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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: 5 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)DescriptionActionsGraphical viewLength
DNA bindingi250 – 269Sequence analysisAdd BLAST20

GO - Molecular functioni

  • damaged DNA binding Source: SGD
  • single-strand break-containing DNA binding Source: SGD
  • single-stranded DNA binding Source: GO_Central

GO - Biological processi

  • DNA topological change Source: SGD
  • mismatch repair Source: GO_Central
  • negative regulation of transcription from RNA polymerase II promoter Source: SGD
  • nucleotide-excision repair Source: SGD
  • 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.
ReactomeiR-SCE-3108214. SUMOylation of DNA damage response and repair proteins.
R-SCE-5696394. DNA Damage Recognition in GG-NER.
R-SCE-5696395. Formation of Incision Complex 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
Proteomesi
  • UP000002311 Componenti: Chromosome V

Organism-specific databases

EuPathDBiFungiDB:YER162C.
SGDiS000000964. RAD4.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
  • nucleotide-excision repair factor 2 complex Source: SGD
  • nucleus Source: SGD
  • XPC complex Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002182981 – 754DNA repair protein RAD4Add BLAST754

Proteomic databases

MaxQBiP14736.
PRIDEiP14736.

Interactioni

Binary interactionsi

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

Protein-protein interaction databases

BioGridi36915. 136 interactors.
DIPiDIP-1547N.
IntActiP14736. 5 interactors.
MINTiMINT-396392.

Structurei

Secondary structure

1754
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni91 – 94Combined sources4
Helixi124 – 129Combined sources6
Helixi134 – 162Combined sources29
Helixi165 – 171Combined sources7
Helixi172 – 174Combined sources3
Helixi177 – 182Combined sources6
Helixi193 – 213Combined sources21
Beta strandi221 – 223Combined sources3
Helixi230 – 235Combined sources6
Turni236 – 239Combined sources4
Helixi248 – 257Combined sources10
Helixi262 – 275Combined sources14
Beta strandi280 – 286Combined sources7
Helixi306 – 309Combined sources4
Beta strandi314 – 321Combined sources8
Turni322 – 325Combined sources4
Beta strandi326 – 335Combined sources10
Beta strandi337 – 339Combined sources3
Turni352 – 355Combined sources4
Beta strandi362 – 366Combined sources5
Beta strandi372 – 374Combined sources3
Helixi376 – 379Combined sources4
Helixi383 – 387Combined sources5
Helixi388 – 390Combined sources3
Helixi392 – 394Combined sources3
Helixi396 – 409Combined sources14
Helixi416 – 431Combined sources16
Beta strandi436 – 438Combined sources3
Helixi439 – 441Combined sources3
Beta strandi445 – 449Combined sources5
Helixi450 – 452Combined sources3
Beta strandi457 – 459Combined sources3
Beta strandi466 – 470Combined sources5
Beta strandi478 – 483Combined sources6
Helixi484 – 486Combined sources3
Beta strandi487 – 489Combined sources3
Helixi493 – 497Combined sources5
Turni498 – 500Combined sources3
Beta strandi501 – 503Combined sources3
Beta strandi510 – 513Combined sources4
Beta strandi529 – 532Combined sources4
Helixi534 – 536Combined sources3
Beta strandi537 – 539Combined sources3
Helixi564 – 566Combined sources3
Beta strandi571 – 575Combined sources5
Helixi579 – 585Combined sources7
Beta strandi591 – 597Combined sources7
Beta strandi601 – 603Combined sources3
Beta strandi607 – 615Combined sources9
Helixi616 – 618Combined sources3
Helixi619 – 627Combined sources9
Helixi629 – 631Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2M14NMR-B76-115[»]
2QSFX-ray2.35A101-632[»]
2QSGX-ray3.10A101-632[»]
2QSHX-ray2.81A101-632[»]
4YIRX-ray3.05A101-632[»]
ProteinModelPortaliP14736.
SMRiP14736.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP14736.

Family & Domainsi

Sequence similaritiesi

Belongs to the XPC family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000005194.
HOGENOMiHOG000074544.
InParanoidiP14736.
KOiK10838.
OMAiCEVWDKF.
OrthoDBiEOG092C3500.

Family and domain databases

InterProiIPR018327. BHD_2.
IPR004583. DNA_repair_Rad4.
IPR018325. Rad4/PNGase_transGLS-fold.
IPR018326. Rad4_beta-hairpin_dom1.
IPR018328. Rad4_beta-hairpin_dom3.
[Graphical view]
PANTHERiPTHR12135. PTHR12135. 1 hit.
PfamiPF10403. BHD_1. 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)DescriptionActionsGraphical viewLength
Sequence conflicti223V → E in AAB64689 (PubMed:9169868).Curated1
Sequence conflicti225L → I in AAA34944 (PubMed:3073107).Curated1
Sequence conflicti225L → I in AAA34945 (PubMed:2649477).Curated1

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2M14NMR-B76-115[»]
2QSFX-ray2.35A101-632[»]
2QSGX-ray3.10A101-632[»]
2QSHX-ray2.81A101-632[»]
4YIRX-ray3.05A101-632[»]
ProteinModelPortaliP14736.
SMRiP14736.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36915. 136 interactors.
DIPiDIP-1547N.
IntActiP14736. 5 interactors.
MINTiMINT-396392.

Proteomic databases

MaxQBiP14736.
PRIDEiP14736.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YER162C.
SGDiS000000964. RAD4.

Phylogenomic databases

GeneTreeiENSGT00390000005194.
HOGENOMiHOG000074544.
InParanoidiP14736.
KOiK10838.
OMAiCEVWDKF.
OrthoDBiEOG092C3500.

Enzyme and pathway databases

BioCyciYEAST:G3O-30323-MONOMER.
ReactomeiR-SCE-3108214. SUMOylation of DNA damage response and repair proteins.
R-SCE-5696394. DNA Damage Recognition in GG-NER.
R-SCE-5696395. Formation of Incision Complex in GG-NER.

Miscellaneous databases

EvolutionaryTraceiP14736.
PROiP14736.

Family and domain databases

InterProiIPR018327. BHD_2.
IPR004583. DNA_repair_Rad4.
IPR018325. Rad4/PNGase_transGLS-fold.
IPR018326. Rad4_beta-hairpin_dom1.
IPR018328. Rad4_beta-hairpin_dom3.
[Graphical view]
PANTHERiPTHR12135. PTHR12135. 1 hit.
PfamiPF10403. BHD_1. 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...

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: November 2, 2016
This is version 151 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

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.