RAD53/YPL153C Summary Help

Standard Name RAD53 1
Systematic Name YPL153C
Alias LSD1 , MEC2 2 , SPK1
Feature Type ORF, Verified
Description DNA damage response protein kinase; required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication; activates the downstream kinase Dun1p; differentially senses mtDNA depletion and mitochondrial ROS; required for regulation of copper genes in response to DNA-damaging agents; relocalizes to cytosol in response to hyoxia (3, 4, 5, 6, 7, 8, 9 and see Summary Paragraph)
Name Description RADiation sensitive
Chromosomal Location
ChrXVI:264192 to 261727 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: -109 cM
Gene Ontology Annotations All RAD53 GO evidence and references
  View Computational GO annotations for RAD53
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 3 genes
Classical genetics
reduction of function
Large-scale survey
630 total interaction(s) for 352 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 76
  • Affinity Capture-Western: 51
  • Biochemical Activity: 70
  • Co-crystal Structure: 1
  • Co-localization: 1
  • Co-purification: 1
  • Protein-peptide: 6
  • Reconstituted Complex: 10
  • Two-hybrid: 28

Genetic Interactions
  • Dosage Growth Defect: 15
  • Dosage Lethality: 5
  • Dosage Rescue: 30
  • Negative Genetic: 38
  • Phenotypic Enhancement: 24
  • Phenotypic Suppression: 25
  • Positive Genetic: 3
  • Synthetic Growth Defect: 124
  • Synthetic Lethality: 61
  • Synthetic Rescue: 61

Expression Summary
Length (a.a.) 821
Molecular Weight (Da) 91,962
Isoelectric Point (pI) 7.82
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrXVI:264192 to 261727 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: -109 cM
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..2466 264192..261727 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | E.C. | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000006074

RAD53 encodes an essential protein kinase required for cell cycle checkpoint function. By modifying the phosphorylation state of protein targets, Rad53p amplifies initial signals from proteins that recognize DNA damage and replication blocks (2, 10, and reviewed in 11). This signal cascade results in the arrest of cells in G1/S, intra-S, or G2/M, transcriptional upregulation of repair genes, transcriptional repression of cyclins, and replication fork stabilization (10, 12, 13, 14, reviewed in 15). Rad53p is also involved in regulating excess levels of histones (16).

Some of the identified targets of Rad53p are the transcriptional regulator Swi6p and the kinases Dun1p and Dbf4p. Activation of these particular targets by Rad53p leads to G1 cyclin induction, ribonucleotide reductase activation, and inhibition of late firing of DNA replication origins, respectively (13, 17, 18, 19).

Rad53p activation occurs both through autophosphorylation and direct phosphorylation by Mec1p (20, 21). Rad53p autophosphorylation is dependent on the presence of Mec1p, and Mec1p-mediated direct phosphorylation appears to depend on the presence of Rad9p (21, 22). Rad9p binds to two Rad53p forkhead-associated (FHA) domains, modular domains that facilitate protein-protein interactions, making Rad53p a suitable substrate for Mec1p (22, 23). The Rad53p N-terminal FHA domain is the interaction site for the type 2C phosphatases Ptc2p and Ptc3p, implicated inhibitors of Rad53p function (24). RAD53 expression has also been shown to depend on the presence of Rad9p (25).

Loss of Rad53p leads to multiple defects, including impaired checkpoint activation, inability to recover from replication blocks, X-ray sensitivity, and excess histone accumulation resulting in slow growth and chromosome loss (10, 14, 26, 16). RAD53 is the homolog of S. pombe CDS1 and human CHK2 (OMIM; 27, 28). Mutations in the human tumor suppressor CHK2 have been associated with sporadic cancer as well as familial breast cancer and Li-Fraumeni syndrome (OMIM; 29, 30).

Last updated: 2006-03-24 Contact SGD

References cited on this page View Complete Literature Guide for RAD53
1) Sitney, K.  (1989) Personal Communication, Mortimer Map Edition 10
2) Weinert TA, et al.  (1994) Mitotic checkpoint genes in budding yeast and the dependence of mitosis on DNA replication and repair. Genes Dev 8(6):652-65
3) Schwartz MF, et al.  (2002) Rad9 phosphorylation sites couple Rad53 to the Saccharomyces cerevisiae DNA damage checkpoint. Mol Cell 9(5):1055-65
4) Toh GW and Lowndes NF  (2003) Role of the Saccharomyces cerevisiae Rad9 protein in sensing and responding to DNA damage. Biochem Soc Trans 31(Pt 1):242-6
5) Dohrmann PR and Sclafani RA  (2006) Novel role for checkpoint Rad53 protein kinase in the initiation of chromosomal DNA replication in Saccharomyces cerevisiae. Genetics 174(1):87-99
6) Ghosh Dastidar R, et al.  (2012) The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation. Cell Biosci 2(1):30
7) Hoch NC, et al.  (2013) Molecular basis of the essential s phase function of the rad53 checkpoint kinase. Mol Cell Biol 33(16):3202-13
8) Dong K, et al.  (2013) The yeast copper response is regulated by DNA damage. Mol Cell Biol 33(20):4041-50
9) Schroeder EA and Shadel GS  (2014) Crosstalk between mitochondrial stress signals regulates yeast chronological lifespan. Mech Ageing Dev 135():41-9
10) Allen JB, et al.  (1994) The SAD1/RAD53 protein kinase controls multiple checkpoints and DNA damage-induced transcription in yeast. Genes Dev 8(20):2401-15
11) Weinert T  (1998) DNA damage checkpoints update: getting molecular. Curr Opin Genet Dev 8(2):185-93
12) Kim EM, et al.  (2002) Phosphorylation of Rph1, a damage-responsive repressor of PHR1 in Saccharomyces cerevisiae, is dependent upon Rad53 kinase. Nucleic Acids Res 30(3):643-8
13) Sidorova JM and Breeden LL  (1997) Rad53-dependent phosphorylation of Swi6 and down-regulation of CLN1 and CLN2 transcription occur in response to DNA damage in Saccharomyces cerevisiae. Genes Dev 11(22):3032-45
14) Lopes M, et al.  (2001) The DNA replication checkpoint response stabilizes stalled replication forks. Nature 412(6846):557-61
15) Elledge SJ  (1996) Cell cycle checkpoints: preventing an identity crisis. Science 274(5293):1664-72
16) Gunjan A and Verreault A  (2003) A Rad53 kinase-dependent surveillance mechanism that regulates histone protein levels in S. cerevisiae. Cell 115(5):537-49
17) Lee SJ, et al.  (2003) Rad53 phosphorylation site clusters are important for Rad53 regulation and signaling. Mol Cell Biol 23(17):6300-14
18) Duncker BP, et al.  (2002) An N-terminal domain of Dbf4p mediates interaction with both origin recognition complex (ORC) and Rad53p and can deregulate late origin firing. Proc Natl Acad Sci U S A 99(25):16087-92
19) Huang M, et al.  (1998) The DNA replication and damage checkpoint pathways induce transcription by inhibition of the Crt1 repressor. Cell 94(5):595-605
20) Ma JL, et al.  (2006) Activation of the checkpoint kinase Rad53 by the phosphatidyl inositol kinase-like kinase Mec1. J Biol Chem 281(7):3954-63
21) Pellicioli A, et al.  (1999) Activation of Rad53 kinase in response to DNA damage and its effect in modulating phosphorylation of the lagging strand DNA polymerase. EMBO J 18(22):6561-72
22) Sweeney FD, et al.  (2005) Saccharomyces cerevisiae Rad9 acts as a Mec1 adaptor to allow Rad53 activation. Curr Biol 15(15):1364-75
23) Durocher D, et al.  (1999) The FHA domain is a modular phosphopeptide recognition motif. Mol Cell 4(3):387-94
24) Leroy C, et al.  (2003) PP2C phosphatases Ptc2 and Ptc3 are required for DNA checkpoint inactivation after a double-strand break. Mol Cell 11(3):827-35
25) Aboussekhra A, et al.  (1996) A novel role for the budding yeast RAD9 checkpoint gene in DNA damage-dependent transcription. EMBO J 15(15):3912-22
26) Game JC  (1975) Radiation-sensitive mutants of yeast. Basic Life Sci 5B:541-4
27) Murakami H and Okayama H  (1995) A kinase from fission yeast responsible for blocking mitosis in S phase. Nature 374(6525):817-9
28) Matsuoka S, et al.  (1998) Linkage of ATM to cell cycle regulation by the Chk2 protein kinase. Science 282(5395):1893-7
29) Bell DW, et al.  (1999) Heterozygous germ line hCHK2 mutations in Li-Fraumeni syndrome. Science 286(5449):2528-31
30) Shaag A, et al.  (2005) Functional and genomic approaches reveal an ancient CHEK2 allele associated with breast cancer in the Ashkenazi Jewish population. Hum Mol Genet 14(4):555-63