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Protein

DNA repair and recombination protein RDH54

Gene

RDH54

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 the recombinational repair of double-strand breaks (DSB) in DNA during mitosis and meiosis. Has DNA dependent ATPase activity. Promotes D-loop (displacement loop) formation with RAD51 recombinase. Modifies the topology of double-stranded DNA during the D-loop reaction to facilitate the invasion of the homologous duplex molecule by the initiating single-stranded DNA substrate. Required for adaptation from G2/M checkpoint arrest induced by a double strand break, by participating in monitoring the extent of single-stranded DNA produced by resection of DNA ends. This role is distinct from its roles in recombination. Promotes colocalization of RAD51 and DMC1 during meiotic recombination. Involved in crossover interference.6 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi380 – 3878ATPPROSITE-ProRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • DNA-dependent ATPase activity Source: SGD
  • DNA topoisomerase activity Source: UniProtKB-KW
  • DNA translocase activity Source: SGD
  • double-stranded DNA binding Source: SGD
  • helicase activity Source: UniProtKB-KW

GO - Biological processi

  • DNA duplex unwinding Source: SGD
  • DNA geometric change Source: SGD
  • DNA recombination Source: SGD
  • DNA repair Source: SGD
  • heteroduplex formation Source: SGD
  • meiotic sister chromatid segregation Source: SGD
  • reciprocal meiotic recombination Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Isomerase, Topoisomerase

Keywords - Biological processi

DNA damage, DNA recombination, DNA repair, Meiosis

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29042-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA repair and recombination protein RDH54
Alternative name(s):
RAD homolog 54
Recombination factor TID1
Two hybrid interaction with DMC1 protein 1
Including the following 2 domains:
DNA topoisomerase (EC:5.99.1.-)
Putative helicase (EC:3.6.4.12)
Gene namesi
Name:RDH54
Synonyms:TID1
Ordered Locus Names:YBR073W
ORF Names:YBR0715
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:YBR073W.
SGDiS000000277. RDH54.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi352 – 3521K → R: 1%-2% of the ATPase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 958958DNA repair and recombination protein RDH54PRO_0000074346Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki649 – 649Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiP38086.

PTM databases

iPTMnetiP38086.

Interactioni

Subunit structurei

Interacts with RAD51 and DMC1.2 Publications

Protein-protein interaction databases

BioGridi32776. 79 interactions.
DIPiDIP-792N.
IntActiP38086. 3 interactions.
MINTiMINT-566887.

Structurei

3D structure databases

ProteinModelPortaliP38086.
SMRiP38086. Positions 284-850.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini333 – 521189Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini665 – 824160Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi506 – 5094DEGH box

Sequence similaritiesi

Belongs to the SNF2/RAD54 helicase family.Curated
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00840000129944.
HOGENOMiHOG000204521.
InParanoidiP38086.
KOiK10877.
OMAiFTIMYRK.
OrthoDBiEOG092C10RV.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR018838. DUF2439.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000330. SNF2_N.
[Graphical view]
PfamiPF10382. DUF2439. 1 hit.
PF00271. Helicase_C. 1 hit.
PF00176. SNF2_N. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P38086-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVISVKPRR REKILQEVKN SSVYQTVFDS GTTQMQIPKY ENKPFKPPRR
60 70 80 90 100
VGSNKYTQLK PTATAVTTAP ISKAKVTVNL KRSISAGPTL NLAKKPNNLS
110 120 130 140 150
SNENTRYFTI MYRKPTTKKH KTWSGDGYAT LKASSDKLCF YNEAGKFLGS
160 170 180 190 200
SMLPSDSDSL FETLFKAGSN EVQLDYELKE NAEIRSAKEA LSQNMGNPSP
210 220 230 240 250
PTTSTTETVP STKNDGGKYQ MPLSQLFSLN TVKRFKSVTK QTNEHMTTVP
260 270 280 290 300
KTSQNSKAKK YYPVFDVNKI DNPIVMNKNA AAEVDVIVDP LLGKFLRPHQ
310 320 330 340 350
REGVKFMYDC LMGLARPTIE NPDIDCTTKS LVLENDSDIS GCLLADDMGL
360 370 380 390 400
GKTLMSITLI WTLIRQTPFA SKVSCSQSGI PLTGLCKKIL VVCPVTLIGN
410 420 430 440 450
WKREFGKWLN LSRIGVLTLS SRNSPDMDKM AVRNFLKVQR TYQVLIIGYE
460 470 480 490 500
KLLSVSEELE KNKHLIDMLV CDEGHRLKNG ASKILNTLKS LDIRRKLLLT
510 520 530 540 550
GTPIQNDLNE FFTIIDFINP GILGSFASFK RRFIIPITRA RDTANRYNEE
560 570 580 590 600
LLEKGEERSK EMIEITKRFI LRRTNAILEK YLPPKTDIIL FCKPYSQQIL
610 620 630 640 650
AFKDILQGAR LDFGQLTFSS SLGLITLLKK VCNSPGLVGS DPYYKSHIKD
660 670 680 690 700
TQSQDSYSRS LNSGKLKVLM TLLEGIRKGT KEKVVVVSNY TQTLDIIENL
710 720 730 740 750
MNMAGMSHCR LDGSIPAKQR DSIVTSFNRN PAIFGFLLSA KSGGVGLNLV
760 770 780 790 800
GASRLILFDN DWNPSVDLQA MSRIHRDGQK KPCFIYRLVT TGCIDEKILQ
810 820 830 840 850
RQLMKNSLSQ KFLGDSEMRN KESSNDDLFN KEDLKDLFSV HTDTKSNTHD
860 870 880 890 900
LICSCDGLGE EIEYPETNQQ QNTVELRKRS TTTWTSALDL QKKMNEAATN
910 920 930 940 950
DDAKKSQYIR QCLVHYKHID PARQDELFDE VITDSFTELK DSITFAFVKP

GEICLREQ
Length:958
Mass (Da):107,946
Last modified:July 27, 2011 - v4
Checksum:iB797375C08FA14FA
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti752 – 7521A → R in CAA53930 (PubMed:7985423).Curated
Sequence conflicti752 – 7521A → R in CAA85017 (PubMed:7813418).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X76294 Genomic DNA. Translation: CAA53930.1.
Z35942 Genomic DNA. Translation: CAA85017.1.
BK006936 Genomic DNA. Translation: DAA07193.2.
PIRiS45466.
RefSeqiNP_009629.6. NM_001178421.4.

Genome annotation databases

EnsemblFungiiYBR073W; YBR073W; YBR073W.
GeneIDi852365.
KEGGisce:YBR073W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X76294 Genomic DNA. Translation: CAA53930.1.
Z35942 Genomic DNA. Translation: CAA85017.1.
BK006936 Genomic DNA. Translation: DAA07193.2.
PIRiS45466.
RefSeqiNP_009629.6. NM_001178421.4.

3D structure databases

ProteinModelPortaliP38086.
SMRiP38086. Positions 284-850.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32776. 79 interactions.
DIPiDIP-792N.
IntActiP38086. 3 interactions.
MINTiMINT-566887.

PTM databases

iPTMnetiP38086.

Proteomic databases

MaxQBiP38086.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYBR073W; YBR073W; YBR073W.
GeneIDi852365.
KEGGisce:YBR073W.

Organism-specific databases

EuPathDBiFungiDB:YBR073W.
SGDiS000000277. RDH54.

Phylogenomic databases

GeneTreeiENSGT00840000129944.
HOGENOMiHOG000204521.
InParanoidiP38086.
KOiK10877.
OMAiFTIMYRK.
OrthoDBiEOG092C10RV.

Enzyme and pathway databases

BioCyciYEAST:G3O-29042-MONOMER.

Miscellaneous databases

PROiP38086.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR018838. DUF2439.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000330. SNF2_N.
[Graphical view]
PfamiPF10382. DUF2439. 1 hit.
PF00271. Helicase_C. 1 hit.
PF00176. SNF2_N. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRDH54_YEAST
AccessioniPrimary (citable) accession number: P38086
Secondary accession number(s): D6VQ73
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: July 27, 2011
Last modified: September 7, 2016
This is version 151 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 1270 molecules/cell in log phase SD medium.1 Publication

Caution

It is uncertain whether Met-1 or Met-35 is the initiator. In many S.cerevisiae strains, it is not possible to extend the sequence at the N-terminus beyond Met-35 because of a framshift in the upstream sequence when compared to strain S288c. However, experimental evidence indicates that the longer protein is made in S288c.Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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