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Protein

DNA polymerase delta subunit 2

Gene

Pold2

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

As a component of the trimeric and tetrameric DNA polymerase delta complexes (Pol-delta3 and Pol-delta4, respectively), plays a role in high fidelity genome replication, including in lagging strand synthesis, and repair. Pol-delta3 and Pol-delta4 are characterized by the absence or the presence of POLD4. They exhibit differences in catalytic activity. Most notably, Pol-delta3 shows higher proofreading activity than Pol-delta4. Although both Pol-delta3 and Pol-delta4 process Okazaki fragments in vitro, Pol-delta3 may also be better suited to fulfill this task, exhibiting near-absence of strand displacement activity compared to Pol-delta4 and stalling on encounter with the 5'-blocking oligonucleotides. Pol-delta3 idling process may avoid the formation of a gap, while maintaining a nick that can be readily ligated. Along with DNA polymerase kappa, DNA polymerase delta carries out approximately half of nucleotide excision repair (NER) synthesis following UV irradiation. Under conditions of DNA replication stress, required for the repair of broken replication forks through break-induced replication (BIR). Involved in the translesion synthesis (TLS) of templates carrying O6-methylguanine or abasic sites performed by Pol-delta4, independently of DNA polymerase zeta (REV3L) or eta (POLH). Facilitates abasic site bypass by DNA polymerase delta by promoting extension from the nucleotide inserted opposite the lesion. Also involved in TLS as a component of the POLZ complex. Along with POLD3, dramatically increases the efficiency and processivity of DNA synthesis of the minimal DNA polymerase zeta complex, consisting of only REV3L and REV7.By similarity

GO - Molecular functioni

  • DNA binding Source: InterPro
  • DNA-directed DNA polymerase activity Source: RGD

GO - Biological processi

  • DNA-dependent DNA replication Source: RGD
  • DNA replication Source: RGD
Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA excision, DNA repair, DNA replication

Enzyme and pathway databases

ReactomeiR-RNO-110314. Recognition of DNA damage by PCNA-containing replication complex.
R-RNO-174411. Polymerase switching on the C-strand of the telomere.
R-RNO-174414. Processive synthesis on the C-strand of the telomere.
R-RNO-174417. Telomere C-strand (Lagging Strand) Synthesis.
R-RNO-174437. Removal of the Flap Intermediate from the C-strand.
R-RNO-5358565. Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha).
R-RNO-5358606. Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta).
R-RNO-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-RNO-5656169. Termination of translesion DNA synthesis.
R-RNO-5685942. HDR through Homologous Recombination (HRR).
R-RNO-5696397. Gap-filling DNA repair synthesis and ligation in GG-NER.
R-RNO-5696400. Dual Incision in GG-NER.
R-RNO-6782135. Dual incision in TC-NER.
R-RNO-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-RNO-69091. Polymerase switching.
R-RNO-69166. Removal of the Flap Intermediate.
R-RNO-69183. Processive synthesis on the lagging strand.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase delta subunit 2
Alternative name(s):
DNA polymerase delta subunit p50
Gene namesi
Name:Pold2
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 14

Organism-specific databases

RGDi1304954. Pold2.

Subcellular locationi

  • Nucleus By similarity

  • Note: Recruited to DNA damage sites within 2 hours following UV irradiation.By similarity

GO - Cellular componenti

  • delta DNA polymerase complex Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002485891 – 469DNA polymerase delta subunit 2Add BLAST469

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineBy similarity1
Modified residuei15PhosphoserineBy similarity1
Modified residuei257PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiQ6AXY4.
PRIDEiQ6AXY4.

PTM databases

SwissPalmiQ6AXY4.

Expressioni

Gene expression databases

BgeeiENSRNOG00000014098.
GenevisibleiQ6AXY4. RN.

Interactioni

Subunit structurei

Component of the tetrameric DNA polymerase delta complex (Pol-delta4), which consists of POLD1/p125, POLD2/p50, POLD3/p66/p68 and POLD4/p12, with POLD1 bearing DNA polymerase and 3' to 5' proofreading exonuclease activities. Within Pol-delta4, directly interacts with POLD1, POLD3 and POLD4. Following stress caused by DNA damaging agents or by replication stress, POLD4 is degraded and Pol-delta4 is converted into a trimeric form of the complex (Pol-delta3), which consists of POLD1, POLD2 and POLD3. Pol-delta3 is the major form occurring at S phase replication sites, as well as DNA damage sites. Also observed as a dimeric complex with POLD2 (Pol-delta2 complex). Pol-delta2 is relatively insensitive to the PCNA stimulation (2-5-fold) compared to Pol-delta4 that is stimulated by over 50-fold. Contrary to the other components of Pol-delta4, does not directly interact with PCNA. As POLD1 and POLD4, directly interacts with WRNIP1; this interaction stimulates DNA polymerase delta-mediated DNA synthesis, independently of the presence of PCNA. This stimulation may be due predominantly to an increase of initiation frequency and also to increased processivity. Directly interacts with POLDIP2 and POLDIP3. Directly interacts with KCTD13/PDIP1; in the presence of PCNA, this interaction may stimulate DNA polymerase activity. Component of the DNA polymerase zeta complex (POLZ), which consists of REV3L, MAD2L2, POLD2 and POLD3, with REV3L bearing DNA polymerase catalytic activity (By similarity). Interacts with KCTD10 (PubMed:15982757).By similarity1 Publication

Protein-protein interaction databases

BioGridi253015. 1 interactor.
STRINGi10116.ENSRNOP00000019288.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG2732. Eukaryota.
COG1311. LUCA.
GeneTreeiENSGT00390000006780.
HOGENOMiHOG000189057.
HOVERGENiHBG051396.
InParanoidiQ6AXY4.
KOiK02328.
OMAiFLENRAQ.
OrthoDBiEOG091G094I.
PhylomeDBiQ6AXY4.
TreeFamiTF101073.

Family and domain databases

InterProiIPR007185. DNA_pol_alpha/epsilon_bsu.
IPR024826. DNA_pol_delta/II_ssu.
[Graphical view]
PANTHERiPTHR10416. PTHR10416. 1 hit.
PfamiPF04042. DNA_pol_E_B. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q6AXY4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFSEQAAQRA HTLLSPPSAS NATFARVPVA TYTNSSQPFR LGERSFNRQY
60 70 80 90 100
AHIYATRLIQ MRPFLVSRAQ QHWGSQVEVK KLCELQPGEQ CCVVGTLFKA
110 120 130 140 150
MPLQPSILRE ISEEHNLIPQ PPRSKYIHPD DELVLEDELQ RIKLKGTIDV
160 170 180 190 200
SKLVTGTVLA VFGSVKDDGK FQVEDHCFAD LAPQNPVPPL DTDRFVLLVS
210 220 230 240 250
GLGLGGGGGE SLLGTQLLVD VVTGQLGDEG EQCSAAHVSR VILAGNLLSH
260 270 280 290 300
NTQSRDSINK AKYLTKKTQA ASVEAVKMLD EILLQLSASV PVDVMPGEFD
310 320 330 340 350
PTNYTLPQQP LHPCMFPLAT AYATLQLVTN PYQATIDGVR FLGTSGQNVS
360 370 380 390 400
DIFRYSSMED HLEILEWTLR VRHISPTAPD TLGCYPFYKT DPFIFAECPH
410 420 430 440 450
VYFCGNTPSF GSKVIRGPED QAVLLVAVPD FSSTQTACLV NLRGLTCQPI
460
SFAGFGAEQD DLEDLGLGP
Length:469
Mass (Da):51,346
Last modified:September 13, 2004 - v1
Checksum:iE6619AD76045911A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC079267 mRNA. Translation: AAH79267.1.
RefSeqiNP_001013068.1. NM_001013050.1.
UniGeneiRn.22989.

Genome annotation databases

EnsembliENSRNOT00000019288; ENSRNOP00000019288; ENSRNOG00000014098.
ENSRNOT00000084633; ENSRNOP00000072093; ENSRNOG00000014098.
GeneIDi289758.
KEGGirno:289758.
UCSCiRGD:1304954. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC079267 mRNA. Translation: AAH79267.1.
RefSeqiNP_001013068.1. NM_001013050.1.
UniGeneiRn.22989.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi253015. 1 interactor.
STRINGi10116.ENSRNOP00000019288.

PTM databases

SwissPalmiQ6AXY4.

Proteomic databases

PaxDbiQ6AXY4.
PRIDEiQ6AXY4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000019288; ENSRNOP00000019288; ENSRNOG00000014098.
ENSRNOT00000084633; ENSRNOP00000072093; ENSRNOG00000014098.
GeneIDi289758.
KEGGirno:289758.
UCSCiRGD:1304954. rat.

Organism-specific databases

CTDi5425.
RGDi1304954. Pold2.

Phylogenomic databases

eggNOGiKOG2732. Eukaryota.
COG1311. LUCA.
GeneTreeiENSGT00390000006780.
HOGENOMiHOG000189057.
HOVERGENiHBG051396.
InParanoidiQ6AXY4.
KOiK02328.
OMAiFLENRAQ.
OrthoDBiEOG091G094I.
PhylomeDBiQ6AXY4.
TreeFamiTF101073.

Enzyme and pathway databases

ReactomeiR-RNO-110314. Recognition of DNA damage by PCNA-containing replication complex.
R-RNO-174411. Polymerase switching on the C-strand of the telomere.
R-RNO-174414. Processive synthesis on the C-strand of the telomere.
R-RNO-174417. Telomere C-strand (Lagging Strand) Synthesis.
R-RNO-174437. Removal of the Flap Intermediate from the C-strand.
R-RNO-5358565. Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha).
R-RNO-5358606. Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta).
R-RNO-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-RNO-5656169. Termination of translesion DNA synthesis.
R-RNO-5685942. HDR through Homologous Recombination (HRR).
R-RNO-5696397. Gap-filling DNA repair synthesis and ligation in GG-NER.
R-RNO-5696400. Dual Incision in GG-NER.
R-RNO-6782135. Dual incision in TC-NER.
R-RNO-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-RNO-69091. Polymerase switching.
R-RNO-69166. Removal of the Flap Intermediate.
R-RNO-69183. Processive synthesis on the lagging strand.

Miscellaneous databases

PROiQ6AXY4.

Gene expression databases

BgeeiENSRNOG00000014098.
GenevisibleiQ6AXY4. RN.

Family and domain databases

InterProiIPR007185. DNA_pol_alpha/epsilon_bsu.
IPR024826. DNA_pol_delta/II_ssu.
[Graphical view]
PANTHERiPTHR10416. PTHR10416. 1 hit.
PfamiPF04042. DNA_pol_E_B. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDPOD2_RAT
AccessioniPrimary (citable) accession number: Q6AXY4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 5, 2006
Last sequence update: September 13, 2004
Last modified: November 30, 2016
This is version 85 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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.