DPOD3_CHICK
ID DPOD3_CHICK Reviewed; 461 AA.
AC Q5ZK28; F1P540;
DT 30-NOV-2016, integrated into UniProtKB/Swiss-Prot.
DT 30-NOV-2016, sequence version 2.
DT 03-AUG-2022, entry version 88.
DE RecName: Full=DNA polymerase delta subunit 3;
DE AltName: Full=DNA polymerase delta subunit p66;
GN Name=POLD3; ORFNames=RCJMB04_13j10;
OS Gallus gallus (Chicken).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae;
OC Phasianinae; Gallus.
OX NCBI_TaxID=9031;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=CB; TISSUE=Bursa of Fabricius;
RX PubMed=15642098; DOI=10.1186/gb-2004-6-1-r6;
RA Caldwell R.B., Kierzek A.M., Arakawa H., Bezzubov Y., Zaim J., Fiedler P.,
RA Kutter S., Blagodatski A., Kostovska D., Koter M., Plachy J., Carninci P.,
RA Hayashizaki Y., Buerstedde J.-M.;
RT "Full-length cDNAs from chicken bursal lymphocytes to facilitate gene
RT function analysis.";
RL Genome Biol. 6:R6.1-R6.9(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Red jungle fowl;
RX PubMed=15592404; DOI=10.1038/nature03154;
RA Hillier L.W., Miller W., Birney E., Warren W., Hardison R.C., Ponting C.P.,
RA Bork P., Burt D.W., Groenen M.A.M., Delany M.E., Dodgson J.B.,
RA Chinwalla A.T., Cliften P.F., Clifton S.W., Delehaunty K.D., Fronick C.,
RA Fulton R.S., Graves T.A., Kremitzki C., Layman D., Magrini V.,
RA McPherson J.D., Miner T.L., Minx P., Nash W.E., Nhan M.N., Nelson J.O.,
RA Oddy L.G., Pohl C.S., Randall-Maher J., Smith S.M., Wallis J.W.,
RA Yang S.-P., Romanov M.N., Rondelli C.M., Paton B., Smith J., Morrice D.,
RA Daniels L., Tempest H.G., Robertson L., Masabanda J.S., Griffin D.K.,
RA Vignal A., Fillon V., Jacobbson L., Kerje S., Andersson L.,
RA Crooijmans R.P., Aerts J., van der Poel J.J., Ellegren H., Caldwell R.B.,
RA Hubbard S.J., Grafham D.V., Kierzek A.M., McLaren S.R., Overton I.M.,
RA Arakawa H., Beattie K.J., Bezzubov Y., Boardman P.E., Bonfield J.K.,
RA Croning M.D.R., Davies R.M., Francis M.D., Humphray S.J., Scott C.E.,
RA Taylor R.G., Tickle C., Brown W.R.A., Rogers J., Buerstedde J.-M.,
RA Wilson S.A., Stubbs L., Ovcharenko I., Gordon L., Lucas S., Miller M.M.,
RA Inoko H., Shiina T., Kaufman J., Salomonsen J., Skjoedt K., Wong G.K.-S.,
RA Wang J., Liu B., Wang J., Yu J., Yang H., Nefedov M., Koriabine M.,
RA Dejong P.J., Goodstadt L., Webber C., Dickens N.J., Letunic I., Suyama M.,
RA Torrents D., von Mering C., Zdobnov E.M., Makova K., Nekrutenko A.,
RA Elnitski L., Eswara P., King D.C., Yang S.-P., Tyekucheva S.,
RA Radakrishnan A., Harris R.S., Chiaromonte F., Taylor J., He J.,
RA Rijnkels M., Griffiths-Jones S., Ureta-Vidal A., Hoffman M.M., Severin J.,
RA Searle S.M.J., Law A.S., Speed D., Waddington D., Cheng Z., Tuzun E.,
RA Eichler E., Bao Z., Flicek P., Shteynberg D.D., Brent M.R., Bye J.M.,
RA Huckle E.J., Chatterji S., Dewey C., Pachter L., Kouranov A.,
RA Mourelatos Z., Hatzigeorgiou A.G., Paterson A.H., Ivarie R., Brandstrom M.,
RA Axelsson E., Backstrom N., Berlin S., Webster M.T., Pourquie O.,
RA Reymond A., Ucla C., Antonarakis S.E., Long M., Emerson J.J., Betran E.,
RA Dupanloup I., Kaessmann H., Hinrichs A.S., Bejerano G., Furey T.S.,
RA Harte R.A., Raney B., Siepel A., Kent W.J., Haussler D., Eyras E.,
RA Castelo R., Abril J.F., Castellano S., Camara F., Parra G., Guigo R.,
RA Bourque G., Tesler G., Pevzner P.A., Smit A., Fulton L.A., Mardis E.R.,
RA Wilson R.K.;
RT "Sequence and comparative analysis of the chicken genome provide unique
RT perspectives on vertebrate evolution.";
RL Nature 432:695-716(2004).
RN [3]
RP FUNCTION IN TRANSLESION SYNTHESIS.
RX PubMed=25628356; DOI=10.1093/nar/gkv023;
RA Hirota K., Yoshikiyo K., Guilbaud G., Tsurimoto T., Murai J., Tsuda M.,
RA Phillips L.G., Narita T., Nishihara K., Kobayashi K., Yamada K.,
RA Nakamura J., Pommier Y., Lehmann A., Sale J.E., Takeda S.;
RT "The POLD3 subunit of DNA polymerase delta can promote translesion
RT synthesis independently of DNA polymerase zeta.";
RL Nucleic Acids Res. 43:1671-1683(2015).
RN [4]
RP FUNCTION IN TRANSLESION SYNTHESIS.
RX PubMed=27185888; DOI=10.1093/nar/gkw439;
RA Hirota K., Tsuda M., Mohiuddin M., Tsurimoto T., Cohen I.S., Livneh Z.,
RA Kobayashi K., Narita T., Nishihara K., Murai J., Iwai S., Guilbaud G.,
RA Sale J.E., Takeda S.;
RT "In vivo evidence for translesion synthesis by the replicative DNA
RT polymerase delta.";
RL Nucleic Acids Res. 44:7242-7250(2016).
CC -!- FUNCTION: Accessory component of both the DNA polymerase delta complex
CC and the DNA polymerase zeta complex. As a component of the trimeric and
CC tetrameric DNA polymerase delta complexes (Pol-delta3 and Pol-delta4,
CC respectively), plays a role in high fidelity genome replication,
CC including in lagging strand synthesis, and repair. Required for optimal
CC Pol-delta activity. Stabilizes the Pol-delta complex and plays a major
CC role in Pol-delta stimulation by PCNA. Pol-delta3 and Pol-delta4 are
CC characterized by the absence or the presence of POLD4. They exhibit
CC differences in catalytic activity. Most notably, Pol-delta3 shows
CC higher proofreading activity than Pol-delta4. Although both Pol-delta3
CC and Pol-delta4 process Okazaki fragments in vitro, Pol-delta3 may also
CC be better suited to fulfill this task, exhibiting near-absence of
CC strand displacement activity compared to Pol-delta4 and stalling on
CC encounter with the 5'-blocking oligonucleotides. Pol-delta3 idling
CC process may avoid the formation of a gap, while maintaining a nick that
CC can be readily ligated. Along with DNA polymerase kappa, DNA polymerase
CC delta carries out approximately half of nucleotide excision repair
CC (NER) synthesis following UV irradiation. In this context, POLD3, along
CC with PCNA and RFC1-replication factor C complex, is required to recruit
CC POLD1, the catalytic subunit of the polymerase delta complex, to DNA
CC damage sites. Under conditions of DNA replication stress, required for
CC the repair of broken replication forks through break-induced
CC replication (BIR). Involved in the translesion synthesis (TLS) of
CC templates carrying O6-methylguanine or abasic sites performed by Pol-
CC delta4, independently of DNA polymerase zeta (REV3L) or eta (POLH).
CC Facilitates abasic site bypass by DNA polymerase delta by promoting
CC extension from the nucleotide inserted opposite the lesion. Also
CC involved in TLS, as a component of the tetrametric DNA polymerase zeta
CC complex. Along with POLD2, dramatically increases the efficiency and
CC processivity of DNA synthesis of the DNA polymerase zeta complex
CC compared to the minimal zeta complex, consisting of only REV3L and
CC REV7. {ECO:0000250|UniProtKB:Q15054}.
CC -!- SUBUNIT: Component of both the DNA polymerase delta and DNA polymerase
CC zeta complexes. The tetrameric DNA polymerase delta complex (Pol-
CC delta4), which consists of POLD1/p125, POLD2/p50, POLD3/p66/p68 and
CC POLD4/p12, with POLD1 bearing DNA polymerase and 3' to 5' proofreading
CC exonuclease activities. {ECO:0000250|UniProtKB:Q15054}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q15054}. Nucleus
CC {ECO:0000250|UniProtKB:Q15054}. Note=Partially colocalizes with PCNA
CC and POLD1 at S phase replication sites. Recruited to DNA damage sites
CC within 2 hours following UV irradiation.
CC {ECO:0000250|UniProtKB:Q15054}.
CC -!- DOMAIN: The PIP-box mediates the interaction with PCNA.
CC {ECO:0000250|UniProtKB:Q15054}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAG31915.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AJ720256; CAG31915.1; ALT_FRAME; mRNA.
DR EMBL; AADN03001032; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; NP_001006284.2; NM_001006284.2.
DR AlphaFoldDB; Q5ZK28; -.
DR SMR; Q5ZK28; -.
DR STRING; 9031.ENSGALP00000027913; -.
DR PRIDE; Q5ZK28; -.
DR GeneID; 419053; -.
DR KEGG; gga:419053; -.
DR CTD; 10714; -.
DR VEuPathDB; HostDB:geneid_419053; -.
DR eggNOG; ENOG502QPSW; Eukaryota.
DR OrthoDB; 1550733at2759; -.
DR PhylomeDB; Q5ZK28; -.
DR TreeFam; TF103006; -.
DR Reactome; R-GGA-353416; Resolution of Abasic Sites (AP sites).
DR PRO; PR:Q5ZK28; -.
DR Proteomes; UP000000539; Unplaced.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0043625; C:delta DNA polymerase complex; IBA:GO_Central.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0006271; P:DNA strand elongation involved in DNA replication; IBA:GO_Central.
DR GO; GO:1904161; P:DNA synthesis involved in UV-damage excision repair; IBA:GO_Central.
DR GO; GO:0006297; P:nucleotide-excision repair, DNA gap filling; IBA:GO_Central.
DR Gene3D; 3.90.1030.20; -; 1.
DR InterPro; IPR019038; POLD3.
DR InterPro; IPR041913; POLD3_sf.
DR PANTHER; PTHR17598; PTHR17598; 1.
DR Pfam; PF09507; CDC27; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; DNA damage; DNA excision; DNA repair; DNA replication; Nucleus;
KW Reference proteome.
FT CHAIN 1..461
FT /note="DNA polymerase delta subunit 3"
FT /id="PRO_0000438549"
FT REGION 148..229
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 249..380
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 399..461
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 451..458
FT /note="PIP-box"
FT /evidence="ECO:0000250|UniProtKB:Q15054"
FT COMPBIAS 151..186
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 281..330
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 399..415
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 426..441
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 275
FT /note="T -> S (in Ref. 1; CAG31915)"
FT CONFLICT 287
FT /note="A -> T (in Ref. 1; CAG31915)"
FT CONFLICT 336
FT /note="L -> P (in Ref. 1; CAG31915)"
SQ SEQUENCE 461 AA; 50751 MW; CA7FC8DA6BEF9D1A CRC64;
MEDELYLENI DEFVTDQNRI VTYKWLSYTL GVHVNQAKQM LYDYVERKRK ENSGAQLHVT
YLVAGNLIQN GHTCHKVAVV REDKLEAMKS KLATVTSVHV YSIQKALLKD SGPLYNTDYD
IIKANLHNCS KFSAIRCADA VPRTPAEVAQ ARTLARSSSQ TPSDTSAVST PPLNGHGPTA
AKQSSQPPKG IMGMFAAKAA SKAQDANKEP KAKEAPSVSA ASSKPSAKGN IMNNFFGKAA
MNKLKVNSVP GQPKEEKEAV KTSVPATEPE SSPNTIVEKP GRKTEPAKIQ QKDKKSKMKR
MDKSDNEEER EPENQKKKRK RIKQLESDSS DEEDVLASPT LEEEKAPSPP PLVPALKAEL
EPASTEASAG GKKRKRKRVL KSKMFVDEEE GCMVTEKVYE SESCTDSEDD FAKTKPPAVP
KQPALPVKKE PKEERKNQKK GAATASRANK QISIMGFCQK K
