DnaA-Hda complex

GO:1990083 · Other · Multiprotein complex · Proposed

A protein complex that inactivates the function of DnaA by inhibiting the phosphorylation of DnaA-ADP to DnaA-ATP and thereby preventing multiple events of replication initiation. In E. coli, this complex is composed of DnaA and Hda. [GO:1990083]

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
DnaA replication initiation protein	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	dnaA		UNKNOWN	Replication initiator constituent bound by Hda during regulatory inactivation of DnaA. `GO:1990083` GO:1990083 defines the DnaA-Hda complex as being composed of DnaA and Hda in E. coli. `PMID:21708944` Keyamura and Katayama 2011 tested DnaA residues needed for E. coli DnaA-Hda interaction during regulatory inactivation of DnaA.
Hda DnaA-related protein	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	hda		UNKNOWN	DnaA-related regulatory inactivation factor that binds DnaA in the DnaA-Hda complex. `GO:1990083` GO:1990083 defines the E. coli DnaA-Hda complex as containing Hda. `PMID:21708944` Keyamura and Katayama 2011 modeled and tested Hda interactions with the DnaA DNA-binding and AAA+ domains.

Taxonomic distribution

NCBITaxon:562 Escherichia coli — COMMON: Keyamura and Katayama 2011 studied E. coli DnaA-Hda interactions during regulatory inactivation of DnaA. [PMID:21708944]

Canonical examples

NCBITaxon:562 Escherichia coli — Keyamura and Katayama 2011 used the E. coli Hda and DnaA proteins to define DnaA-Hda contacts needed for DnaA-ATP hydrolysis in the regulatory inactivation of DnaA system. [PMID:21708944]

Functions

negative regulation of DNA-templated DNA replication initiation GO:0032297 — The E. coli DnaA-Hda complex participates in regulatory inactivation of DnaA to prevent extra DNA replication initiation events.
- GO:1990083 GO:1990083 defines the complex by inactivation of DnaA 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:21708944 Keyamura and Katayama 2011 analyzed DnaA-Hda interaction during regulatory inactivation of DnaA, the E. coli pathway that represses extra initiations.

Mechanism graphs

Hda binds DnaA for RIDA (FUNCTION)

Hda binds DnaA in a protein complex that supports regulatory inactivation of DnaA and thereby suppresses extra replication initiation events.

Subject	Predicate	Object	Evidence
DnaA replication initiation protein	contributes to	DnaA-Hda complex	`GO:1990083` GO:1990083 defines the E. coli complex as being composed of DnaA and Hda.
Hda DnaA-related protein	contributes to	DnaA-Hda complex	`GO:1990083` GO:1990083 defines the E. coli complex as being composed of DnaA and Hda.
DnaA-Hda complex	supports	negative regulation of DNA-templated DNA replication initiation	`GO:1990083` GO:1990083 defines the complex by inactivation of DnaA and prevention of multiple replication initiation events. `PMID:21708944` Keyamura and Katayama 2011 showed that functional DnaA-Hda interactions are needed for regulatory inactivation of DnaA.

Discussions

CURATION_TODO (OPEN): Resolve exact source-neutral DnaA and Hda family groundings for the DnaA-Hda complex. GO:1990083 names DnaA and Hda as the E. coli constituents of the DnaA-Hda complex. Exact source-neutral InterPro, Pfam, NCBIfam or UniProt family CURIEs need narrower curation before these components can be grounded.
INTERPRETATION (RESOLVED): Keep the DnaA-Hda complex distinct from the Hda-beta clamp complex. GO:1990083 denotes the DnaA-Hda complex, whereas GO:1990085 separately denotes Hda bound to the DnaN beta clamp. Keyamura and Katayama 2011 studied DnaA-Hda contacts during RIDA in the context of DNA-loaded clamp-Hda but do not make the beta clamp a required constituent of the GO:1990083 entity.

Evidence

GO:1990083 Gene Ontology cellular-component term for the DnaA-Hda complex.
GO:1990078 OLS reports GO:1990078 replication inhibiting complex as the direct GO:1990083 is-a parent.
GO:1990085 Gene Ontology cellular-component term for the separately scoped Hda-beta clamp complex.
GO:0032297 Gene Ontology biological-process term for negative regulation of DNA-templated DNA replication initiation.
PMID:21708944 PubMed identifier for Keyamura and Katayama 2011, the Journal of Biological Chemistry paper cited by GO:1990083.
DOI:10.1074/jbc.M111.233403 DOI for Keyamura and Katayama 2011, 'DnaA protein DNA-binding domain binds to Hda protein to promote inter-AAA+ domain interaction involved in regulatory inactivation of DnaA', as reported by PubMed.
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

2026-10-01T12:06:54Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-10-01T12:07:51Z codex · EXPANDED_RECORD — Added replication-inhibiting-complex parentage, reviewed-label-only DnaA and Hda components, E. coli RIDA evidence, negative-DNA-replication-initiation function evidence, GO/PubMed/DOI evidence, a nonmechanistic DnaA-Hda regulatory graph, and grounding/boundary discussions.
2026-10-01T12:09:16Z codex · FIX_GRAPH_PREDICATE — Changed the DnaA-Hda graph edge to support the negative-regulation process instead of negatively regulating that process.

Source: data/structures/other/dnaa_hda_complex.yaml