uvrB

Gene Description

UvrB is the central DNA damage-verification subunit of the bacterial UvrABC nucleotide excision repair (NER) system, which removes a structurally diverse range of helix-distorting DNA lesions such as bulky adducts and UV-induced photoproducts. UvrB is an ATP-dependent superfamily-2 (SF2) helicase-family protein containing tandem RecA-like helicase domains, a P-loop ATP-binding site, a characteristic damage-sensing beta-hairpin, and a C-terminal UVR domain that mediates interactions with partner Uvr proteins. Within NER, the UvrA(2)B(2) complex scans DNA for abnormalities; ATP-dependent wrapping of DNA around a UvrB monomer locally melts the duplex and inserts the UvrB beta-hairpin between the strands so that UvrB can probe one strand for a lesion. When a lesion is verified, UvrA dissociates and a stable UvrB-DNA pre-incision complex forms, which then recruits the UvrC endonuclease for dual incision flanking the lesion. UvrB acts in the cytoplasm on chromosomal DNA and is a core component of the cellular response to DNA damage, including the SOS response.

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0003677 DNA binding	IEA GO_REF:0000120	MODIFY	Summary: UvrB binds DNA as part of damage scanning and pre-incision complex formation; its beta-hairpin motif inserts between DNA strands for lesion probing. Reason: DNA binding is genuine, but GO:0003684 captures UvrB's lesion-verification substrate specificity more precisely. Proposed replacements: damaged DNA binding Supporting Evidence: file:PSEPK/uvrB/uvrB-uniprot.txt probes one DNA strand for the presence of a lesion.
GO:0005524 ATP binding	IEA GO_REF:0000120	ACCEPT	Summary: UvrB possesses a P-loop (Walker A) ATP-binding site (residues 38-45); ATP binding drives DNA wrapping and helix melting required for lesion verification. Reason: ATP binding is intrinsic to the SF2 helicase fold of UvrB and is supported by the conserved Walker A motif annotated in the UniProt record. Core molecular function.
GO:0005737 cytoplasm	IEA GO_REF:0000120	ACCEPT	Summary: UvrB acts on chromosomal DNA in the bacterial cytoplasm/nucleoid. Reason: Consistent with UniProt subcellular location (Cytoplasm) and the biology of a cytoplasmic DNA repair protein in a bacterium lacking a nucleus.
GO:0006281 DNA repair	IEA GO_REF:0000104	KEEP AS NON CORE	Summary: UvrB is a core DNA repair protein acting in nucleotide excision repair. Reason: Correct but general. The more specific child term GO:0006289 (nucleotide-excision repair) is also annotated and better captures the precise role, so this broad parent is retained as non-core context rather than as the representative core function.
GO:0006289 nucleotide-excision repair	IEA GO_REF:0000120	ACCEPT	Summary: UvrB is the damage-verification subunit of the UvrABC excinuclease, central to bacterial nucleotide excision repair. Reason: This is the core biological process of UvrB, strongly supported by family conservation and the UvrB HAMAP rule. Captures the precise role of the gene.
GO:0009380 excinuclease repair complex	IEA GO_REF:0000002	ACCEPT	Summary: UvrB forms a heterotetramer (UvrA2B2) with UvrA during lesion scanning and interacts with UvrC in the incision complex. Reason: Accurately reflects UvrB's role as a component of the UvrABC excinuclease complex; supported by the UniProt SUBUNIT annotation. Core cellular component.
GO:0009381 excinuclease ABC activity	IEA GO_REF:0000104	MARK AS OVER ANNOTATED	Summary: GO:0009381 describes the dual-incision chemistry of the assembled UvrABC system; UvrB verifies the lesion and forms the preincision complex rather than independently catalyzing incision. Reason: The term is meaningful only as a contribution to the UvrABC complex. The `enables` qualifier overstates UvrB's individual activity because UvrC supplies the endonuclease chemistry. Supporting Evidence: file:PSEPK/uvrB/uvrB-uniprot.txt Interacts with UvrC in an incision complex.
GO:0009432 SOS response	IEA GO_REF:0000104	KEEP AS NON CORE	Summary: uvrB is part of the bacterial DNA-damage/SOS regulon in many bacteria, contributing to the cellular response to DNA damage. Reason: In E. coli uvrB is SOS-inducible (LexA-regulated), and this electronic annotation is propagated by the UvrB UniRule. However, SOS regulation is not universal among bacteria (notably reported as not SOS-regulated in some Pseudomonas species), and it reflects regulatory context rather than UvrB's core molecular/repair function. Retained as non-core.
GO:0016787 hydrolase activity	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: Very general hydrolase parent term; UvrB's relevant hydrolase activity is ATP hydrolysis. Reason: GO:0016787 is an uninformative high-level parent of the more specific and also-annotated GO:0016887 (ATP hydrolysis activity). It adds no functional specificity beyond the ATPase annotation.
GO:0016887 ATP hydrolysis activity	IEA GO_REF:0000002	ACCEPT	Summary: UvrB hydrolyzes ATP via its SF2 helicase ATPase machinery; ATP hydrolysis is essential for forming the UvrB-DNA pre-incision complex. Reason: ATP hydrolysis (ATPase activity) is a well-established core molecular function of UvrB, supported by the conserved helicase motifs and Walker A/B-containing helicase ATP-binding domain.

Gene Description

Existing Annotations Review

Core Functions

UvrB is the DNA damage-verification subunit of the bacterial UvrABC excinuclease, using ATP-dependent helicase/ATPase activity to engage and probe DNA and form a stable pre-incision complex at helix-distorting lesions.

ATP-dependent DNA engagement, with ATP binding and hydrolysis driving DNA wrapping, local duplex melting, and insertion of the damage-sensing beta-hairpin for lesion probing.

References

Deep Research

Falcon

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