FlyBase Gene Report: Dmel\PolD1

General Information

Symbol

Dmel\PolD1

Species

D. melanogaster

Name

DNA polymerase delta subunit 1

Annotation Symbol

CG5949

Feature Type

protein_coding_gene

FlyBase ID

FBgn0263600

Gene Model Status

Current

Stock Availability

8 publicly available

Enzyme Name (EC)

DNA-directed DNA polymerase (2.7.7.7)

Gene Summary

As the catalytic component of the DNA polymerase delta complex, plays a crucial role in high fidelity genome replication, including lagging strand synthesis, DNA recombination and repair (By similarity). Exhibits both DNA polymerase and 3'- to 5'-exonuclease activities (PubMed:7907087, PubMed:8415662, PubMed:1360647). Required at the nucleus of rapidly dividing embryonic cells to activate genome replication during the earliest cell cycles (PubMed:31100062). Likely to require the presence of accessory proteins PolD2 and PolD3 for full activity (PubMed:31100062). (UniProt, P54358)

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All Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

DNApol-delta, DNApol-δ, DNA polymerase delta, DNA-polymerase-δ, Polδ

Key Links

Genomic Location

Cytogenetic map

72C1-72C1

Sequence location

3L:15,984,322..15,987,815 [-]

Recombination map

3-43

RefSeq locus

NT_037436 REGION:15984322..15987815

Sequence

Get Decorated FASTA

Genomic Maps

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Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (12 terms)

Molecular Function (5 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

enables 3'-5'-exodeoxyribonuclease activity

inferred from direct assay

(Aoyagi et al., 1994, Chiang et al., 1993, Peck et al., 1992)

enables DNA-directed DNA polymerase activity

inferred from direct assay

(Aoyagi et al., 1994, Chiang et al., 1993, Peck et al., 1992)

enables protein binding

inferred from physical interaction with UniProtKB:Q9VIT0

(assigned by UniProt )

(Ruike et al., 2006)

inferred from physical interaction with UniProtKB:Q9W088,UniProtKB:Q9Y118

(assigned by UniProt )

(Ji et al., 2019)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

enables 3'-5'-exodeoxyribonuclease activity

inferred from biological aspect of ancestor with PANTHER:PTN000035478

(assigned by GO_Central )

(Gaudet et al., 2011)

enables DNA binding

inferred from electronic annotation with InterPro:IPR006134

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

enables DNA-directed DNA polymerase activity

inferred from biological aspect of ancestor with PANTHER:PTN000035346

(assigned by GO_Central )

(Gaudet et al., 2011)

enables nucleotide binding

inferred from electronic annotation with InterPro:IPR006134, InterPro:IPR006172, InterPro:IPR017964

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

Biological Process (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

involved_in DNA replication proofreading

inferred from direct assay

(Aoyagi et al., 1994)

involved_in DNA-dependent DNA replication

inferred from direct assay

(Aoyagi et al., 1994, Chiang et al., 1993, Peck et al., 1992)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

involved_in base-excision repair, gap-filling

inferred from biological aspect of ancestor with PANTHER:PTN000035478

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in DNA replication proofreading

inferred from biological aspect of ancestor with PANTHER:PTN000035478

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in DNA-dependent DNA replication

inferred from biological aspect of ancestor with PANTHER:PTN000035346

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in nucleotide-excision repair, DNA gap filling

inferred from biological aspect of ancestor with PANTHER:PTN000035478

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

part_of delta DNA polymerase complex

inferred from direct assay

(Ji et al., 2019, Peck et al., 1992)

located_in nucleoplasm

inferred from direct assay

(assigned by UniProt )

(Ji et al., 2019)

located_in nucleus

inferred from direct assay

(Ji et al., 2019)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of delta DNA polymerase complex

inferred from biological aspect of ancestor with PANTHER:PTN000035478

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

DNA POLYMERASE DELTA

DNA POLYMERASE CATALYTIC SUBUNITS

3'-5'-EXODEOXYRIBONUCLEASES

Protein Family (UniProt)

Belongs to the DNA polymerase type-B family. (P54358)

Protein Signatures (InterPro)

Catalytic Activity (EC)

Experimental Evidence

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (2.7.7.7)

Predictions / Assertions

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (2.7.7.7)

Summaries

Gene Group (FlyBase)

DNA POLYMERASE DELTA -: DNA polymerase delta functions as a leading strand polymerase during nuclear DNA synthesis. It is a multi-subunit enzyme in which DNApol-δ encodes the catalytic subunit with polymerase and 3'-5' exonuclease proofreading activities. (Adapted from PMID:30005324.)
DNA POLYMERASE CATALYTIC SUBUNITS -: Multiple DNA polymerases are required for DNA replication and/or repair in eukaryotic cells. The alpha-primase, delta, epsilon, zeta and gamma polymerases exist as multi-subunit complexes in which one of the subunits has catalytic activity, whereas other DNA polymerases act as single molecules. (Adapted from PMID:30005324.)
3'-5'-EXODEOXYRIBONUCLEASES -: 3'-5'-exodeoxyribonucleases catalyze the sequential degradation of double-stranded DNA acting progressively in a 3'-to-5' direction, releasing nucleoside 5'-phosphates.

Protein Function (UniProtKB)

(UniProt, P54358)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\PolD1 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)

Isoform displayed:

Pfam protein domains

InterPro name

classification

start

end

Protein Domains (via SMART)

Isoform displayed:

SMART protein domains

InterPro name

classification

start

end

Structure New Section

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry P54358)

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Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Comments on Gene Model

Gene model reviewed during 5.44

Gene model reviewed during 5.46

Sequence Ontology: Class of Gene

gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

PolD1-RA

FBtr0075522

NM_079375

3440

1092

Additional Transcript Data and Comments

Reported size (kB)

4 (northern blot)

(Chiang and Lehman, 1995)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

PolD1-PA

FBpp0075277

124.9

1092

6.90

NP_524099

AAF49555

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments

Reported size (kDa)

1092 (aa); 120 (kD observed); 125 (kD predicted)

(Chiang and Lehman, 1995)

Comments

The DNApol-δ protein sequence contains a number of homology boxes and conserved residues that are characteristic of δ DNA polymerases. Insect cells infected with the DNApol-δ cDNA show increased DNA polymerase activity.

(Chiang and Lehman, 1995)

External Data

Subunit Structure (UniProtKB)

Catalytic component of the DNA polymerase delta complex consisting of three subunits: the catalytic subunit PolD1 and two accessory subunits PolD2/Pol31 and PolD3/Pol32 (PubMed:31100062). Within the delta complex, interacts with both PolD2 and PolD3, and is able to interact with PolD2 in the absence of PolD3 (PubMed:31100062). Interacts with PCNA AND PCNA2 (PubMed:17087725).

(UniProt, P54358)

Domain

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

(UniProt, P54358)

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

P54358

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\PolD1 using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

DNApol-delta_1

Linkouts

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 7 -- 8

antennal anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

central brain anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

dorsal head epidermis anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

visual anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

ventral nerve cord primordium

Comment: reported as ventral nerve cord anlage

(Fisher et al., 2012)

embryonic stage 9 -- 10

antennal primordium