Gene Description

LigA is the essential bacterial NAD-dependent DNA ligase. It uses NAD to adenylate and seal phosphodiester nicks between adjacent 5'-phosphate and 3'-hydroxyl DNA ends, completing Okazaki-fragment maturation during chromosome replication and also sealing intermediates generated during DNA repair.

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0003677 DNA binding	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: Correct substrate-binding property of DNA ligase. Reason: LigA recognizes nicked duplex DNA through multiple DNA-binding domains before phosphodiester-bond formation.
GO:0003911 DNA ligase (NAD+) activity	IEA GO_REF:0000120	ACCEPT	Summary: Correct core catalytic activity with the appropriate bacterial NAD cofactor specificity. Reason: The reviewed UniProt record gives the NAD-dependent nick-sealing reaction and EC 6.5.1.2.
GO:0005829 cytosol	IEA GO_REF:0000118	ACCEPT	Summary: Appropriate localization for an intracellular bacterial DNA ligase. Reason: LigA acts on chromosomal DNA in the cytosol/nucleoid and has no secretion or membrane-targeting features.
GO:0006259 DNA metabolic process	IEA GO_REF:0000104	MARK AS OVER ANNOTATED	Summary: True but too broad relative to replication and repair. Reason: The specific DNA replication and DNA repair annotations better define the biological settings for nick sealing.
GO:0006260 DNA replication	IEA GO_REF:0000002	ACCEPT	Summary: Correct core process annotation. Reason: LigA seals nicks left during lagging-strand maturation and is essential for chromosome replication.
GO:0006281 DNA repair	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: Correct secondary biological role outside the focused replication module. Reason: The reviewed UniProt record supports DNA repair as a genuine LigA role, while Okazaki-fragment sealing is the core module function.

Core Functions

NAD-dependent sealing of phosphodiester nicks during lagging-strand maturation in bacterial chromosome replication.

Molecular Function:

DNA ligase (NAD+) activity

Directly Involved In:

DNA replication

Cellular Locations:

cytosol

References

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📚 Additional Documentation

Notes

(ligA-notes.md)

ligA curation notes

Annotation-reviewer pass (2026-09-01)

Consulted the annotation-reviewer workflow against all 6 current GOA rows and reviewed UniProt Q88F25. Accepted NAD-dependent DNA ligase activity, cytosolic localization, and DNA replication; retained generic DNA binding as non-core. Kept DNA repair as a genuine non-core role outside the focused replication boundary and marked generic DNA metabolism as over-annotated. No GOA row remains pending.

ligA