DPB11 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: DPB11
Primary source: FungiDB:YJL090C
Locus tag: YJL090C
See related: SGD:S000003626; AllianceGenome:SGD:S000003626; VEuPathDB:YJL090C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables DNA polymerase binding activity and protein kinase activator activity. Involved in several processes, including DNA integrity checkpoint signaling; DNA metabolic process; and positive regulation of DNA replication origin binding activity. Located in replication fork. Part of DNA replication preinitiation complex. Orthologous to human TOPBP1 (DNA topoisomerase II binding protein 1). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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Location:: chromosome: X

Exon count:: 1

Sequence:: Chromosome: X; NC_001142.9 (262757..265051, complement)

Chromosome X - NC_001142.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001142.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Dpb11 obtained by endogenous purification strongly stimulates the Mec1 kinase activity and promotes the changes in conformational distribution. This observation suggests the Dpb11 activates Mec1 kinase probably through modulation in the kinase conformations.
Title: Preparation of endogenous TopBP1/Dpb11 and effect on central checkpoint kinase Mec1- Ddc2 (human ATR-ATRIP homolog).
Budding yeast Fun30 and human SMARCAD1 are cell cycle-regulated by interaction with the DNA double strand break-localized scaffold protein Dpb11/TOPBP1, respectively. In yeast, this protein assembly additionally comprises the 9-1-1 damage sensor, is involved in localizing Fun30 to damaged chromatin, and thus is required for efficient long-range resection of DNA double strand breaks.
Title: Targeting of the Fun30 nucleosome remodeller by the Dpb11 scaffold facilitates cell cycle-regulated DNA end resection.
The Slx4-Dpb11 scaffold complex coordinates the response to replication fork stalling in S-phase and the subsequent mitosis.
Title: The Slx4-Dpb11 scaffold complex: coordinating the response to replication fork stalling in S-phase and the subsequent mitosis.
Upon extrusion of ssDNA from the central channel of Mcm2-7, Dpb11 dissociates from Mcm2-7, and Dpb11 binds to ssDNA, thereby allowing GINS to bind to Cdc45.Mcm2-7
Title: Dpb11 protein helps control assembly of the Cdc45·Mcm2-7·GINS replication fork helicase.
The ddc2-S4 mutation decreases phosphorylation of histone H2A more significantly than the absence of Ddc1 and Dpb11 function does.
Title: Ddc2 mediates Mec1 activation through a Ddc1- or Dpb11-independent mechanism.
Depletion of TopBP1/Dpb11 led to an accumulation of chromatin bridges.
Title: TopBP1/Dpb11 binds DNA anaphase bridges to prevent genome instability.
the inter-BRCT region of Dpb11 is a functionally conserved GINS interaction domain that is important for the initiation of DNA replication
Title: Efficient initiation of DNA replication in eukaryotes requires Dpb11/TopBP1-GINS interaction.
a ternary complex of Dpb11, Mec1 and another key mediator protein Rad9 is required for efficient Rad9 phosphorylation by Mec1 in vitro, and for checkpoint activation in vivo.
Title: Dpb11 coordinates Mec1 kinase activation with cell cycle-regulated Rad9 recruitment.
Dpb11 plays distinct roles in replication, checkpoint response and recombination processes, thereby contributing to chromosomal stability
Title: Dpb11/TopBP1 plays distinct roles in DNA replication, checkpoint response and homologous recombination.
Multiple fork repair factors associate with Rtt107 or Slx4, supporting that Mec1-dependent assembly of the Rtt107-Slx4-Dpb11 complex functions to coordinate fork repair.
Title: DNA damage signaling recruits the Rtt107-Slx4 scaffolds via Dpb11 to mediate replication stress response.

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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 DNA polymerase binding	IDA Inferred from Direct Assay more info	PubMed
enables protein kinase activator activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
involved_in DNA replication checkpoint signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA replication initiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA replication initiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in double-strand break repair via break-induced replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mating type switching	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic DNA replication checkpoint signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitotic G2 DNA damage checkpoint signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitotic G2 DNA damage checkpoint signaling	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of DNA replication origin binding	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in recombinational repair	IDA Inferred from Direct Assay more info	PubMed
involved_in recombinational repair	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
part_of DNA replication preinitiation complex	IMP Inferred from Mutant Phenotype more info	PubMed
located_in nucleus	HDA more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in replication fork	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: protein kinase activating protein DPB11

NP_012445.1

DNA replication initiation protein; loads DNA pol epsilon onto pre-replication complexes at origins; checkpoint sensor recruited to stalled replication forks by the checkpoint clamp complex where it activates Mec1p; along with Rfa1p, binds to ultrafine anaphase bridges in mitotic cells and prevents accumulation of chromatin bridges by stimulating the Mec1p kinase and suppressing homologous recombination; ortholog of human TopBP1; 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_001142.9 Reference assembly

Range

262757..265051 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001181523.1 → NP_012445.1 TPA: protein kinase activating protein DPB11 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_012445.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VW94, P47027, Q05712

UniProtKB/TrEMBL

B3LQ23, C7GR24, N1P327

Conserved Domains (3) summary

cd18433
Location:326 → 410

BRCT_Rad4_rpt3; third BRCT domain of Schizosaccharomyces pombe S-M checkpoint control protein Rad4 and similar proteins

pfam00533
Location:111 → 206

BRCT; BRCA1 C-terminus (BRCT) domain

cl00038
Location:2 → 85

BRCT; C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains