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Protein

DNA polymerase zeta catalytic subunit

Gene

REV3

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

Nonessential DNA polymerase. Required for DNA damage induced mutagenesis. Involved in DNA repair, mitochondrial DNA repair and translesion synthesis. Translesion synthesis in S.cerevisiae may use a specialized DNA polymerase that is not required for other DNA replicative processes. Has a role in the bypass of abasic (AP) sites. Highly inefficient in incorporating nucleotides opposite the AP site, but efficiently extends from nucleotides, particularly an A, inserted opposite the lesion.4 Publications

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).1 Publication

Cofactori

[4Fe-4S] cluster1 PublicationNote: Binds 1 [4Fe-4S] cluster.1 Publication

Kineticsi

  1. KM=543 µM for dGTP (insertion opposite abasic site)1 Publication
  2. KM=81 µM for dATP (insertion opposite abasic site)1 Publication
  3. KM=125 µM for dTTP (insertion opposite abasic site)1 Publication
  4. KM=113 µM for dCTP (insertion opposite abasic site)1 Publication
  5. KM=0.11 µM for dGTP (insertion opposite C)1 Publication
  6. KM=267 µM for dATP (insertion opposite C)1 Publication
  7. KM=552 µM for dTTP (insertion opposite C)1 Publication
  8. KM=321 µM for dCTP (insertion opposite C)1 Publication
  9. KM=344 µM for dGTP (insertion opposite G)1 Publication
  10. KM=118 µM for dATP (insertion opposite G)1 Publication
  11. KM=428 µM for dTTP (insertion opposite G)1 Publication
  12. KM=0.14 µM for dCTP (insertion opposite G)1 Publication
  13. KM=6.5 µM for dTTP (extension from G, A, T, or C opposite abasic site)1 Publication
  14. KM=2.3 µM for dTTP (extension from G, A, T, or C opposite abasic site)1 Publication
  15. KM=49 µM for dTTP (extension from G, A, T, or C opposite abasic site)1 Publication
  16. KM=21 µM for dTTP (extension from G, A, T, or C opposite abasic site)1 Publication
  17. KM=0.35 µM for dTTP (extension from G, A, T, or C opposite C)1 Publication
  18. KM=2.3 µM for dTTP (extension from G, A, T, or C opposite C)1 Publication
  19. KM=15 µM for dTTP (extension from G, A, T, or C opposite C)1 Publication
  20. KM=26 µM for dTTP (extension from G, A, T, or C opposite C)1 Publication
  21. KM=6.9 µM for dTTP (extension from G, A, T, or C opposite G)1 Publication
  22. KM=2.1 µM for dTTP (extension from G, A, T, or C opposite G)1 Publication
  23. KM=28.8 µM for dTTP (extension from G, A, T, or C opposite G)1 Publication
  24. KM=0.23 µM for dTTP (extension from G, A, T, or C opposite G)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi1398 – 13981ZincBy similarity
    Metal bindingi1401 – 14011ZincBy similarity
    Metal bindingi1414 – 14141ZincBy similarity
    Metal bindingi1417 – 14171ZincBy similarity
    Metal bindingi1446 – 14461Iron-sulfur (4Fe-4S)By similarity
    Metal bindingi1449 – 14491Iron-sulfur (4Fe-4S)By similarity
    Metal bindingi1468 – 14681Iron-sulfur (4Fe-4S)By similarity
    Metal bindingi1473 – 14731Iron-sulfur (4Fe-4S)By similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri1398 – 141720CysA-typeAdd
    BLAST

    GO - Molecular functioni

    GO - Biological processi

    • DNA replication Source: UniProtKB-KW
    • error-free translesion synthesis Source: SGD
    • error-prone translesion synthesis Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    DNA-directed DNA polymerase, Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    DNA damage, DNA repair, DNA replication

    Keywords - Ligandi

    4Fe-4S, DNA-binding, Iron, Iron-sulfur, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciYEAST:G3O-34063-MONOMER.
    ReactomeiR-SCE-5655862. Translesion synthesis by POLK.
    R-SCE-5656121. Translesion synthesis by POLI.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA polymerase zeta catalytic subunit (EC:2.7.7.7)
    Alternative name(s):
    Protein reversionless 3
    Gene namesi
    Name:REV3
    Synonyms:PSO1
    Ordered Locus Names:YPL167C
    ORF Names:P2535
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome XVI

    Organism-specific databases

    EuPathDBiFungiDB:YPL167C.
    SGDiS000006088. REV3.

    Subcellular locationi

    GO - Cellular componenti

    • mitochondrion Source: SGD
    • nucleus Source: UniProtKB-SubCell
    • zeta DNA polymerase complex Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Mitochondrion, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 15041504DNA polymerase zeta catalytic subunitPRO_0000046470Add
    BLAST

    Proteomic databases

    PRIDEiP14284.

    Interactioni

    Subunit structurei

    Forms DNA polymerase zeta with REV7.

    Protein-protein interaction databases

    BioGridi36016. 98 interactions.
    DIPiDIP-8024N.
    IntActiP14284. 1 interaction.
    MINTiMINT-2731570.

    Structurei

    3D structure databases

    ProteinModelPortaliP14284.
    SMRiP14284. Positions 739-1355.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi1446 – 147328CysB motifAdd
    BLAST

    Domaini

    The CysB motif binds 1 4Fe-4S cluster and is required for the formation of polymerase complexes.By similarity

    Sequence similaritiesi

    Belongs to the DNA polymerase type-B family.Curated
    Contains 1 CysA-type zinc finger.Curated

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri1398 – 141720CysA-typeAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    GeneTreeiENSGT00550000074640.
    HOGENOMiHOG000194392.
    InParanoidiP14284.
    KOiK02350.
    OMAiDRWGYTH.
    OrthoDBiEOG715QCC.

    Family and domain databases

    Gene3Di3.30.420.10. 1 hit.
    3.90.1600.10. 2 hits.
    InterProiIPR006172. DNA-dir_DNA_pol_B.
    IPR017964. DNA-dir_DNA_pol_B_CS.
    IPR006133. DNA-dir_DNA_pol_B_exonuc.
    IPR006134. DNA-dir_DNA_pol_B_multi_dom.
    IPR023211. DNA_pol_palm_dom.
    IPR030559. PolZ_Rev3.
    IPR012337. RNaseH-like_dom.
    IPR025687. Znf-C4pol.
    [Graphical view]
    PANTHERiPTHR10322:SF5. PTHR10322:SF5. 5 hits.
    PfamiPF00136. DNA_pol_B. 1 hit.
    PF03104. DNA_pol_B_exo1. 2 hits.
    PF14260. zf-C4pol. 1 hit.
    [Graphical view]
    PRINTSiPR00106. DNAPOLB.
    SMARTiSM00486. POLBc. 1 hit.
    [Graphical view]
    SUPFAMiSSF53098. SSF53098. 4 hits.
    PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P14284-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSRESNDTIQ SDTVRSSSKS DYFRIQLNNQ DYYMSKPTFL DPSHGESLPL
    60 70 80 90 100
    NQFSQVPNIR VFGALPTGHQ VLCHVHGILP YMFIKYDGQI TDTSTLRHQR
    110 120 130 140 150
    CAQVHKTLEV KIRASFKRKK DDKHDLAGDK LGNLNFVADV SVVKGIPFYG
    160 170 180 190 200
    YHVGWNLFYK ISLLNPSCLS RISELIRDGK IFGKKFEIYE SHIPYLLQWT
    210 220 230 240 250
    ADFNLFGCSW INVDRCYFRS PVLNSILDID KLTINDDLQL LLDRFCDFKC
    260 270 280 290 300
    NVLSRRDFPR VGNGLIEIDI LPQFIKNREK LQHRDIHHDF LEKLGDISDI
    310 320 330 340 350
    PVKPYVSSAR DMINELTMQR EELSLKEYKE PPETKRHVSG HQWQSSGEFE
    360 370 380 390 400
    AFYKKAQHKT STFDGQIPNF ENFIDKNQKF SAINTPYEAL PQLWPRLPQI
    410 420 430 440 450
    EINNNSMQDK KNDDQVNASF TEYEICGVDN ENEGVKGSNI KSRSYSWLPE
    460 470 480 490 500
    SIASPKDSTI LLDHQTKYHN TINFSMDCAM TQNMASKRKL RSSVSANKTS
    510 520 530 540 550
    LLSRKRKKVM AAGLRYGKRA FVYGEPPFGY QDILNKLEDE GFPKIDYKDP
    560 570 580 590 600
    FFSNPVDLEN KPYAYAGKRF EISSTHVSTR IPVQFGGETV SVYNKPTFDM
    610 620 630 640 650
    FSSWKYALKP PTYDAVQKWY NKVPSMGNKK TESQISMHTP HSKFLYKFAS
    660 670 680 690 700
    DVSGKQKRKK SSVHDSLTHL TLEIHANTRS DKIPDPAIDE VSMIIWCLEE
    710 720 730 740 750
    ETFPLDLDIA YEGIMIVHKA SEDSTFPTKI QHCINEIPVM FYESEFEMFE
    760 770 780 790 800
    ALTDLVLLLD PDILSGFEIH NFSWGYIIER CQKIHQFDIV RELARVKCQI
    810 820 830 840 850
    KTKLSDTWGY AHSSGIMITG RHMINIWRAL RSDVNLTQYT IESAAFNILH
    860 870 880 890 900
    KRLPHFSFES LTNMWNAKKS TTELKTVLNY WLSRAQINIQ LLRKQDYIAR
    910 920 930 940 950
    NIEQARLIGI DFHSVYYRGS QFKVESFLIR ICKSESFILL SPGKKDVRKQ
    960 970 980 990 1000
    KALECVPLVM EPESAFYKSP LIVLDFQSLY PSIMIGYNYC YSTMIGRVRE
    1010 1020 1030 1040 1050
    INLTENNLGV SKFSLPRNIL ALLKNDVTIA PNGVVYAKTS VRKSTLSKML
    1060 1070 1080 1090 1100
    TDILDVRVMI KKTMNEIGDD NTTLKRLLNN KQLALKLLAN VTYGYTSASF
    1110 1120 1130 1140 1150
    SGRMPCSDLA DSIVQTGRET LEKAIDIIEK DETWNAKVVY GDTDSLFVYL
    1160 1170 1180 1190 1200
    PGKTAIEAFS IGHAMAERVT QNNPKPIFLK FEKVYHPSIL ISKKRYVGFS
    1210 1220 1230 1240 1250
    YESPSQTLPI FDAKGIETVR RDGIPAQQKI IEKCIRLLFQ TKDLSKIKKY
    1260 1270 1280 1290 1300
    LQNEFFKIQI GKVSAQDFCF AKEVKLGAYK SEKTAPAGAV VVKRRINEDH
    1310 1320 1330 1340 1350
    RAEPQYKERI PYLVVKGKQG QLLRERCVSP EEFLEGENLE LDSEYYINKI
    1360 1370 1380 1390 1400
    LIPPLDRLFN LIGINVGNWA QEIVKSKRAS TTTTKVENIT RVGTSATCCN
    1410 1420 1430 1440 1450
    CGEELTKICS LQLCDDCLEK RSTTTLSFLI KKLKRQKEYQ TLKTVCRTCS
    1460 1470 1480 1490 1500
    YRYTSDAGIE NDHIASKCNS YDCPVFYSRV KAERYLRDNQ SVQREEALIS

    LNDW
    Length:1,504
    Mass (Da):172,957
    Last modified:January 1, 1990 - v1
    Checksum:i54C2C6B664F734F5
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M29683 Genomic DNA. Translation: AAA34968.1.
    X96770 Genomic DNA. Translation: CAA65554.1.
    Z73523 Genomic DNA. Translation: CAA97873.1.
    BK006949 Genomic DNA. Translation: DAA11267.1.
    PIRiA33602.
    RefSeqiNP_015158.1. NM_001183981.1.

    Genome annotation databases

    EnsemblFungiiYPL167C; YPL167C; YPL167C.
    GeneIDi855936.
    KEGGisce:YPL167C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M29683 Genomic DNA. Translation: AAA34968.1.
    X96770 Genomic DNA. Translation: CAA65554.1.
    Z73523 Genomic DNA. Translation: CAA97873.1.
    BK006949 Genomic DNA. Translation: DAA11267.1.
    PIRiA33602.
    RefSeqiNP_015158.1. NM_001183981.1.

    3D structure databases

    ProteinModelPortaliP14284.
    SMRiP14284. Positions 739-1355.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi36016. 98 interactions.
    DIPiDIP-8024N.
    IntActiP14284. 1 interaction.
    MINTiMINT-2731570.

    Proteomic databases

    PRIDEiP14284.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYPL167C; YPL167C; YPL167C.
    GeneIDi855936.
    KEGGisce:YPL167C.

    Organism-specific databases

    EuPathDBiFungiDB:YPL167C.
    SGDiS000006088. REV3.

    Phylogenomic databases

    GeneTreeiENSGT00550000074640.
    HOGENOMiHOG000194392.
    InParanoidiP14284.
    KOiK02350.
    OMAiDRWGYTH.
    OrthoDBiEOG715QCC.

    Enzyme and pathway databases

    BioCyciYEAST:G3O-34063-MONOMER.
    ReactomeiR-SCE-5655862. Translesion synthesis by POLK.
    R-SCE-5656121. Translesion synthesis by POLI.

    Miscellaneous databases

    NextBioi980687.
    PROiP14284.

    Family and domain databases

    Gene3Di3.30.420.10. 1 hit.
    3.90.1600.10. 2 hits.
    InterProiIPR006172. DNA-dir_DNA_pol_B.
    IPR017964. DNA-dir_DNA_pol_B_CS.
    IPR006133. DNA-dir_DNA_pol_B_exonuc.
    IPR006134. DNA-dir_DNA_pol_B_multi_dom.
    IPR023211. DNA_pol_palm_dom.
    IPR030559. PolZ_Rev3.
    IPR012337. RNaseH-like_dom.
    IPR025687. Znf-C4pol.
    [Graphical view]
    PANTHERiPTHR10322:SF5. PTHR10322:SF5. 5 hits.
    PfamiPF00136. DNA_pol_B. 1 hit.
    PF03104. DNA_pol_B_exo1. 2 hits.
    PF14260. zf-C4pol. 1 hit.
    [Graphical view]
    PRINTSiPR00106. DNAPOLB.
    SMARTiSM00486. POLBc. 1 hit.
    [Graphical view]
    SUPFAMiSSF53098. SSF53098. 4 hits.
    PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "REV3, a Saccharomyces cerevisiae gene whose function is required for induced mutagenesis, is predicted to encode a nonessential DNA polymerase."
      Morrison A., Christensen R.B., Alley J., Beck A.K., Bernstine E.G., Lemontt J.F., Lawrence C.W.
      J. Bacteriol. 171:5659-5667(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
    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.
      , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
      Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    5. "Thymine-thymine dimer bypass by yeast DNA polymerase zeta."
      Nelson J.R., Lawrence C.W., Hinkle D.C.
      Science 272:1646-1649(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH REV7.
    6. "Roles of yeast DNA polymerases delta and zeta and of Rev1 in the bypass of abasic sites."
      Haracska L., Unk I., Johnson R.E., Johansson E., Burgers P.M.J., Prakash S., Prakash L.
      Genes Dev. 15:945-954(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
    7. "Saccharomyces cerevisiae polymerase zeta functions in mitochondria."
      Zhang H., Chatterjee A., Singh K.K.
      Genetics 172:2683-2688(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION.
    8. "Eukaryotic DNA polymerases require an iron-sulfur cluster for the formation of active complexes."
      Netz D.J., Stith C.M., Stumpfig M., Kopf G., Vogel D., Genau H.M., Stodola J.L., Lill R., Burgers P.M., Pierik A.J.
      Nat. Chem. Biol. 8:125-132(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: COFACTOR, IRON-SULFUR-BINDING.

    Entry informationi

    Entry nameiDPOZ_YEAST
    AccessioniPrimary (citable) accession number: P14284
    Secondary accession number(s): D6W3K1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1990
    Last sequence update: January 1, 1990
    Last modified: May 11, 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

    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 XVI
      Yeast (Saccharomyces cerevisiae) chromosome XVI: 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.