LCD1 Lcd1p [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: LCD1
Official Full Name: Lcd1p
Primary source: SGD:S000002907
Locus tag: YDR499W
See related: AllianceGenome:SGD:S000002907; FungiDB:YDR499W; VEuPathDB:YDR499W
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: DDC2; PIE1
Summary: Enables damaged DNA binding activity. Involved in DNA damage checkpoint signaling; establishment of protein localization; and telomere maintenance via telomerase. Located in nuclear chromosome. [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See LCD1 in Genome Data Viewer

Location:: chromosome: IV

Exon count:: 1

Sequence:: Chromosome: IV; NC_001136.10 (1447830..1450073)

Chromosome IV - NC_001136.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001136.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

the C-terminal of Ddc1 has structural flexibility and it plays a critical role for Mec1/Ddc2 activation in G1/G2 phase; the 9-1-1 complex and Rad24-RFC interact
Title: The structure of the checkpoint clamp 9-1-1 complex and clamp loader Rad24-RFC in Saccharomyces cerevisiae.
This study presents functional and structural characterization of the physical interaction between Dpb11 and Mec1-Ddc2 complex.
Title: Preparation of endogenous TopBP1/Dpb11 and effect on central checkpoint kinase Mec1- Ddc2 (human ATR-ATRIP homolog).
Study shows that Ddc2 promotes Mec1 activation independently of Ddc1/Dpb11/Dna2 function in vivo and through ssDNA recognition in vitro. The ddc2-S4 mutation diminishes damage-induced phosphorylation of the checkpoint mediators, Rad9 and Mrc1. Rad9 controls checkpoint throughout the cell-cycle whereas Mrc1 is specifically required for the S-phase checkpoint.
Title: Ddc2ATRIP promotes Mec1ATR activation at RPA-ssDNA tracts.
Rad52-RFP and Rad51-GFP co-localize to the same DSB, but a significant minority of foci have Rad51-GFP without visible Rad52-RFP. We conclude that co-localization of foci in cells with 3 DSBs does not represent formation of a homologous recombination "repair center," as the same distribution of Ddc2-GFP foci was found in the absence of the Rad52 protein.
Title: Live cell monitoring of double strand breaks in S. cerevisiae.
this study determined the structure of intact Mec1-Ddc2 (the yeast homolog of ATR-ATRIP), which is poised for catalysis, at a resolution of 3.9 angstroms.
Title: 3.9 Å structure of the yeast Mec1-Ddc2 complex, a homolog of human ATR-ATRIP.
RPA-dependent recruitment of Mec1-Ddc2 is crucial for maintaining its homodimeric state at ssDNA and that Ddc2's recruitment domain and CCD are important for Mec1-dependent survival of UV-light-induced DNA damage.
Title: Structural Basis of Mec1-Ddc2-RPA Assembly and Activation on Single-Stranded DNA at Sites of Damage.
Physical interaction between Pph3 and Mec1, mediated by cofactors Psy2 and Ddc2, is important for regulating the checkpoint response in yeast.
Title: Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling.
Our results suggest that Ddc2 plays a critical role in Mec1 activation as well as Mec1 localization at sites of DNA damage
Title: Ddc2 mediates Mec1 activation through a Ddc1- or Dpb11-independent mechanism.
Results point to an evolutionary conserved role for Ddc2/ATRIP in monitoring meiotic chromosome metabolism.
Title: The Ddc2/ATRIP checkpoint protein monitors meiotic recombination intermediates.
Results show that DNA damage response at eroded telomeres is characterized by the recruitment of Cdc13, replication protein A, DNA damage checkpoint proteins and the DNA repair protein Rad52 into a single focus.
Title: The DNA damage response at eroded telomeres and tethering to the nuclear pore complex.

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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 damaged DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA damage checkpoint signaling	IEA Inferred from Electronic Annotation more info
involved_in DNA damage checkpoint signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in establishment of protein localization	IDA Inferred from Direct Assay more info	PubMed
involved_in establishment of protein localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in telomere maintenance via telomerase	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nuclear chromosome	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	HDA more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Lcd1p

NP_010787.3

Essential protein required for the DNA integrity checkpoint pathways; interacts physically with Mec1p and contributes to its activation; putative homolog of S. pombe Rad26 and human ATRIP; forms nuclear foci upon DNA replication stress

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_001136.10 Reference assembly

Range

1447830..1450073

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001180807.3 → NP_010787.3 TPA: Lcd1p [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_010787.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VTC1, Q04377

UniProtKB/TrEMBL

G2WBM7, N1P5T4

Conserved Domains (1) summary

pfam09798
Location:77 → 745

LCD1; DNA damage checkpoint protein