi1) cleavage is tightly regulated in vivo as it only takes place in yeast when calcium increases but under specific metabolic conditions.
Title: DNA-damage inducible protein 1 is a conserved metacaspase substrate that is cleaved and further destabilized in yeast under specific metabolic conditions.
The dual functionality of Ddi1-ubiquitin-like domain, capable of binding both ubiquitin and proteasome, suggests an intriguing mechanism for Ddi1 as a proteasomal shuttle.
Title: DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin.
The current study identifies residues in the LRR1 domain of Rpn1 that contribute to shuttle receptor docking. It validates Ddi1 as a proteasomal shuttle receptor whose stable binding to the proteasome depends on Rpn1 residue D517.
Title: Identification of a functional docking site in the Rpn1 LRR domain for the UBA-UBL domain protein Ddi1.
Results substantiate the hypothesis that Ddi1 functions in vivo as a catalytically-active aspartic proteinase.
Title: The retroviral proteinase active site and the N-terminus of Ddi1 are required for repression of protein secretion.
Ddi1 participates in multiple cellular processes via its different domains and phosphorylation may regulate exocytic functions
Title: Different domains of the UBL-UBA ubiquitin receptor, Ddi1/Vsm1, are involved in its multiple cellular roles.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables SNARE binding	IDA Inferred from Direct Assay more info	PubMed
enables aspartic-type endopeptidase activity	IDA Inferred from Direct Assay more info	PubMed
enables aspartic-type endopeptidase activity	IEA Inferred from Electronic Annotation more info
enables aspartic-type endopeptidase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables polyubiquitin modification-dependent protein binding	IDA Inferred from Direct Assay more info	PubMed
enables polyubiquitin modification-dependent protein binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables proteasome regulatory particle binding	IDA Inferred from Direct Assay more info	PubMed
enables protein-macromolecule adaptor activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in positive regulation of DNA replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
involved_in ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Ddi1p

NP_011070.3

Aspartic-type endopeptidase; involved in the cleavage of long-chain polyubiquitinated substrates; role in proteasome-independent, ubiquitin (Ub)-dependent proteolysis and DNA-protein crosslink repair; Ub-shuttle receptor for HO and Ufo1p; DNA damage-inducible v-SNARE binding protein and negative regulator of constitutive exocytosis; possible role in the S-phase checkpoint; UBL-UBA family member containing Ub-like (UBL), helical, Ub-associated (UBA) and retroviral-like proteinase (RVP) domains

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_001137.3 Reference assembly

Range

456319..457605

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001179033.3 → NP_011070.3 TPA: Ddi1p [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_011070.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D3DM50, P40087

UniProtKB/TrEMBL

A0A6A5Q0F6, B3LRQ6, B5VHR8, C7GQ53, C8Z7G3, N1P542

Conserved Domains (4) summary

cd05479
Location:188 → 310

RP_DDI; retropepsin-like domain of DNA damage inducible protein

cd14309
Location:392 → 427

UBA_scDdi1_like; UBA domain found in Saccharomyces cerevisiae DNA-damage response protein Ddi1 and similar proteins

TIGR00601
Location:324 → 427

rad23; UV excision repair protein Rad23

cd01796
Location:1 → 74

Ubl_Ddi1_like; ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family