Hda-beta clamp complex

GO:1990085 · Other · Multiprotein complex · Proposed

A protein complex involved in inactivating the function of DnaA and thereby preventing multiple events of replication initiation. In E. coli, this complex is composed of the beta clamp (DnaN) and Hda. [GO:1990085]

Synonyms: Hda-DnaN complex; Hda-dpo3b complex

Has part: DNA polymerase III, beta sliding clamp processivity factor complex (GO:0044775)

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Stoichiometry	Essential	Role
Hda DnaA-related protein	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	hda		UNKNOWN	DnaA-related regulatory protein that binds the DnaN beta clamp in the Hda-beta clamp complex. `GO:1990085` GO:1990085 defines the E. coli Hda-beta clamp complex as containing Hda. `PMID:15150238` Kurz et al. 2004 purified E. coli Hda and beta proteins and assayed their direct interaction.
DNA polymerase III, beta sliding clamp processivity factor complex	Protein complex	part of	`GO:0044775`	dnaN		UNKNOWN	DnaN beta sliding-clamp ring bound by Hda during regulatory inactivation of DnaA. `GO:1990085` GO:1990085 defines the E. coli Hda-beta clamp complex as containing the beta clamp, DnaN. `GO:0044775` GO:0044775 is the Gene Ontology cellular-component term for the DNA polymerase III beta sliding-clamp processivity factor complex. `PMID:15150238` Kurz et al. 2004 showed direct interaction between E. coli Hda and the sliding-clamp beta subunit.

Taxonomic distribution

NCBITaxon:562 Escherichia coli — COMMON: Kurz et al. 2004 studied the interaction between E. coli Hda and the DnaN beta sliding clamp. [PMID:15150238]

Canonical examples

NCBITaxon:562 Escherichia coli — Kurz et al. 2004 used purified E. coli Hda and beta sliding-clamp proteins to define the Hda-beta interaction. [PMID:15150238]

Functions

negative regulation of DNA-templated DNA replication initiation GO:0032297 — The E. coli Hda-beta clamp complex participates in regulatory inactivation of DnaA to prevent multiple replication initiation events.
- GO:1990085 GO:1990085 defines the Hda-beta clamp complex by DnaA inactivation and prevention of multiple replication initiation events.
- GO:0032297 GO:0032297 is the Gene Ontology biological-process term for negative regulation of DNA-templated DNA replication initiation.
- PMID:15150238 Kurz et al. 2004 connected Hda-beta interaction to accelerated hydrolysis of DnaA-bound ATP and prevention of excess replication initiation.

Mechanism graphs

Hda binds the beta clamp for RIDA (FUNCTION)

Hda binds the DnaN beta sliding clamp to form a replication inhibiting complex that supports regulatory inactivation of DnaA.

Subject	Predicate	Object	Evidence
Hda DnaA-related protein	contributes to	Hda-beta clamp complex	`GO:1990085` GO:1990085 names Hda as a constituent of the Hda-beta clamp complex.
DNA polymerase III, beta sliding clamp processivity factor complex	contributes to	Hda-beta clamp complex	`GO:1990085` GO:1990085 names the beta clamp, DnaN, as a constituent of the Hda-beta clamp complex. `GO:0044775` GO:0044775 denotes the DNA polymerase III beta sliding-clamp complex.
Hda-beta clamp complex	supports	negative regulation of DNA-templated DNA replication initiation	`GO:1990085` GO:1990085 defines the complex by DnaA inactivation and prevention of multiple replication initiation events. `PMID:15150238` Kurz et al. 2004 established Hda-beta binding and proposed its importance in DnaA inactivation.

Discussions

CURATION_TODO (OPEN): Resolve exact source-neutral Hda family grounding for the Hda-beta clamp complex. GO:1990085 names Hda as an E. coli constituent of the Hda-beta clamp complex. Exact source-neutral InterPro, Pfam, NCBIfam or UniProt family CURIEs need narrower curation before this component can be grounded.
INTERPRETATION (RESOLVED): Keep the Hda-beta clamp complex distinct from the DnaA-Hda complex. GO:1990085 denotes Hda bound to the DnaN beta clamp, whereas GO:1990083 separately denotes the DnaA-Hda complex. Kurz et al. 2004 established direct Hda-beta interaction, and GO:1990085 scopes that Hda-beta entity to the replication-inhibiting state.

Evidence

GO:1990085 Gene Ontology cellular-component term for the Hda-beta clamp complex and its Hda-DnaN/Hda-dpo3b exact synonyms.
GO:1990078 QuickGO reports GO:1990085 Hda-beta clamp complex as an is-a child of GO:1990078 replication inhibiting complex.
GO:0044775 Gene Ontology cellular-component term for the DNA polymerase III beta sliding-clamp processivity factor complex.
GO:1990083 Gene Ontology cellular-component term for the separately scoped DnaA-Hda complex.
GO:0032297 Gene Ontology biological-process term for negative regulation of DNA-templated DNA replication initiation.
PMID:15150238 PubMed identifier for Kurz et al. 2004, the Journal of Bacteriology paper cited by GO:1990085.
DOI:10.1128/JB.186.11.3508-3515.2004 DOI for Kurz et al. 2004, 'Interaction of the sliding clamp beta-subunit and Hda, a DnaA-related protein', as reported by PubMed.

Curation history

2026-10-01T12:42:41Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-10-01T12:43:52Z codex · EXPANDED_RECORD — Added Hda-beta clamp GO synonymy, replication-inhibiting-complex parentage, beta sliding-clamp substructure and component links, a reviewed-label-only Hda component, E. coli Hda-beta evidence, negative-DNA-replication-initiation function evidence, GO/PubMed/DOI evidence, a nonmechanistic Hda-beta RIDA graph, and grounding/boundary discussions.
2026-10-01T12:45:20Z codex · FIX_COMPONENT_LABEL — Matched the beta sliding-clamp component label to GO:0044775 and narrowed the Hda-beta/DnaA-Hda boundary discussion rationale to the directly cited GO and Kurz et al. 2004 sources.
2026-10-01T13:05:25Z codex · FIX_REVIEW_ISSUE — Addressed PR #1871 review issue #1872 by narrowing the Hda-beta/DnaA-Hda boundary discussion so Kurz et al. 2004 supports direct Hda-beta binding while GO:1990085 supports the replication-inhibiting scope.

Source: data/structures/other/hda_beta_clamp_complex.yaml