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Protein

DNA polymerase delta subunit 2

Gene

pold2

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at transcript 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

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA excision, DNA repair, DNA replication

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase delta subunit 2
Alternative name(s):
XlCdc1
Gene namesi
Name:pold2
Synonyms:cdc1
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-999393. pold2.

Subcellular locationi

  • Nucleus By similarity

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

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000961681 – 463DNA polymerase delta subunit 2Add BLAST463

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. 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). 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

Protein-protein interaction databases

IntActiO93610. 1 interactor.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

HOVERGENiHBG051396.
KOiK02328.

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.

O93610-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFTDLAISGG PGLLTAPSEV QSTFTRVSNT QYSNCSSIFR LGERTFTRQY
60 70 80 90 100
AHIYATRLEQ MRPLLIKSAK QRWGDDIAVR KLCELQGGEK CCVIGTLFKS
110 120 130 140 150
MELQPSILRE ISEEHNLLPQ PARQKYISDS DELILEDELQ RIKLEGATDV
160 170 180 190 200
QQLVTGAVLA VLGAEEDAGK FVVEDFCLTS LPVQSPLPRL SEDRFVLLTS
210 220 230 240 250
GLGLGGGSGD SLMGLQLLLD LVTGQAGAEE DQGCAARISR VILAGNLLSE
260 270 280 290 300
NTQGKDSLNK AKYLSKKTQA ASVEAVKMLD EILLQMSGSV SVDVMPGAFD
310 320 330 340 350
PTNYILPQQP LHRCMFPQSA LYSTLQLVTN PYEAEIDGVR FLGTSGQNIG
360 370 380 390 400
DIYKYSSMQD YLDILEWTLQ VGHLCPTAPD TLGCYPFYKS DPFILQNCPH
410 420 430 440 450
VYFCGSAPKF SCKEVTGAEG QRVLLLTVPE FCSTQTACLV NLRTLQCQPI
460
SFSGFGADDE LGD
Length:463
Mass (Da):50,648
Last modified:November 1, 1998 - v1
Checksum:i77026EF1897A638D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ010836 mRNA. Translation: CAA09373.1.
BC047262 mRNA. Translation: AAH47262.1.
RefSeqiNP_001080101.1. NM_001086632.1.
UniGeneiXl.4169.

Genome annotation databases

GeneIDi379793.
KEGGixla:379793.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ010836 mRNA. Translation: CAA09373.1.
BC047262 mRNA. Translation: AAH47262.1.
RefSeqiNP_001080101.1. NM_001086632.1.
UniGeneiXl.4169.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiO93610. 1 interactor.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi379793.
KEGGixla:379793.

Organism-specific databases

CTDi5425.
XenbaseiXB-GENE-999393. pold2.

Phylogenomic databases

HOVERGENiHBG051396.
KOiK02328.

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_XENLA
AccessioniPrimary (citable) accession number: O93610
Secondary accession number(s): Q5D0A2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: November 1, 1998
Last modified: November 30, 2016
This is version 70 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

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.