dnaN

UniProt ID: P0A120
Organism: Pseudomonas putida KT2440
Review Status: COMPLETE
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Gene Description

DnaN is the homodimeric beta sliding clamp of bacterial DNA polymerase III. The clamp forms a ring around duplex DNA after ATP-dependent loading by the clamp-loader complex and tethers replicative polymerases to DNA, thereby supporting processive chromosome synthesis.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003677 DNA binding
IEA
GO_REF:0000002
ACCEPT
Summary: The beta clamp directly encircles and interacts with DNA.
Reason: The beta clamp directly encircles and interacts with DNA. DNA binding is intrinsic to clamp function rather than a peripheral consequence.
Supporting Evidence:
file:PSEPK/dnaN/dnaN-uniprot.txt
Belongs to the beta sliding clamp family.
PMID:15611049
Efficient primer elongation requires the presence of alphaepsilon, beta, and tau(3)deltadelta'.
GO:0003887 DNA-directed DNA polymerase activity
IEA
GO_REF:0000002
REMOVE
Summary: The clamp is a non-catalytic processivity factor; polymerase chemistry is performed by DnaE.
Reason: The clamp is a non-catalytic processivity factor; polymerase chemistry is performed by DnaE. Pseudomonas reconstitution separates beta from the alpha-epsilon catalytic complex.
Supporting Evidence:
file:PSEPK/dnaN/dnaN-uniprot.txt
Belongs to the beta sliding clamp family.
PMID:15611049
Efficient primer elongation requires the presence of alphaepsilon, beta, and tau(3)deltadelta'.
GO:0005737 cytoplasm
IEA
GO_REF:0000044
ACCEPT
Summary: The beta clamp operates on bacterial chromosome DNA in the cytoplasm.
Reason: The beta clamp operates on bacterial chromosome DNA in the cytoplasm. The ISS donor supports a conserved location rather than target-specific imaging.
Supporting Evidence:
file:PSEPK/dnaN/dnaN-uniprot.txt
Belongs to the beta sliding clamp family.
PMID:15611049
Efficient primer elongation requires the presence of alphaepsilon, beta, and tau(3)deltadelta'.
GO:0006260 DNA replication
IEA
GO_REF:0000002
MODIFY
Summary: The direct processivity contribution supports strand elongation during replication, a descendant already present.
Reason: The direct processivity contribution supports strand elongation during replication, a descendant already present.
Supporting Evidence:
file:PSEPK/dnaN/dnaN-uniprot.txt
Belongs to the beta sliding clamp family.
PMID:15611049
Efficient primer elongation requires the presence of alphaepsilon, beta, and tau(3)deltadelta'.
GO:0006271 DNA strand elongation involved in DNA replication
IEA
GO_REF:0000118
ACCEPT
Summary: The clamp physically tethers polymerase to its DNA template, thereby performing structural work required for processive strand elongation.
Reason: The clamp physically tethers polymerase to its DNA template, thereby performing structural work required for processive strand elongation.
Supporting Evidence:
file:PSEPK/dnaN/dnaN-uniprot.txt
Belongs to the beta sliding clamp family.
PMID:15611049
Efficient primer elongation requires the presence of alphaepsilon, beta, and tau(3)deltadelta'.
GO:0008408 3'-5' exonuclease activity
IEA
GO_REF:0000002
REMOVE
Summary: The beta clamp lacks the DnaQ proofreading catalytic role; the editing activity of the holoenzyme must not be assigned to this processivity subunit.
Reason: The beta clamp lacks the DnaQ proofreading catalytic role; the editing activity of the holoenzyme must not be assigned to this processivity subunit.
Supporting Evidence:
file:PSEPK/dnaN/dnaN-uniprot.txt
Belongs to the beta sliding clamp family.
PMID:15611049
Efficient primer elongation requires the presence of alphaepsilon, beta, and tau(3)deltadelta'.
GO:0009360 DNA polymerase III complex
IEA
GO_REF:0000002
ACCEPT
Summary: The beta clamp is a polymerase III holoenzyme component, corroborated by Pseudomonas replicase reconstitution.
Reason: The beta clamp is a polymerase III holoenzyme component, corroborated by Pseudomonas replicase reconstitution.
Supporting Evidence:
file:PSEPK/dnaN/dnaN-uniprot.txt
Belongs to the beta sliding clamp family.
PMID:15611049
Efficient primer elongation requires the presence of alphaepsilon, beta, and tau(3)deltadelta'.
GO:0042802 identical protein binding
IEA
GO_REF:0000117
ACCEPT
Summary: Head-to-tail homodimerization forms the functional DNA-encircling ring.
Reason: Head-to-tail homodimerization forms the functional DNA-encircling ring. Identical-protein binding therefore describes a specific core assembly property; it is not the uninformative bare GO0005515 term.
Supporting Evidence:
file:PSEPK/dnaN/dnaN-uniprot.txt
Belongs to the beta sliding clamp family.
PMID:15611049
Efficient primer elongation requires the presence of alphaepsilon, beta, and tau(3)deltadelta'.
GO:0071897 DNA biosynthetic process
IEA
GO_REF:0000108
ACCEPT
Summary: The clamp contributes the DNA-tethering scaffold that enables processive DNA production.
Reason: The clamp contributes the DNA-tethering scaffold that enables processive DNA production. Its non-catalytic status does not exclude structural participation in biosynthesis, and no nonexistent ancestor relationship with replication is assumed.
Supporting Evidence:
file:PSEPK/dnaN/dnaN-uniprot.txt
Belongs to the beta sliding clamp family.
PMID:15611049
Efficient primer elongation requires the presence of alphaepsilon, beta, and tau(3)deltadelta'.
GO:0005737 cytoplasm
ISS
GO_REF:0000024
ACCEPT
Summary: The beta clamp operates on bacterial chromosome DNA in the cytoplasm.
Reason: The beta clamp operates on bacterial chromosome DNA in the cytoplasm. The ISS donor supports a conserved location rather than target-specific imaging.
Supporting Evidence:
file:PSEPK/dnaN/dnaN-uniprot.txt
Belongs to the beta sliding clamp family.
PMID:15611049
Efficient primer elongation requires the presence of alphaepsilon, beta, and tau(3)deltadelta'.
GO:0030337 DNA polymerase processivity factor activity
IEA
file:PSEPK/dnaN/dnaN-uniprot.txt
NEW
Summary: Retain the inherited proposal and original payload.
Reason: Retain the inherited proposal and original payload. The target belongs to the beta-clamp family, and Pseudomonas reconstitution directly separates the beta processivity factor from polymerase and loader. The processivity activity adds a distinct regulator function, not polymerization or nuclease chemistry.
Supporting Evidence:
file:PSEPK/dnaN/dnaN-uniprot.txt
Belongs to the beta sliding clamp family.
PMID:15611049
Efficient primer elongation requires the presence of alphaepsilon, beta, and tau(3)deltadelta'.

Core Functions

Homodimeric beta sliding clamp that encircles DNA and tethers DNA polymerase III for processive strand elongation.

Supporting Evidence:
  • file:PSEPK/dnaN/dnaN-uniprot.txt
    Belongs to the beta sliding clamp family.
  • PMID:15611049
    Efficient primer elongation requires the presence of alphaepsilon, beta, and tau(3)deltadelta'.

References

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Notes

(dnaN-notes.md)

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