POLD2 (p50) is the non-catalytic B subunit of DNA polymerase delta, the B-family replicative polymerase that synthesizes lagging-strand (and some leading-strand) DNA and performs gap-filling synthesis in nucleotide excision repair, base excision repair, mismatch repair and break-induced replication. POLD2 bridges the catalytic subunit POLD1 and the PCNA-binding subunit POLD3 and is required for the stability of the heterotetrameric holoenzyme. POLD2 and POLD3 are also shared accessory subunits of the translesion polymerase zeta (REV3L-REV7-POLD2-POLD3), where they raise the efficiency and processivity of lesion bypass and provide a platform for switching between the delta and zeta catalytic subunits. POLD2 also binds the Y-family polymerase eta. The protein acts in the nucleoplasm. The donkey protein is 95.5% identical to human POLD2 over its full length and carries an 18-residue N-terminal extension.
Summary: InterPro2GO DNA binding from the DNA polymerase alpha/delta/epsilon subunit B family (IPR007185). POLD2 is a structural accessory subunit; DNA engagement is by the catalytic subunit and by POLD3/PCNA, and the PolD2-PolD3 structure lacks an evident DNA-binding surface.
Reason: The family-level mapping asserts a direct DNA-binding activity for which there is no POLD2-specific evidence; the structural observation argues against a dedicated DNA-binding surface. Same call as the human POLD2 review. Not removed because the subunit is part of a DNA-bound holoenzyme.
The cocrystal structure of human PolD2 and the NTD of PolD3 has been determined ( 35 ) and shows a primarily negatively charged molecular surface without obvious features for DNA binding.
Summary: Nuclear localization from the UniProt subcellular-location vocabulary; POLD2 acts in nuclear DNA replication and repair as part of Pol delta and Pol zeta.
Reason: Correct location for a replicative polymerase subunit; nucleoplasm (also annotated) is the more specific location.
Summary: Ensembl Compara transfer of DNA-templated DNA replication from human POLD2 (IDA in human).
Reason: Correct core process for a Pol delta subunit; the donkey protein is conserved over its full length.
Supporting Evidence:
file:EQUAS/POLD2/POLD2-bioinformatics/RESULTS.md
The donkey sequence A0A9L0IND0 (487 residues) aligns to human P49005 (469 residues) with 95.52% identity among 469 paired residues.
GO:0006271 DNA strand elongation involved in DNA replication
IEA GO_REF:0000118
ACCEPT
Summary: TreeGrafter assignment of DNA strand elongation involved in DNA replication from PANTHER node PTN001311496 (PTHR10416:SF0, DNA polymerase delta subunit 2). The donkey protein falls in the POLD2 subfamily and is 95.5% identical to human POLD2 over its full length.
Reason: Pol delta, with POLD2 as an essential subunit, performs processive strand elongation in replication (lagging strand and Okazaki fragment maturation). Correct at an appropriate level of specificity, matching the human IBA.
Summary: Ensembl Compara transfer of enzyme activator activity from human POLD2. POLD2 and POLD3 raise the catalytic efficiency (kcat/KM) and processivity of the REV3L-REV7 catalytic core of Pol zeta. A PAINT curator has placed this term (IBD, seeded by human P49005) on PANTHER node PTN000045935, the same node that carries zeta DNA polymerase complex and error-prone translesion synthesis.
Reason: Revised in the 2026-10-21 re-review from MARK_AS_OVER_ANNOTATED. The earlier objection (a constitutive subunit is not a separate activator) is a modelling preference, not a biological contradiction; GO uses activator terms for regulatory subunits that stimulate a catalytic partner, the human experiment shows exactly that stimulation of Pol zeta, and a PAINT curator judged the activity ancestral at PTN000045935, a node whose descendants include the donkey protein (TreeGrafter places it in PTHR10416:SF0, and the yeast and human seeds of this node bracket mammals). It is kept as non-core because the subunit's role is more fully captured by its contribution to the DNA-directed DNA polymerase activity of the delta and zeta complexes, and the term does not name the target enzyme.
In human Pol ฮถ4, the presence of PolD2 and PolD3, even at submolar ratios to Rev3 (TR4-2), dramatically increased the efficiency ( k cat / K M ) and processivity of DNA synthesis
The purified four-subunit Pol ฮถ4 (Rev3โRev7โPolD2โPolD3) is much more efficient and more processive at bypassing a 1,2-intrastrand d(GpG)-cisplatin cross-link than the two-subunit Pol ฮถ2 (Rev3โRev7).
Summary: Error-prone translesion synthesis, transferred from human POLD2, as a subunit of Pol zeta4.
Reason: Supported through Pol zeta4, in which POLD2 is a constitutive accessory subunit that raises lesion-bypass efficiency and processivity; recorded as the second core function. (The human review keeps this as non-core; the difference is one of emphasis, not of correctness.) Evolutionary grounding - a PAINT curator placed error-prone translesion synthesis and zeta DNA polymerase complex (IBD, seeded by yeast Pol31 and human POLD2) on PANTHER node PTN000045935, from which the donkey protein descends.
The purified four-subunit Pol ฮถ4 (Rev3โRev7โPolD2โPolD3) is much more efficient and more processive at bypassing a 1,2-intrastrand d(GpG)-cisplatin cross-link than the two-subunit Pol ฮถ2 (Rev3โRev7).
Summary: DNA polymerase binding, transferred from human POLD2. POLD2 binds the catalytic subunits of Pol delta and Pol zeta and binds Pol eta.
Reason: Supported by binding of POLD2 to the Pol delta/zeta catalytic subunits and to Pol eta; it describes the subunit's bridging role but is less informative than complex membership and the contributed polymerase activity.
Only POLD2, the B-subunit of Polฮด, was found to bind to Polฮท in a two-hybrid experiment and this interaction was further confirmed in a pull-down assay.
ISS file:EQUAS/POLD2/POLD2-bioinformatics/human-P49005-uniprot.txt
NEW
Summary: Pol delta performs repair synthesis in nucleotide excision repair and in break-induced replication, and POLD2 is required for holoenzyme integrity. The term is absent from donkey GOA (error-prone translesion synthesis sits under DNA damage tolerance, not DNA repair).
Reason: Supported by human POLD2 experimental findings (curated UniProt FUNCTION text with ECO:0000269 citations for NER synthesis and break-induced replication) transferred through a 95.5%-identical full-length ortholog in the same PANTHER subfamily (PTHR10416:SF0); the human review also carries DNA repair (accepted). The term is absent from donkey GOA because the human DNA repair row is a keyword (GO_REF:0000043) mapping, a pipeline retired for cellular organisms, not because a PAINT curator declined to propagate an experimental repair term (no experimental DNA repair annotation exists on the PAINT seeds). POLD2 is a subunit of the polymerase that performs the repair synthesis, so this is participation, not mere necessity; kept at the general DNA repair level because the pathway-specific evidence is on the holoenzyme rather than on POLD2 itself.
required for the repair of broken replication forks through break-induced replication (BIR)
Core Functions
Non-catalytic B subunit of the replicative DNA polymerase delta holoenzyme; bridges POLD1 and POLD3 and contributes to processive DNA-templated DNA synthesis in nuclear genome replication.
The purified four-subunit Pol ฮถ4 (Rev3โRev7โPolD2โPolD3) is much more efficient and more processive at bypassing a 1,2-intrastrand d(GpG)-cisplatin cross-link than the two-subunit Pol ฮถ2 (Rev3โRev7).
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
Assessment of the 2 ProtNLM2 GO predictions for donkey POLD2 (A0A9L0IND0, DONKEY40 cohort), using the reviewed human ortholog P49005, Pol delta/zeta literature, and a full-length donkey-human alignment (95.52% identity, complete human coverage). DNA replication is correct but less precise than the strand-elongation and DNA-templated replication terms already in donkey GOA (LSP). DNA repair is correct and absent from donkey GOA, whose damage-related row (error-prone translesion synthesis) is classed under DNA damage tolerance rather than DNA repair (COR). ProtNLM2 emitted no function text or subcellular-location statement for this accession in the snapshot.
LSP โ Less precise than existing annotation Review score: 2/2
Prediction method: ProtNLM2 ยท Version: UniProt API snapshot 2026-10-14
Review rationale: POLD2 is the essential B subunit of the replicative polymerase delta, and the donkey protein is 95.5% identical to human POLD2 across the whole human sequence, so DNA replication is biologically correct. The exact term is already in donkey GOA (InterPro2GO), and GOA also carries the more specific DNA strand elongation involved in DNA replication (TreeGrafter) and DNA-templated DNA replication (Ensembl Compara), both supported. The prediction is therefore less precise than existing annotation. The ProtNLM2 evidence record links it to the strand-elongation term. Training-set membership is unknown.
Supporting Evidence:
PMID:31449058: "The mammalian polymerase ฮด complex is a heterotetramer consisting of the catalytic subunit POLD1 and the accessory subunits POLD2, POLD3, and POLD4"
Prediction method: ProtNLM2 ยท Version: UniProt API snapshot 2026-10-14
Review rationale: Human Pol delta, with POLD2 as an obligate subunit, performs about half of nucleotide excision repair synthesis and break-induced replication at broken forks (experimental evidence in the reviewed human record), and the donkey protein is conserved over the full length. DNA repair is absent from donkey GOA; the error-prone translesion synthesis row is a DNA damage tolerance process in GO, not a DNA repair descendant (QuickGO ancestor check). The prediction is a justified ortholog-based transfer that adds coverage to the target record. Novelty refers to target annotation coverage only; training-set membership is unknown.
PMID:31449058: "Beyond DNA replication, the polymerase ฮด complex has emerged as a central element in the safeguarding of genome integrity by controlling processes such as break-induced replication"