YgfF is a glucose 1-dehydrogenase (EC 1.1.1.47) belonging to the short-chain dehydrogenases/reductases (SDR) family (SDR63C subgroup). It catalyzes the NAD(+)-dependent oxidation of D-glucose to D-glucono-1,5-lactone, which spontaneously hydrolyzes to D-gluconate. The enzymatic function was predicted by the DeepECtransformer deep learning tool (prediction score 0.6331) and experimentally validated in vitro by Kim et al. 2023, who measured a specific activity of 305.55 U/mg, comparable to characterized glucose 1-dehydrogenases from other organisms. Full kinetic parameters (Km, kcat) have not yet been determined. YgfF was one of only three genuinely correct novel predictions (out of 464) made by DeepECtransformer for the E. coli y-ome. The protein contains a conserved NAD(P)-binding Rossmann-fold domain and predicted binding sites for both NAD(+) and D-glucose. A physical interaction with LpdA (dihydrolipoyl dehydrogenase) was detected by affinity purification-mass spectrometry, though the biological significance of this interaction is unclear. The physiological role of YgfF in E. coli metabolism remains to be established.
Summary: YgfF is experimentally confirmed as a glucose 1-dehydrogenase (EC 1.1.1.47), which is a type of oxidoreductase (PMID:37963869). The IBA annotation to oxidoreductase activity is correct but much less specific than what is now known. The more specific term GO:0047934 (glucose 1-dehydrogenase (NAD+) activity) is supported by direct experimental evidence.
Reason: This IBA annotation is consistent with the experimentally validated function of YgfF. While more specific terms exist (and are annotated separately), the IBA at this level is not wrong and reflects phylogenetic inference that is consistent with experimental data. Glucose 1-dehydrogenase activity is a subtype of oxidoreductase activity.
YgfF exhibited a specific glucose 1-dehydrogenase activity of 305.55 U mg−1
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
IEA GO_REF:0000117
ACCEPT
Summary: This IEA annotation from ARBA is consistent with the experimentally validated glucose 1-dehydrogenase activity. Glucose 1-dehydrogenase acts on the CH-OH group of D-glucose, so this intermediate-level annotation is correct. It is less specific than GO:0047934 but appropriately reflects the ARBA computational prediction.
Reason: The term is a correct parent of the experimentally validated specific function (glucose 1-dehydrogenase (NAD+) activity). The IEA evidence code is appropriate for a computationally derived annotation, and the term is consistent with the SDR family classification and the known catalytic mechanism.
Summary: This IEA annotation is derived from Rhea reaction mapping (RHEA:14293), which corresponds to the reaction D-glucose + NAD(+) = D-glucono-1,5-lactone + NADH + H(+). This matches the experimentally validated catalytic activity of YgfF exactly as described by Kim et al. 2023 and annotated by UniProt (PMID:37963869).
Reason: The Rhea-derived IEA correctly captures the specific enzymatic activity of YgfF. This is also independently supported by the IDA annotation from PMID:37963869 using the same GO term.
Summary: This IEA annotation is derived from the EC number mapping (EC:1.1.1.47). GO:0047936 describes glucose 1-dehydrogenase that can use either NAD+ or NADP+ as cofactor. However, the EC number 1.1.1.47 specifically refers to the NAD+-dependent form, and the experimental validation by Kim et al. used an NAD+-dependent assay (PMID:37963869). UniProt annotates the catalytic activity with the Rhea reaction that specifies NAD+ specifically. The more precise term GO:0047934 (NAD+ specific) is the better annotation.
Reason: The EC:1.1.1.47 mapping to GO:0047936 is potentially an overly broad mapping, since EC:1.1.1.47 is the NAD+-dependent glucose 1-dehydrogenase, not the dual-cofactor NAD(P)+ form (which would be EC:1.1.1.119). The experimental data from Kim et al. 2023 validated activity using an NAD+-dependent assay kit, and UniProt annotates the Rhea reaction (RHEA:14293) specifically with NAD+. The NAD+-specific GO term GO:0047934 is more accurate.
IPI PMID:15690043 Interaction network containing conserved and essential prote...
MARK AS OVER ANNOTATED
Summary: This annotation is based on a high-throughput affinity purification-mass spectrometry study by Butland et al. 2005 that detected a physical interaction between YgfF and LpdA (dihydrolipoyl dehydrogenase, P0A9P0). The interaction is recorded in IntAct with 2 experiments supporting it. However, the GO term GO:0005515 (protein binding) is uninformative per curation guidelines and does not convey any specific functional information about this interaction.
Reason: Per curation guidelines, GO:0005515 (protein binding) is too vague and uninformative. The Butland et al. 2005 study was a large-scale screen that detected many interactions, and the biological significance of the YgfF-LpdA interaction is unknown. LpdA functions in the pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes, and there is no clear functional connection to glucose 1-dehydrogenase activity. Without understanding the functional nature of this interaction, a generic protein binding annotation provides little value.
no large-scale analysis of protein complexes in Escherichia coli has yet been reported. To this end, we have targeted DNA cassettes into the E. coli chromosome to create carboxy-terminal, affinity-tagged alleles of 1,000 open reading frames
IDA PMID:37963869 Functional annotation of enzyme-encoding genes using deep le...
ACCEPT
Summary: This is the key experimentally validated annotation. Kim et al. 2023 expressed and purified recombinant His-tagged YgfF from E. coli BL21(DE3) and measured glucose 1-dehydrogenase activity in vitro using a colorimetric GDH assay kit. The specific activity was 305.55 U/mg, comparable to the previously reported value of 205.70 U/mg for glucose 1-dehydrogenase from Lysinibacillus sphaericus. The activity was predicted by DeepECtransformer with EC number EC:1.1.1.47 and confirmed by the enzyme assay. This represents a validated core function.
Reason: Direct experimental evidence from in vitro enzyme assay demonstrates glucose 1-dehydrogenase (NAD+) activity. The specific activity (305.55 U/mg) is robust and comparable to characterized homologs. This is the most specific and well-supported annotation for YgfF. UniProt has adopted this function based on this study (EC:1.1.1.47).
For YgfF, DeepECtransformer predicted its EC number to be EC:1.1.1.47 (glucose 1-dehydrogenase). The enzyme assay results showed that YgfF exhibited a specific glucose 1-dehydrogenase activity of 305.55 U mg−1
which was comparable to the previously reported value of 205.70 U mg−1 for the glucose 1-dehydrogenase from Lysinibacillus sphaericus G10
file:ECOLI/ygfF/ygfF-deep-research-falcon.md
Falcon deep research confirms YgfF as EC 1.1.1.47 glucose 1-dehydrogenase validated by in vitro assay with 305.55 U/mg specific activity, and notes SDR63C subgroup classification supports this assignment.
IDA PMID:37963869 Functional annotation of enzyme-encoding genes using deep le...
NEW
Summary: YgfF requires NAD+ as a cofactor for its glucose 1-dehydrogenase activity. The catalytic reaction (D-glucose + NAD(+) = D-glucono-1,5-lactone + NADH + H(+)) directly involves NAD+ binding. UniProt annotates extensive NAD+ binding residues (positions 11, 13, 59, 60, 86, 88, 110, 156, 160, 189, 191, 194) based on similarity to characterized SDR family members. The in vitro enzyme assay demonstrating NAD+-dependent glucose oxidation provides experimental evidence for NAD binding.
Reason: The experimentally validated glucose 1-dehydrogenase activity requires NAD+ as a cofactor, and UniProt annotates multiple NAD+ binding residues. NAD binding is an inherent aspect of the catalytic mechanism and should be annotated. This is not currently present in the GO annotations.
For YgfF, DeepECtransformer predicted its EC number to be EC:1.1.1.47 (glucose 1-dehydrogenase). The enzyme assay results showed that YgfF exhibited a specific glucose 1-dehydrogenase activity of 305.55 U mg−1
IDA PMID:37963869 Functional annotation of enzyme-encoding genes using deep le...
NEW
Summary: YgfF catalyzes the oxidation of D-glucose to D-glucono-1,5-lactone, which spontaneously hydrolyzes to D-gluconate. This places YgfF as a participant in D-gluconate metabolism. No biological process annotations currently exist for YgfF, yet the experimentally validated enzymatic activity directly implicates it in this metabolic pathway. However, the in vivo physiological role has not been established, so this annotation should be considered with caution.
Reason: There are currently no biological process annotations for YgfF, which is a significant gap. The experimentally validated glucose 1-dehydrogenase activity produces D-glucono-1,5-lactone (a precursor to D-gluconate), directly linking YgfF to D-gluconate metabolic process. UniProt states the protein catalyzes the NAD(+)-dependent oxidation of D-glucose to D-gluconate via gluconolactone.
IDA PMID:37963869 Functional annotation of enzyme-encoding genes using deep le...
NEW
Summary: YgfF was expressed as a soluble protein and purified from the cytosolic fraction (supernatant after cell lysis and centrifugation) by Kim et al. 2023. The protein was predicted to be soluble by NetSolP and was successfully purified from the soluble fraction. While there are no dedicated localization studies, the solubility data and lack of any signal peptide or transmembrane domain strongly suggest cytosolic localization. No cellular component annotations currently exist for YgfF.
Reason: There are currently no cellular component annotations for YgfF, which is a gap. The protein was purified from the soluble cytoplasmic fraction and has no predicted signal peptide or transmembrane domains, consistent with cytosolic localization. However, the evidence is indirect (protein was soluble when overexpressed) rather than from a dedicated localization study.
Cell debris was separated by centrifugation at 15,044 × g for 40 min, and the resulting supernatants were loaded onto Talon metal affinity resin
Core Functions
NAD(+)-dependent glucose 1-dehydrogenase activity. YgfF catalyzes the oxidation of D-glucose to D-glucono-1,5-lactone using NAD+ as the electron acceptor. This is the sole experimentally validated enzymatic function, demonstrated by in vitro assay with a specific activity of 305.55 U/mg (PMID:37963869). YgfF belongs to the SDR family (SDR63C subgroup) and contains a conserved NAD(P)-binding Rossmann-fold domain.
For YgfF, DeepECtransformer predicted its EC number to be EC:1.1.1.47 (glucose 1-dehydrogenase). The enzyme assay results showed that YgfF exhibited a specific glucose 1-dehydrogenase activity of 305.55 U mg−1
Q: What is the physiological role of YgfF glucose 1-dehydrogenase activity in E. coli K-12 metabolism? Is it involved in glucose catabolism via the Entner-Doudoroff pathway or another metabolic route?
Suggested experts: Lee SY, Kim GB
Q: What is the biological significance of the YgfF-LpdA physical interaction detected by Butland et al. 2005? Does YgfF participate in a metabolic complex with pyruvate dehydrogenase components?
Suggested experts: Emili A, Butland G
Q: Does YgfF have any activity with NADP+ as cofactor, or is it strictly NAD+-dependent? The current annotations include both NAD+ and NAD(P)+ terms.
Suggested experts: Kim GB, Lee SY
Suggested Experiments
Experiment: Construct a ygfF knockout in E. coli K-12 and test growth phenotypes on minimal media with glucose as the sole carbon source under aerobic and anaerobic conditions. Compare with wild-type to determine if YgfF contributes to glucose utilization in vivo.
Hypothesis: YgfF deletion affects growth on glucose as sole carbon source under specific metabolic conditions.
Type: growth phenotype assay
Experiment: Perform in vitro enzyme assays with purified YgfF using NADP+ instead of NAD+ as the cofactor to determine cofactor specificity. This would resolve whether GO:0047936 (NAD(P)+ form) or GO:0047934 (NAD+ specific) is the correct annotation.
Hypothesis: YgfF is NAD+-specific and does not use NADP+ as an electron acceptor.
Type: enzyme kinetics
Experiment: Perform co-purification experiments with tagged YgfF under physiological expression levels and test whether LpdA affects YgfF enzymatic activity in vitro. Also test if ygfF deletion affects pyruvate dehydrogenase complex activity.
Hypothesis: The YgfF-LpdA interaction has functional significance in glucose metabolism.
Type: protein interaction validation
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
YgfF DeepECTF prediction review. The DeepECTF prediction of glucose 1-dehydrogenase (EC 1.1.1.47) is a successful prediction, validated by SDR nomenclature classification (SDR63C subgroup) and consistent with published biochemical data.
Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.
Review rationale: Correct prediction. YgfF belongs to the SDR63C/Glucose 1-dehydrogenase subgroup of the SDR superfamily (IPR002347), as classified by the Oppermann/Persson HMM-based nomenclature system. The DeepECTF prediction matches this classification and was validated by in vitro assay. However, the actual in vivo substrate is NAD+ not NADP+, and the physiological substrate may be D-gluconate rather than glucose.
Supporting Evidence:
PMID:40703034: "YgfF is a member of the large short-chain dehydrogenase/reductase (SDR) superfamily (IPR002347)...This resource predicts YgfF is part of the SDR63C/Glucose 1-dehydrogenase subgroup, the activity predicted and validated in the Kim et al. (2023) study. This prediction demonstrates the accurate propagation of functional annotation and is a successful prediction."