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Protein

DNA repair protein RAD4

Gene

RAD4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi250 – 26920Sequence AnalysisAdd
BLAST

GO - Molecular functioni

  1. damaged DNA binding Source: SGD

GO - Biological processi

  1. nucleotide-excision repair Source: SGD
  2. proteasome-mediated ubiquitin-dependent protein catabolic process Source: SGD
Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-30323-MONOMER.
ReactomeiREACT_233196. Formation of incision complex in GG-NER.
REACT_250453. Dual incision reaction in GG-NER.
REACT_252357. DNA Damage Recognition in GG-NER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA repair protein RAD4
Gene namesi
Name:RAD4
Ordered Locus Names:YER162C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome V

Organism-specific databases

SGDiS000000964. RAD4.

Subcellular locationi

Cytoplasm 1 Publication. Nucleus 1 Publication

GO - Cellular componenti

  1. cytosol Source: SGD
  2. nucleotide-excision repair factor 2 complex Source: SGD
  3. nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 754754DNA repair protein RAD4PRO_0000218298Add
BLAST

Proteomic databases

MaxQBiP14736.
PaxDbiP14736.
PeptideAtlasiP14736.

Expressioni

Gene expression databases

GenevestigatoriP14736.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
RAD23P326283EBI-14766,EBI-14668

Protein-protein interaction databases

BioGridi36915. 136 interactions.
DIPiDIP-1547N.
IntActiP14736. 5 interactions.
MINTiMINT-396392.
STRINGi4932.YER162C.

Structurei

Secondary structure

1
754
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni91 – 944Combined sources
Helixi124 – 1296Combined sources
Helixi134 – 16229Combined sources
Helixi165 – 1717Combined sources
Helixi172 – 1743Combined sources
Helixi177 – 1826Combined sources
Helixi193 – 21321Combined sources
Beta strandi221 – 2233Combined sources
Helixi230 – 2356Combined sources
Turni236 – 2394Combined sources
Helixi248 – 25710Combined sources
Helixi262 – 27514Combined sources
Beta strandi280 – 2867Combined sources
Helixi306 – 3094Combined sources
Beta strandi314 – 3218Combined sources
Turni322 – 3254Combined sources
Beta strandi326 – 33510Combined sources
Beta strandi337 – 3393Combined sources
Turni352 – 3554Combined sources
Beta strandi362 – 3665Combined sources
Beta strandi372 – 3743Combined sources
Helixi376 – 3794Combined sources
Helixi383 – 3875Combined sources
Helixi388 – 3903Combined sources
Helixi392 – 3943Combined sources
Helixi396 – 40914Combined sources
Helixi416 – 43116Combined sources
Beta strandi436 – 4383Combined sources
Helixi439 – 4413Combined sources
Beta strandi445 – 4495Combined sources
Helixi450 – 4523Combined sources
Beta strandi457 – 4593Combined sources
Beta strandi466 – 4705Combined sources
Beta strandi478 – 4836Combined sources
Helixi484 – 4863Combined sources
Beta strandi487 – 4893Combined sources
Helixi493 – 4975Combined sources
Turni498 – 5003Combined sources
Beta strandi501 – 5033Combined sources
Beta strandi510 – 5134Combined sources
Beta strandi529 – 5324Combined sources
Helixi534 – 5363Combined sources
Beta strandi537 – 5393Combined sources
Helixi564 – 5663Combined sources
Beta strandi571 – 5755Combined sources
Helixi579 – 5857Combined sources
Beta strandi591 – 5977Combined sources
Beta strandi601 – 6033Combined sources
Beta strandi607 – 6159Combined sources
Helixi616 – 6183Combined sources
Helixi619 – 6279Combined sources
Helixi629 – 6313Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2M14NMR-B76-115[»]
2QSFX-ray2.35A101-632[»]
2QSGX-ray3.10A101-632[»]
2QSHX-ray2.81A101-632[»]
ProteinModelPortaliP14736.
SMRiP14736. Positions 123-632.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP14736.

Family & Domainsi

Sequence similaritiesi

Belongs to the XPC family.Curated

Phylogenomic databases

eggNOGiCOG5535.
GeneTreeiENSGT00390000005194.
HOGENOMiHOG000074544.
InParanoidiP14736.
KOiK10838.
OMAiCEVWDKF.
OrthoDBiEOG7H79C5.

Family and domain databases

InterProiIPR004583. DNA_repair_Rad4.
IPR018325. Rad4/PNGase_transGLS-fold.
IPR018326. Rad4_beta-hairpin_dom1.
IPR018327. Rad4_beta-hairpin_dom2.
IPR018328. Rad4_beta-hairpin_dom3.
[Graphical view]
PANTHERiPTHR12135. PTHR12135. 1 hit.
PfamiPF10403. BHD_1. 1 hit.
PF10404. BHD_2. 1 hit.
PF10405. BHD_3. 1 hit.
PF03835. Rad4. 1 hit.
[Graphical view]
SMARTiSM01030. BHD_1. 1 hit.
SM01031. BHD_2. 1 hit.
SM01032. BHD_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P14736-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNEDLPKEYF ELIRKALNEK EAEKAPLSRR RRVRRKNQPL PDAKKKFKTG
60 70 80 90 100
LNELPRESVV TVNLDSSDDG VVTVPTDDSV EEIQSSEEDY DSEEFEDVTD
110 120 130 140 150
GNEVAGVEDI SVEIKPSSKR NSDARRTSRN VCSNEERKRR KYFHMLYLVC
160 170 180 190 200
LMVHGFIRNE WINSKRLSRK LSNLVPEKVF ELLHPQKDEE LPLRSTRKLL
210 220 230 240 250
DGLKKCMELW QKHWKITKKY DNVGLYMRTW KEIEMSANNK RKFKTLKRSD
260 270 280 290 300
FLRAVSKGHG DPDISVQGFV AMLRACNVNA RLIMSCQPPD FTNMKIDTSL
310 320 330 340 350
NGNNAYKDMV KYPIFWCEVW DKFSKKWITV DPVNLKTIEQ VRLHSKLAPK
360 370 380 390 400
GVACCERNML RYVIAYDRKY GCRDVTRRYA QWMNSKVRKR RITKDDFGEK
410 420 430 440 450
WFRKVITALH HRKRTKIDDY EDQYFFQRDE SEGIPDSVQD LKNHPYYVLE
460 470 480 490 500
QDIKQTQIVK PGCKECGYLK VHGKVGKVLK VYAKRDIADL KSARQWYMNG
510 520 530 540 550
RILKTGSRCK KVIKRTVGRP KGEAEEEDER LYSFEDTELY IPPLASASGE
560 570 580 590 600
ITKNTFGNIE VFAPTMIPGN CCLVENPVAI KAARFLGVEF APAVTSFKFE
610 620 630 640 650
RGSTVKPVLS GIVVAKWLRE AIETAIDGIE FIQEDDNRKE HLLGALESWN
660 670 680 690 700
TLLLKLRIRS KLNSTYGKIA EEEPNVTKEQ NIADNHDNTE TFMGGGFLPG
710 720 730 740 750
IANHEARPYS EPSEPEDSLD YVSVDKAEES ATDDDVGEDY SDFMKELEMS

EESD
Length:754
Mass (Da):87,174
Last modified:September 21, 2011 - v3
Checksum:i788D3B6F580D2BF8
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti223 – 2231V → E in AAB64689. (PubMed:9169868)Curated
Sequence conflicti225 – 2251L → I in AAA34944. (PubMed:3073107)Curated
Sequence conflicti225 – 2251L → I in AAA34945. (PubMed:2649477)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M26050 Genomic DNA. Translation: AAA34944.1.
M24928 Genomic DNA. Translation: AAA34945.1.
U18917 Genomic DNA. Translation: AAB64689.1.
BK006939 Genomic DNA. Translation: DAA07824.2.
PIRiS30814. DDBYD4.
RefSeqiNP_011089.4. NM_001179052.4.

Genome annotation databases

EnsemblFungiiYER162C; YER162C; YER162C.
GeneIDi856909.
KEGGisce:YER162C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M26050 Genomic DNA. Translation: AAA34944.1.
M24928 Genomic DNA. Translation: AAA34945.1.
U18917 Genomic DNA. Translation: AAB64689.1.
BK006939 Genomic DNA. Translation: DAA07824.2.
PIRiS30814. DDBYD4.
RefSeqiNP_011089.4. NM_001179052.4.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2M14NMR-B76-115[»]
2QSFX-ray2.35A101-632[»]
2QSGX-ray3.10A101-632[»]
2QSHX-ray2.81A101-632[»]
ProteinModelPortaliP14736.
SMRiP14736. Positions 123-632.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36915. 136 interactions.
DIPiDIP-1547N.
IntActiP14736. 5 interactions.
MINTiMINT-396392.
STRINGi4932.YER162C.

Proteomic databases

MaxQBiP14736.
PaxDbiP14736.
PeptideAtlasiP14736.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYER162C; YER162C; YER162C.
GeneIDi856909.
KEGGisce:YER162C.

Organism-specific databases

SGDiS000000964. RAD4.

Phylogenomic databases

eggNOGiCOG5535.
GeneTreeiENSGT00390000005194.
HOGENOMiHOG000074544.
InParanoidiP14736.
KOiK10838.
OMAiCEVWDKF.
OrthoDBiEOG7H79C5.

Enzyme and pathway databases

BioCyciYEAST:G3O-30323-MONOMER.
ReactomeiREACT_233196. Formation of incision complex in GG-NER.
REACT_250453. Dual incision reaction in GG-NER.
REACT_252357. DNA Damage Recognition in GG-NER.

Miscellaneous databases

EvolutionaryTraceiP14736.
NextBioi983347.
PROiP14736.

Gene expression databases

GenevestigatoriP14736.

Family and domain databases

InterProiIPR004583. DNA_repair_Rad4.
IPR018325. Rad4/PNGase_transGLS-fold.
IPR018326. Rad4_beta-hairpin_dom1.
IPR018327. Rad4_beta-hairpin_dom2.
IPR018328. Rad4_beta-hairpin_dom3.
[Graphical view]
PANTHERiPTHR12135. PTHR12135. 1 hit.
PfamiPF10403. BHD_1. 1 hit.
PF10404. BHD_2. 1 hit.
PF10405. BHD_3. 1 hit.
PF03835. Rad4. 1 hit.
[Graphical view]
SMARTiSM01030. BHD_1. 1 hit.
SM01031. BHD_2. 1 hit.
SM01032. BHD_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and nucleotide sequence analysis of the Saccharomyces cerevisiae RAD4 gene required for excision repair of UV-damaged DNA."
    Gietz R.D., Prakash S.
    Gene 74:535-541(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Nucleotide sequence of the wild-type RAD4 gene of Saccharomyces cerevisiae and characterization of mutant rad4 alleles."
    Couto L.B., Friedberg E.C.
    J. Bacteriol. 171:1862-1869(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 223.
    Strain: ATCC 204508 / S288c.
  5. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiRAD4_YEAST
AccessioniPrimary (citable) accession number: P14736
Secondary accession number(s): D3DM70
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: September 21, 2011
Last modified: February 4, 2015
This is version 134 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 876 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

External Data

Dasty 3

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 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.