id: Q88I83 gene_symbol: imuB taxon: id: NCBITaxon:160488 label: Pseudomonas putida KT2440 status: COMPLETE locus_tag: PP_3118 description: >- NCBI PGAP names WP_010954010.1 "Y-family DNA polymerase" from the SPARCLE CDD domain architecture 10131054 (a single PolY_like domain, cd03468) and passes on EC 2.7.7.7 and five GO terms: damaged DNA binding, DNA-directed DNA polymerase activity, metal ion binding, DNA replication and DNA repair. ImuB keeps the Y-family polymerase fold but has lost the active-site carboxylates; in the characterized mycobacterial system it is a polymerase-inactive adaptor that links ImuA and the catalytic DnaE2/ImuC to the beta clamp. In the KT2440 sequence every CDD-annotated active-site position carries a non-acidic residue except one. The polymerase activity, the EC number and the metal ion binding are therefore wrong (pseudoenzyme over-annotation). DNA replication and DNA repair are broad processes that the main review refines to translesion synthesis, and damaged DNA binding is unverified for ImuB. The error lies on the architecture: a bare PolY_like architecture cannot distinguish active Y-family polymerases from ImuB, so the product name and GO reach every ImuB with it. references: - id: PMID:33270901 title: 'RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation.' - id: PMID:20615954 title: Essential roles for imuA'- and imuB-encoded accessory factors in DnaE2-dependent mutagenesis in Mycobacterium tuberculosis. - id: PMID:28118378 title: DNA Polymerases ImuC and DinB Are Involved in DNA Alkylation Damage Tolerance in Pseudomonas aeruginosa and Pseudomonas putida. - id: PMID:17331811 title: Study of involvement of ImuB and DnaE2 in stationary-phase mutagenesis in Pseudomonas putida. - id: file:PSEPK/imuB/imuB-pgap-prediction-evidence/WP_010954010.1.gp title: RefSeq GenPept record WP_010954010.1 - id: file:PSEPK/imuB/imuB-pgap-prediction-evidence/pgap_models.yaml title: PGAP naming model and matched NCBI HMMs for imuB source_documents: - genes/PSEPK/imuB/imuB-pgap-prediction-evidence/WP_010954010.1.gp - genes/PSEPK/imuB/imuB-pgap-prediction-evidence/pgap_models.yaml predictions: - source_method: NCBI PGAP source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: GO:0003684 label: damaged DNA binding predicted_term_type: GO_MF review: assessment: UNC confidence_score: 1 summary: >- Uncertain. The term is inherited from active Y-family polymerases, which bind lesion-containing primer-template DNA in their catalytic cleft. The CDD annotation maps a DNA-binding site onto ImuB, but no study has shown that ImuB binds DNA, damaged or otherwise; the characterized interactions are protein-protein (ImuA, DnaE2 and the beta clamp). In the mycobacterial mutasome the predicted DNA-binding component is ImuA', not ImuB. Neither in GOA nor proposed in the main review. supported_by: - reference_id: PMID:20615954 supporting_text: "a putative polymerase-inactive Y-family homolog that binds β as well as the other cassette components, and a predicted DNA-binding protein" - source_method: NCBI PGAP source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: GO:0003887 label: DNA-directed DNA polymerase activity predicted_term_type: GO_MF review: assessment: NPI confidence_score: 0 error_type: PSEUDOENZYME_OVERANNOTATION summary: >- Wrong. ImuB homologs keep the Y-family fold but lack the active-site carboxylates that coordinate the catalytic metals. In the GenPept record, the CDD active-site positions (7-8, 11-12, 44, 47, 101-102, 154) carry L, L, L, A, P, A, R, A and D in the KT2440 sequence: only one acidic residue remains and the two-metal palm carboxylates are gone. In the ImuA-ImuB-DnaE2 cassette, DNA synthesis is done by DnaE2/ImuC, and ImuB is the polymerase-inactive adaptor (main review core function: protein-macromolecule adaptor activity). The SPARCLE architecture is a single PolY_like domain shared with active polymerases, so it cannot separate ImuB from them. supported_by: - reference_id: PMID:20615954 supporting_text: "Despite retaining structural features characteristic of Y-family members, ImuB homologs lack conserved active-site amino acids required for polymerase activity." - reference_id: PMID:20615954 supporting_text: "However, the absence of active-site carboxylates appears incompatible with catalytic function in ImuB" - reference_id: PMID:28118378 supporting_text: "ImuB lacks catalytic residues essential for polymerase activities, but possesses β-clamp-binding motif." - source_method: NCBI PGAP source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: GO:0046872 label: metal ion binding predicted_term_type: GO_MF review: assessment: NPI confidence_score: 0 error_type: PSEUDOENZYME_OVERANNOTATION summary: >- Not supported. In Y-family polymerases, metal ion binding is the coordination of the two catalytic Mg2+/Mn2+ ions by the active-site carboxylates. ImuB has lost those carboxylates, so the basis for the prediction is absent; no other metal site is known in ImuB. The term follows from the same pseudoenzyme over-annotation as the polymerase activity. supported_by: - reference_id: PMID:20615954 supporting_text: "However, the absence of active-site carboxylates appears incompatible with catalytic function in ImuB" - source_method: NCBI PGAP source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: GO:0006260 label: DNA replication predicted_term_type: GO_BP review: assessment: LSP confidence_score: 2 summary: >- Broadly true but less precise. ImuB takes part in damage-induced, DnaE2-dependent translesion synthesis, which the main review proposes as GO:0019985; in GO, translesion synthesis is part of DNA replication, so this term is an ancestor of the specific process. It is not in GOA. ImuB takes part in replication only through lesion bypass, not in normal replicative synthesis. supported_by: - reference_id: PMID:28118378 supporting_text: "Therefore, the study in Mycobacterium tuberculosis suggested that ImuB mediates the access of the cassette components to the replication fork through interaction with the β-clamp [46]." - reference_id: PMID:17331811 supporting_text: "accumulation of stationary-phase mutants up to two-fold." - source_method: NCBI PGAP source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: GO:0006281 label: DNA repair predicted_term_type: GO_BP review: assessment: LSP confidence_score: 2 summary: >- In GOA (InterPro IEA), where the main review MODIFIES it to translesion synthesis (GO:0019985) on the grounds that ImuB is an accessory of error-prone lesion bypass rather than a repair enzyme. Scored as less precise for consistency with that action. Strictly, the refinement is lateral rather than a descendant: in GO, translesion synthesis falls under DNA damage tolerance and DNA replication, not DNA repair, because bypass tolerates the lesion rather than removing it. The damage-response context is right; ImuB contributes to alkylation damage tolerance in P. putida. supported_by: - reference_id: PMID:28118378 supporting_text: "This cassette encodes an in silico predicted SulA/RecA like DNA-binding protein ImuA, a nonfunctional homolog of Y-family DNA polymerases ImuB and an error-prone TLS DNA polymerase DnaE2 (later ImuC) [42–45]." - source_method: NCBI PGAP source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: EC:2.7.7.7 label: EC 2.7.7.7 predicted_term_type: EC review: assessment: NPI confidence_score: 0 error_type: PSEUDOENZYME_OVERANNOTATION summary: >- Wrong, for the same reason as GO:0003887: EC 2.7.7.7 (DNA-directed DNA polymerase) requires the catalytic carboxylates that ImuB lacks. The UniProt entry carries no EC number. supported_by: - reference_id: PMID:20615954 supporting_text: "Despite retaining structural features characteristic of Y-family members, ImuB homologs lack conserved active-site amino acids required for polymerase activity."