id: P10378 gene_symbol: entE taxon: id: NCBITaxon:83333 label: Escherichia coli K-12 status: COMPLETE locus_tag: b0594 description: >- NCBI PGAP names WP_000026812.1 "(2,3-dihydroxybenzoyl)adenylate synthase EntE" from BlastRule NBR012093 and assigns three EC numbers (2.5.1.-, 6.2.1.71, 6.3.2.14) but no GO terms. The GO gap comes from how PGAP propagates GO: it passes on GO only from the model that names the protein, and NBR012093 carries none. EntE also matches two equivalog HMMs with the same product name, NF008192 and TIGR02275, and both carry GO:0008668 (2,3-dihydroxybenzoate--[aryl-carrier protein] ligase activity) and GO:0019290 (siderophore biosynthetic process). Because a BlastRule outranks them for naming, their GO is discarded, so PGAP omits EntE's core molecular function. GOA supports that function with five EXP annotations and one IDA annotation. Judged against the literature, EC 6.2.1.71 is exactly EntE's activity: ATP-dependent adenylation of 2,3-dihydroxybenzoate (DHB) and transfer onto holo-EntB ArCP. EC 6.3.2.14, the overall enterobactin synthase reaction, is defensible only as a component-level assignment, since EntF forms the amide and ester bonds; UniProt makes the same assignment. EC 2.5.1.- (transferase of alkyl or aryl groups other than methyl) is not supported. DHB transfer onto the phosphopantetheine thiol is an aroyl (acyl) transfer, and it is the second half-reaction of EC 6.2.1.71, not a separate alkyl/aryl-transferase activity. source_documents: - genes/ECOLI/entE/entE-pgap-prediction-evidence/WP_000026812.1.gp - genes/ECOLI/entE/entE-pgap-prediction-evidence/pgap_models.yaml references: - id: PMID:33270901 title: 'RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation.' - id: PMID:9214294 title: 'Enterobactin biosynthesis in Escherichia coli: isochorismate lyase (EntB) is a bifunctional enzyme that is phosphopantetheinylated by EntD and then acylated by EntE using ATP and 2,3-dihydroxybenzoate.' - id: PMID:9485415 title: Reconstitution and characterization of the Escherichia coli enterobactin synthetase from EntB, EntE, and EntF. - id: PMID:20359185 title: Kinetic and inhibition studies of dihydroxybenzoate-AMP ligase from Escherichia coli. - id: file:ECOLI/entE/entE-uniprot.txt title: entE-uniprot.txt - id: file:ECOLI/entE/entE-pgap-prediction-evidence/WP_000026812.1.gp title: WP_000026812.1.gp - id: file:ECOLI/entE/entE-pgap-prediction-evidence/pgap_models.yaml title: pgap_models.yaml predictions: - source_method: NCBI PGAP source_version: current WP_ records (wp); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: EC:2.5.1.- label: EC 2.5.1.- predicted_term_type: EC review: assessment: NPI confidence_score: 0 error_type: CURATION_MISTAKE summary: >- EC 2.5.1 covers transfer of alkyl or aryl groups other than methyl. EntE has no such activity. Its second half-reaction moves the 2,3-dihydroxybenzoyl group from DHB-AMP onto the phosphopantetheine thiol of holo-EntB. That is an aroyl (acyl) transfer, which UniProt records as "S-dihydroxybenzoyltransferase" kinetics with no EC number, and it is already part of the EC 6.2.1.71 overall reaction. The EC 2.5.1.- assignment looks like an outdated or misclassified label for that half-reaction, carried by the naming BlastRule. Its exact provenance is not recorded in the evidence files. It should be dropped, not replaced. supported_by: - reference_id: file:ECOLI/entE/entE-pgap-prediction-evidence/WP_000026812.1.gp supporting_text: /EC_number="2.5.1.-" - reference_id: PMID:9214294 supporting_text: This holo-EntB is then acylated with 2,3-DHB in a reaction catalyzed by EntE, previously described as the 2,3-DHB-AMP ligase, with a kcat of 100 min-1 - reference_id: file:ECOLI/entE/entE-uniprot.txt supporting_text: Reaction=2,3-dihydroxybenzoyl-5'-AMP + holo-[ACP] = 2,3- - source_method: NCBI PGAP source_version: current WP_ records (wp); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: EC:6.2.1.71 label: EC 6.2.1.71 predicted_term_type: EC review: assessment: CNN confidence_score: 2 summary: >- Correct. EC 6.2.1.71 (2,3-dihydroxybenzoate--[aryl-carrier protein] ligase) is EntE's experimentally established activity: ATP-dependent adenylation of DHB and transfer of the DHB moiety onto the phosphopantetheine of holo-EntB ArCP. The equivalog HMMs NF008192 and TIGR02275 carry the same EC. UniProt already holds it with experimental evidence, and GOA holds the corresponding GO:0008668, so the prediction is correct but not novel. PGAP misses the matching GO term only because the naming BlastRule has no GO. supported_by: - reference_id: file:ECOLI/entE/entE-pgap-prediction-evidence/WP_000026812.1.gp supporting_text: /EC_number="6.2.1.71" - reference_id: file:ECOLI/entE/entE-pgap-prediction-evidence/pgap_models.yaml supporting_text: 'model: TIGR02275' - reference_id: PMID:20359185 supporting_text: 'Belonging to the family of aryl acid adenylating enzymes (AAAE), EntE is characterized by a two-step adenylation/ligation reaction: first, the enzyme catalyzes the condensation of DHB and ATP to form an adenylate intermediate, followed by the ligation of DHB onto the phosphopantetheinylated cofactor that is bound to the ArCP of EntB' - source_method: NCBI PGAP source_version: current WP_ records (wp); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: EC:6.3.2.14 label: EC 6.3.2.14 predicted_term_type: EC review: assessment: CNN confidence_score: 2 summary: >- Defensible as a component-level assignment, not as EntE's own catalytic activity. EC 6.3.2.14 (enterobactin synthase) is the overall reaction 3 DHB + 3 L-serine + 6 ATP -> enterobactin, carried out jointly by EntB, EntD, EntE and EntF. EntF makes the amide and ester bonds, using the DHB-loaded holo-EntB that EntE produces. UniProt follows a component-level convention here: it assigns the synthase EC 6.3.2.14 to each component of the system, EntE included, citing experimental evidence. The PGAP prediction therefore matches the existing record under that convention, but it should not be read as EntE catalysing the full reaction by itself. For GO, this reaction is better represented on EntE by GO:0008668 than by GO:0047527. supported_by: - reference_id: file:ECOLI/entE/entE-pgap-prediction-evidence/WP_000026812.1.gp supporting_text: /EC_number="6.3.2.14" - reference_id: PMID:9485415 supporting_text: The holo-EntF monomer acts as the catalyst for the formation of the three amide and three ester bonds in enterobactin using ATP, L-serine, and acyl-holo-EntB, acylated with 2,3-dihydroxybenzoate by EntE, as substrates