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Protein

DNA damage-responsive transcriptional repressor RPH1

Gene

RPH1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Transcriptional repressor of photolyase PHR1. Recognizes and binds the sequence AG4 in the upstream repressing sequence of PHR1. Derepresses PHR1 transcription when phosphorylated.2 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri709 – 732C2H2-type 1PROSITE-ProRule annotationAdd BLAST24
Zinc fingeri738 – 763C2H2-type 2; atypicalPROSITE-ProRule annotationAdd BLAST26

GO - Molecular functioni

  • histone demethylase activity (H3-K36 specific) Source: SGD
  • histone demethylase activity (H3-K9 specific) Source: SGD
  • metal ion binding Source: UniProtKB-KW
  • sequence-specific DNA binding Source: SGD
  • transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding Source: SGD

GO - Biological processi

  • histone demethylation Source: SGD
  • negative regulation of autophagy Source: SGD
  • negative regulation of transcription from RNA polymerase II promoter Source: SGD
  • positive regulation of transcription elongation from RNA polymerase II promoter Source: SGD
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-30330-MONOMER.
BRENDAi1.14.11.27. 984.
ReactomeiR-SCE-3214842. HDMs demethylate histones.
R-SCE-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA damage-responsive transcriptional repressor RPH1
Gene namesi
Name:RPH1
Ordered Locus Names:YER169W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome V

Organism-specific databases

EuPathDBiFungiDB:YER169W.
SGDiS000000971. RPH1.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000468491 – 796DNA damage-responsive transcriptional repressor RPH1Add BLAST796

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei399PhosphothreonineCombined sources1
Modified residuei430PhosphoserineCombined sources1
Modified residuei459PhosphoserineCombined sources1
Modified residuei557PhosphoserineCombined sources1
Modified residuei561PhosphoserineCombined sources1
Modified residuei575PhosphoserineCombined sources1
Modified residuei584PhosphoserineCombined sources1
Modified residuei652PhosphoserineCombined sources1
Modified residuei689PhosphoserineCombined sources1

Post-translational modificationi

RAD53-dependent phosphorylated in response to DNA damage.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP39956.
PRIDEiP39956.

PTM databases

iPTMnetiP39956.

Interactioni

Protein-protein interaction databases

BioGridi36922. 38 interactors.
DIPiDIP-5418N.
IntActiP39956. 2 interactors.
MINTiMINT-518485.

Structurei

Secondary structure

1796
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi9 – 17Combined sources9
Helixi21 – 24Combined sources4
Helixi27 – 32Combined sources6
Helixi35 – 38Combined sources4
Beta strandi41 – 46Combined sources6
Helixi50 – 53Combined sources4
Helixi62 – 67Combined sources6
Beta strandi69 – 72Combined sources4
Beta strandi74 – 91Combined sources18
Beta strandi95 – 97Combined sources3
Helixi98 – 104Combined sources7
Turni105 – 107Combined sources3
Helixi142 – 148Combined sources7
Turni149 – 151Combined sources3
Helixi157 – 160Combined sources4
Helixi162 – 174Combined sources13
Turni175 – 178Combined sources4
Beta strandi182 – 188Combined sources7
Beta strandi201 – 203Combined sources3
Beta strandi222 – 226Combined sources5
Beta strandi231 – 235Combined sources5
Helixi238 – 240Combined sources3
Beta strandi242 – 251Combined sources10
Beta strandi253 – 257Combined sources5
Helixi260 – 262Combined sources3
Helixi263 – 272Combined sources10
Helixi275 – 278Combined sources4
Turni285 – 287Combined sources3
Beta strandi290 – 292Combined sources3
Helixi294 – 298Combined sources5
Turni299 – 301Combined sources3
Beta strandi305 – 309Combined sources5
Beta strandi314 – 317Combined sources4
Beta strandi323 – 338Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3OPTX-ray2.20A1-373[»]
3OPWX-ray2.50A1-373[»]
ProteinModelPortaliP39956.
SMRiP39956.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP39956.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini14 – 55JmjNPROSITE-ProRule annotationAdd BLAST42
Domaini193 – 355JmjCPROSITE-ProRule annotationAdd BLAST163

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi455 – 471Bipartite nuclear localization signalAdd BLAST17

Sequence similaritiesi

Contains 2 C2H2-type zinc fingers.PROSITE-ProRule annotation
Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 JmjN domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri709 – 732C2H2-type 1PROSITE-ProRule annotationAdd BLAST24
Zinc fingeri738 – 763C2H2-type 2; atypicalPROSITE-ProRule annotationAdd BLAST26

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00530000063342.
HOGENOMiHOG000112726.
InParanoidiP39956.
KOiK19799.
OMAiYWKTLNF.
OrthoDBiEOG092C2SZJ.

Family and domain databases

Gene3Di3.30.160.60. 2 hits.
InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00355. ZnF_C2H2. 2 hits.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 1 hit.
PS50157. ZINC_FINGER_C2H2_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P39956-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKLIAPSEI VGGVPVFKPT YEQFEDFYAY CKAINKYGMK SGVVKVIPPK
60 70 80 90 100
EWKDKLDLPY SAETLQKIKI KSPIQQHISG NKGLFMVQNV EKNKTYNIIQ
110 120 130 140 150
WKDLSKDYVP PEDPKARRNS RKGSVSKSTK LKLKNFESSF NIDDFEQFRT
160 170 180 190 200
EYTIDLSDFQ NTERLKFLEE YYWKTLNFTT PMYGADTPGS IFPEGLNVWN
210 220 230 240 250
VAKLPNILDH METKVPGVND SYLYAGLWKA SFSWHLEDQD LYSINYIHFG
260 270 280 290 300
APKQWYSIPQ EDRFKFYKFM QEQFPEEAKN CPEFLRHKMF LASPKLLQEN
310 320 330 340 350
GIRCNEIVHH EGEFMITYPY GYHAGFNYGY NLAESVNFAL EEWLPIGKKA
360 370 380 390 400
GKCHCISDSV EIDVKKLAKS WRDNNKESKG TPPLNQLPNP AMPLLHRPTL
410 420 430 440 450
KEMESSSLRS TSPDVGHFSN FKSKSSGVSS PLLSRMKDYS NIVEPTLEDP
460 470 480 490 500
TLKLKRISSF QEQPLNKLLK RETSQTAMLT DHEDNIVAMS LTSMANSAAS
510 520 530 540 550
SPRLPLSRLN SSNELSNAQP LLDMTNNTLA FPRPNGPSGL NPLLYISNKN
560 570 580 590 600
ISGISHSAPH SPVNPNISLI KRVKSPNIVT LNISRESSRS PIALNYEARQ
610 620 630 640 650
QHSQQHSFST PSTVSNLSTS VLGPLSDTND IKTPHPERPN HKTANRILKK
660 670 680 690 700
ESPVETSKSN LILSKVASTR QEDSFTSRND DLDKEQGSSP LNSKFAPEEI
710 720 730 740 750
VLSGKNKIYI CKECQRKFSS GHHLTRHKKS VHSGEKPHSC PKCGKRFKRR
760 770 780 790
DHVLQHLNKK IPCISNETTV DAPIMNPTVQ PQDGKAAINQ QSTPLN
Length:796
Mass (Da):90,211
Last modified:February 1, 1995 - v1
Checksum:i606C27836E1600F5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18922 Genomic DNA. Translation: AAB64696.1.
BK006939 Genomic DNA. Translation: DAA07831.1.
PIRiS50672.
RefSeqiNP_011096.1. NM_001179059.1.

Genome annotation databases

EnsemblFungiiYER169W; YER169W; YER169W.
GeneIDi856916.
KEGGisce:YER169W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18922 Genomic DNA. Translation: AAB64696.1.
BK006939 Genomic DNA. Translation: DAA07831.1.
PIRiS50672.
RefSeqiNP_011096.1. NM_001179059.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3OPTX-ray2.20A1-373[»]
3OPWX-ray2.50A1-373[»]
ProteinModelPortaliP39956.
SMRiP39956.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36922. 38 interactors.
DIPiDIP-5418N.
IntActiP39956. 2 interactors.
MINTiMINT-518485.

PTM databases

iPTMnetiP39956.

Proteomic databases

MaxQBiP39956.
PRIDEiP39956.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYER169W; YER169W; YER169W.
GeneIDi856916.
KEGGisce:YER169W.

Organism-specific databases

EuPathDBiFungiDB:YER169W.
SGDiS000000971. RPH1.

Phylogenomic databases

GeneTreeiENSGT00530000063342.
HOGENOMiHOG000112726.
InParanoidiP39956.
KOiK19799.
OMAiYWKTLNF.
OrthoDBiEOG092C2SZJ.

Enzyme and pathway databases

BioCyciYEAST:G3O-30330-MONOMER.
BRENDAi1.14.11.27. 984.
ReactomeiR-SCE-3214842. HDMs demethylate histones.
R-SCE-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.

Miscellaneous databases

EvolutionaryTraceiP39956.
PROiP39956.

Family and domain databases

Gene3Di3.30.160.60. 2 hits.
InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00355. ZnF_C2H2. 2 hits.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 1 hit.
PS50157. ZINC_FINGER_C2H2_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRPH1_YEAST
AccessioniPrimary (citable) accession number: P39956
Secondary accession number(s): D3DM77
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: November 30, 2016
This is version 151 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2229 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome V
    Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.