Serine/threonine-protein kinase RAD53 - RAD53 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P22216 (RAD53_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 163. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Serine/threonine-protein kinase RAD53
EC=2.7.12.1

Alternative name(s):
CHEK2 homolog
Serine-protein kinase 1

Gene names

Name:	RAD53
Synonyms:	MEC2, SAD1, SPK1
Ordered Locus Names:	YPL153C
ORF Names:	P2588

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	821 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Controls S-phase checkpoint as well as G1 and G2 DNA damage checkpoints. Phosphorylates proteins on serine, threonine, and tyrosine. Prevents entry into anaphase and mitotic exit after DNA damage via regulation of the Polo kinase CDC5. Seems to be involved in the phosphorylation of RPH1. Ref.6 Ref.7 Ref.9 Ref.10 Ref.12
Catalytic activity	ATP + a protein = ADP + a phosphoprotein.
Subunit structure	Interacts with PIN4. Ref.12
Subcellular location	Nucleus Ref.6.
Domain	FHA domains are phosphothreonine recognition modules, FHA 1 strongly selects for Asp at position +3 relative to phosphothreonine, whereas FHA 2 selects for Ile in this position.
Post-translational modification	Autophosphorylated. Ref.8
Miscellaneous	Present with 6900 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the protein kinase superfamily. CAMK Ser/Thr protein kinase family. CHEK2 subfamily. Contains 2 FHA domains. Contains 1 protein kinase domain.

Ontologies

Keywords
Biological process	Cell cycle DNA damage
Cellular component	Nucleus
Domain	Repeat
Ligand	ATP-binding Nucleotide-binding
Molecular function	Kinase Serine/threonine-protein kinase Transferase Tyrosine-protein kinase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA damage checkpoint Inferred from genetic interaction PubMed 7926756. Source: SGD DNA repair Inferred from mutant phenotype Ref.6. Source: SGD DNA replication initiation Inferred from mutant phenotype PubMed 16816422. Source: SGD deoxyribonucleoside triphosphate biosynthetic process Inferred from mutant phenotype PubMed 17188244. Source: SGD negative regulation of phosphorylation Inferred from mutant phenotype PubMed 24130507. Source: SGD nucleobase-containing compound metabolic process Inferred from genetic interaction PubMed 9744871. Source: SGD protein localization Inferred from mutant phenotype PubMed 18045534. Source: SGD
Cellular_component	cytosol Inferred from direct assay PubMed 22932476. Source: SGD nucleus Inferred from direct assay PubMed 22932476 Ref.6. Source: SGD
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA replication origin binding Inferred from direct assay PubMed 16816422. Source: SGD protein binding Inferred from physical interaction PubMed 10688190 PubMed 11805826 Ref.12 PubMed 15755447 PubMed 16429126 PubMed 21179020 PubMed 22820947 PubMed 9657725. Source: IntAct protein serine/threonine kinase activity Inferred from electronic annotation. Source: UniProtKB-KW protein serine/threonine/tyrosine kinase activity Inferred from direct assay Ref.6. Source: SGD protein tyrosine kinase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct
ASF1	P32447	8	EBI-17843,EBI-3003
PIN4	P34217	3	EBI-17843,EBI-21256
RAD9	P14737	3	EBI-17843,EBI-14788
SGS1	P35187	3	EBI-17843,EBI-17059

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 821

821

Serine/threonine-protein kinase RAD53

PRO_0000086595

Regions

Domain

66 – 116

FHA 1

Domain

198 – 466

269

Protein kinase

Domain

601 – 664

FHA 2

Nucleotide binding

204 – 212

ATP By similarity

Sites

Active site

319

Proton acceptor

Binding site

227

ATP By similarity

Amino acid modifications

Modified residue

Phosphoserine Ref.14

Modified residue

175

Phosphoserine Ref.14

Modified residue

547

Phosphoserine Ref.14

Modified residue

560

Phosphoserine Ref.14

Modified residue

774

Phosphoserine Ref.14 Ref.15

Modified residue

793

Phosphoserine Ref.14

Experimental info

Sequence conflict

204

V → A in AAT93028. Ref.5

Secondary structure

821

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P22216 [UniParc].

Last modified August 1, 1991. Version 1.
Checksum: 84A9612229CA72D1
Show »

FASTA

821

91,962

        10         20         30         40         50         60 
MENITQPTQQ STQATQRFLI EKFSQEQIGE NIVCRVICTT GQIPIRDLSA DISQVLKEKR 

        70         80         90        100        110        120 
SIKKVWTFGR NPACDYHLGN ISRLSNKHFQ ILLGEDGNLL LNDISTNGTW LNGQKVEKNS 

       130        140        150        160        170        180 
NQLLSQGDEI TVGVGVESDI LSLVIFINDK FKQCLEQNKV DRIRSNLKNT SKIASPGLTS 

       190        200        210        220        230        240 
STASSMVANK TGIFKDFSII DEVVGQGAFA TVKKAIERTT GKTFAVKIIS KRKVIGNMDG 

       250        260        270        280        290        300 
VTRELEVLQK LNHPRIVRLK GFYEDTESYY MVMEFVSGGD LMDFVAAHGA VGEDAGREIS 

       310        320        330        340        350        360 
RQILTAIKYI HSMGISHRDL KPDNILIEQD DPVLVKITDF GLAKVQGNGS FMKTFCGTLA 

       370        380        390        400        410        420 
YVAPEVIRGK DTSVSPDEYE ERNEYSSLVD MWSMGCLVYV ILTGHLPFSG STQDQLYKQI 

       430        440        450        460        470        480 
GRGSYHEGPL KDFRISEEAR DFIDSLLQVD PNNRSTAAKA LNHPWIKMSP LGSQSYGDFS 

       490        500        510        520        530        540 
QISLSQSLSQ QKLLENMDDA QYEFVKAQRK LQMEQQLQEQ DQEDQDGKIQ GFKIPAHAPI 

       550        560        570        580        590        600 
RYTQPKSIEA ETREQKLLHS NNTENVKSSK KKGNGRFLTL KPLPDSIIQE SLEIQQGVNP 

       610        620        630        640        650        660 
FFIGRSEDCN CKIEDNRLSR VHCFIFKKRH AVGKSMYESP AQGLDDIWYC HTGTNVSYLN 

       670        680        690        700        710        720 
NNRMIQGTKF LLQDGDEIKI IWDKNNKFVI GFKVEINDTT GLFNEGLGML QEQRVVLKQT 

       730        740        750        760        770        780 
AEEKDLVKKL TQMMAAQRAN QPSASSSSMS AKKPPVSDTN NNGNNSVLND LVESPINANT 

       790        800        810        820 
GNILKRIHSV SLSQSQIDPS KKVKRAKLDQ TSKGPENLQF S

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Spk1, a new kinase from Saccharomyces cerevisiae, phosphorylates proteins on serine, threonine, and tyrosine." Stern D.F., Zheng P., Beidler D.R., Zerillo C. Mol. Cell. Biol. 11:987-1001(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The sequence of 55 kb on the left arm of yeast chromosome XVI identifies a small nuclear RNA, a new putative protein kinase and two new putative regulators." Purnelle B., Coster F., Goffeau A. Yeast 12:1483-1492(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI." Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M. Hani J. Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	"The reference genome sequence of Saccharomyces cerevisiae: Then and now." Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M. G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract] Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[6]	"SPK1 is an essential S-phase-specific gene of Saccharomyces cerevisiae that encodes a nuclear serine/threonine/tyrosine kinase." Zheng P., Fay D.S., Burton J., Xiao H., Pinkham J.L., Stern D.F. Mol. Cell. Biol. 13:5829-5842(1993) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[7]	"The SAD1/RAD53 protein kinase controls multiple checkpoints and DNA damage-induced transcription in yeast." Allen J.B., Zhou Z., Siede W., Friedberg E.C., Elledge S.J. Genes Dev. 8:2401-2415(1994) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[8]	"Activation of Rad53 kinase in response to DNA damage and its effect in modulating phosphorylation of the lagging strand DNA polymerase." Pellicioli A., Lucca C., Liberi G., Marini F., Lopes M., Plevani P., Romano A., Di Fiore P.P., Foiani M. EMBO J. 18:6561-6572(1999) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION.
[9]	"Control of the DNA damage checkpoint by chk1 and rad53 protein kinases through distinct mechanisms." Sanchez Y., Bachant J., Wang H., Hu F., Liu D., Tetzlaff M., Elledge S.J. Science 286:1166-1171(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[10]	"Phosphorylation of Rph1, a damage-responsive repressor of PHR1 in Saccharomyces cerevisiae, is dependent upon Rad53 kinase." Kim E.M., Jang Y.K., Park S.D. Nucleic Acids Res. 30:643-648(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN PHOSPHORYLATION OF RPH1.
[11]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[12]	"Mdt1, a novel Rad53 FHA1 domain-interacting protein, modulates DNA damage tolerance and G(2)/M cell cycle progression in Saccharomyces cerevisiae." Pike B.L., Yongkiettrakul S., Tsai M.-D., Heierhorst J. Mol. Cell. Biol. 24:2779-2788(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH PIN4.
[13]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-24; SER-175; SER-547; SER-560; SER-774 AND SER-793, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]	"Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution." Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O. Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-774, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[16]	"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB." Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R. Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[17]	"Structure and function of a new phosphopeptide-binding domain containing the FHA2 of Rad53." Liao H., Byeon I.-J.L., Tsai M.-D. J. Mol. Biol. 294:1041-1049(1999) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 573-730.
[18]	"Structure of the FHA1 domain of yeast Rad53 and identification of binding sites for both FHA1 and its target protein Rad9." Liao H., Yuan C., Su M.I., Yongkiettrakul S., Qin D., Li H., Byeon I.J., Pei D., Tsai M.D. J. Mol. Biol. 304:941-951(2000) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 2-164.
[19]	"The molecular basis of FHA domain:phosphopeptide binding specificity and implications for phospho-dependent signaling mechanisms." Durocher D., Taylor I.A., Sarbassova D., Haire L.F., Westcott S.L., Jackson S.P., Smerdon S.J., Yaffe M.B. Mol. Cell 6:1169-1182(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 29-155.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M55623 Genomic DNA. Translation: AAA35070.1.
X96770 Genomic DNA. Translation: CAA65568.1.
Z73509 Genomic DNA. Translation: CAA97858.1.
AY693009 Genomic DNA. Translation: AAT93028.1.
BK006949 Genomic DNA. Translation: DAA11281.1.

PIR

A39616.

RefSeq

NP_015172.1. NM_001183967.1.

3D structure databases

PDBe
RCSB-PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DMZ	NMR	-	A	573-730	[»]
1FHQ	NMR	-	A	573-730	[»]
1FHR	NMR	-	A	573-730	[»]
1G3G	NMR	-	A	1-164	[»]
1G6G	X-ray	1.60	A/B	29-155	[»]
1J4K	NMR	-	A	573-730	[»]
1J4L	NMR	-	A	573-730	[»]
1J4O	NMR	-	A	14-164	[»]
1J4P	NMR	-	A	14-164	[»]
1J4Q	NMR	-	A	14-164	[»]
1K2M	NMR	-	A	573-730	[»]
1K2N	NMR	-	A	573-730	[»]
1K3J	NMR	-	A	14-164	[»]
1K3N	NMR	-	A	14-164	[»]
1K3Q	NMR	-	A	14-164	[»]
1QU5	NMR	-	A	549-730	[»]
2A0T	NMR	-	A	14-164	[»]
2JQI	NMR	-	A	14-164	[»]
			B	3-12	[»]
2JQL	NMR	-	B	3-12	[»]
2YGV	X-ray	2.94	E/F/G/H	800-821	[»]

ProteinModelPortal

P22216.

SMR

P22216. Positions 2-490, 549-730.

ModBase

Search...

MobiDB

Search...

Protein-protein interaction databases

BioGrid

36030. 353 interactions.

DIP

DIP-2322N.

IntAct

P22216. 14 interactions.

MINT

MINT-364105.

STRING

4932.YPL153C.

Proteomic databases

MaxQB

P22216.

PaxDb

P22216.

PeptideAtlas

P22216.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YPL153C; YPL153C; YPL153C.

GeneID

855950.

KEGG

sce:YPL153C.

Organism-specific databases

CYGD

YPL153c.

SGD

S000006074. RAD53.

Phylogenomic databases

eggNOG

COG0515.

GeneTree

ENSGT00710000106821.

HOGENOM

HOG000074515.

K02831.

OMA

HLPFNGK.

OrthoDB

EOG7XWPXG.

Enzyme and pathway databases

BioCyc

YEAST:G3O-34050-MONOMER.

BRENDA

2.7.12.1. 984.

Gene expression databases

Genevestigator

P22216.

Family and domain databases

Gene3D

2.60.200.20. 2 hits.

InterPro

IPR000253. FHA_dom.
IPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
IPR002290. Ser/Thr_dual-sp_kinase_dom.
IPR008271. Ser/Thr_kinase_AS.
IPR016256. Ser/Thr_kinase_Rad53.
IPR008984. SMAD_FHA_domain.
[Graphical view]

Pfam

PF00498. FHA. 2 hits.
PF00069. Pkinase. 1 hit.
[Graphical view]

PIRSF

PIRSF000661. Ser/Thr_PK_RAD53. 1 hit.

SMART

SM00240. FHA. 2 hits.
SM00220. S_TKc. 1 hit.
[Graphical view]

SUPFAM

SSF49879. SSF49879. 2 hits.
SSF56112. SSF56112. 1 hit.

PROSITE

PS50006. FHA_DOMAIN. 2 hits.
PS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00108. PROTEIN_KINASE_ST. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P22216.

NextBio

980729.

PRO

P22216.

Entry information

Entry name

RAD53_YEAST

Accession

Primary (citable) accession number: P22216
Secondary accession number(s): D6W3L5, Q6B1S1

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1991
Last sequence update:	August 1, 1991
Last modified:	July 9, 2014
This is version 163 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast chromosome XVI

Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents