D-ribose pyranase (EC 5.4.99.62) that catalyzes the interconversion of beta-D-ribopyranose and beta-D-ribofuranose. This enzyme was originally misidentified as a high-affinity ribose transport protein based on its genomic location in the rbs operon, but NMR studies (PMID:15060078) definitively demonstrated its enzymatic function as a pyranase. The enzyme also catalyzes the conversion between beta-allofuranose and beta-allopyranose. RbsD forms a homodecameric toroidal structure with active sites formed at the interface between adjacent subunits. The catalytic mechanism involves His-20 as a proton donor. This enzyme is essential for D-ribose catabolism, converting the pyranose form of ribose (which enters the cell via the RbsB transporter) into the furanose form that can be phosphorylated by ribokinase (RbsK) for entry into the pentose phosphate pathway [file:ECOLI/rbsD/rbsD-deep-research-falcon.md].
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0019303 D-ribose catabolic process | IMP PMID:15060078 NMR application probes a novel and ubiquitous family of enzy... | ACCEPT | Summary: RbsD functions in the D-ribose degradation pathway, converting beta-D-ribopyranose (the form that enters the cell) to beta-D-ribofuranose, which can then be phosphorylated by ribokinase for entry into the pentose phosphate pathway [file:ECOLI/rbsD/rbsD-deep-research-falcon.md]. Reason: This accurately describes the biological process context for RbsD function. The enzyme performs step 1 of 2 in the pathway from beta-D-ribopyranose to D-ribose 5-phosphate (UniPathway UPA00916). This is the core biological process for this enzyme. Supporting Evidence: file:ECOLI/rbsD/rbsD-deep-research-falcon.md This reaction facilitates efficient phosphorylation by ribokinase (RbsK), which produces D-ribose-5-phosphate for entry into central metabolism |
| GO:0016853 isomerase activity | IEA GO_REF:0000120 | MODIFY | Summary: This is the top-level isomerase activity term, representing EC class 5. D-ribose pyranase is indeed an isomerase (EC 5.4.99.62). Reason: Isomerase activity is correct but general; refine to D-ribose pyranase activity (GO:0062193), already on this gene by IDA. Proposed replacements: D-ribose pyranase activity |
| GO:0016866 intramolecular transferase activity | IBA GO_REF:0000033 | MODIFY | Summary: Phylogenetically-inferred annotation for the parent term of D-ribose pyranase activity. EC 5.4.99.62 belongs to the EC 5.4 class (intramolecular transferases), making this parent term appropriate. Reason: Intramolecular transferase activity is correct but general; refine to D-ribose pyranase activity (GO:0062193), already on this gene by IDA. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002208836 · PANTHER:PTN002208836 SUPPORTS TRANSFER The node transfers a true but generic EC 5.4 parent; the specific pyranase activity is carried on this gene by IDA. UniProtKB:P04982 · RbsD SUPPORTS TRANSFER RbsD's own experimental pyranase evidence is valid descendant evidence for the node, not circular. Proposed replacements: D-ribose pyranase activity |
| GO:0016872 intramolecular lyase activity | IEA GO_REF:0000120 | REMOVE | Summary: This IEA annotation from UniRule maps to intramolecular lyase activity. However, this is enzymatically inconsistent with the correct EC classification. Reason: This annotation appears to be INCORRECT. D-ribose pyranase (EC 5.4.99.62) is classified under EC 5.4 (intramolecular transferases), NOT EC 4.x (lyases). The GO term GO:0016872 (intramolecular lyase activity) describes "catalysis of certain rearrangements of a molecule to break or form a ring" which superficially sounds similar, but the enzyme is definitively an intramolecular transferase per IUBMB/ExpaSy classification. The correct parent term is GO:0016866 (intramolecular transferase activity), as correctly captured by the IBA annotation. This UniRule mapping should be corrected. |
| GO:0042802 identical protein binding | IDA PMID:16731978 Stepwise disassembly and apparent nonstepwise reassembly for... | ACCEPT | Summary: This annotation reflects the homodecameric quaternary structure of RbsD, as characterized by Feng et al. (2006) studying the stepwise assembly/disassembly of the oligomer [PMID:16731978]. Kim et al. (2003) also demonstrated the decameric structure crystallographically [PMID:12738765]. Reason: The homodecameric structure is well-established by both crystallographic and biochemical studies. This self-association is required for enzymatic activity, as active sites are formed at interfaces between subunits. This represents a core structural feature of the functional enzyme. |
| GO:0048029 monosaccharide binding | IEA GO_REF:0000002 | ACCEPT | Summary: This annotation reflects the substrate binding capability of RbsD for D-ribose (a monosaccharide). The enzyme must bind its substrate to catalyze the pyranose-to-furanose conversion. Reason: As an enzyme that acts on D-ribose, RbsD necessarily binds monosaccharides. The UniProt entry documents substrate binding residues at positions 28, 106, and 128-130. This annotation is consistent with the catalytic function and supported by structural data. |
| GO:0062193 D-ribose pyranase activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation based on EC number 5.4.99.62. This correctly maps the enzyme classification to the GO term for D-ribose pyranase activity. Reason: This IEA annotation is redundant with the IDA annotation from PMID:15060078 but correctly captures the core function via EC number mapping. The EC classification 5.4.99.62 accurately reflects the experimentally determined activity. |
| GO:0062193 D-ribose pyranase activity | IDA PMID:15060078 NMR application probes a novel and ubiquitous family of enzy... | ACCEPT | Summary: This is the core enzymatic function of RbsD, definitively established by Ryu et al. (2004) using NMR spectroscopy. The paper demonstrated that RbsD catalyzes the interconversion of beta-D-ribopyranose and beta-D-ribofuranose, correcting the earlier misidentification as a ribose transport protein [file:ECOLI/rbsD/rbsD-deep-research-falcon.md]. Reason: This annotation represents the primary, experimentally validated molecular function of RbsD. The NMR-based evidence from PMID:15060078 directly demonstrated pyranase activity, and mutagenesis of the catalytic His-20 residue abolished activity. This is the core evolved function of this enzyme. Supporting Evidence: file:ECOLI/rbsD/rbsD-deep-research-falcon.md RbsD is a D-ribose pyranase (EC 5.4.99.62), commonly referred to as a ribose mutarotase, catalyzing interconversion between the beta-pyranose and beta-furanose forms of D-ribose |
| GO:0005996 monosaccharide metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: This is a general parent term for monosaccharide metabolism. D-ribose catabolism is a child of this process. Reason: Monosaccharide metabolic process is correct but general; refine to D-ribose catabolic process (GO:0019303), already on this gene by IMP. Proposed replacements: D-ribose catabolic process |
| GO:0019303 D-ribose catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically-inferred annotation for D-ribose catabolic process, consistent with the experimental IMP annotation. Reason: This IBA annotation is consistent with the IMP annotation from PMID:15060078 and reflects the conserved function of RbsD family members across bacteria. |
| GO:0019303 D-ribose catabolic process | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation based on UniPathway mapping to the D-ribose degradation pathway. Reason: This correctly maps the enzyme to the D-ribose catabolic process based on its role in the UniPathway D-ribose degradation pathway (UPA00916), consistent with experimental evidence. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically-inferred cytosol localization, consistent with the IDA annotation. Reason: This IBA annotation is consistent with the experimental IDA annotation and reflects conserved cytoplasmic localization across the RbsD family. |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | MODIFY | Summary: This IEA annotation for cytoplasm is based on UniProt subcellular location annotation. Cytoplasm is the parent term of cytosol. Reason: Cytoplasm is correct but general; the gene carries cytosol (GO:0005829) by IDA and IBA, the specific location of this soluble enzyme. Proposed replacements: cytosol |
| GO:0005829 cytosol | IDA PMID:18304323 Protein abundance profiling of the Escherichia coli cytosol. | ACCEPT | Summary: This annotation is based on EcoCyc curation from PMID:18304323 (protein abundance profiling of E. coli cytosol). RbsD is a soluble cytoplasmic enzyme with no membrane-targeting signals [file:ECOLI/rbsD/rbsD-deep-research-falcon.md]. Reason: The cytosolic localization is consistent with the biochemical function of RbsD as a soluble enzyme acting on ribose that has been transported into the cell. UniProt also indicates cytoplasmic localization. Supporting Evidence: file:ECOLI/rbsD/rbsD-deep-research-falcon.md RbsD functions in the cytoplasm where it enhances the phosphorylation of internalized ribose via its mutarotase activity |
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Download this section (compressed HTML)Q: What is the physiological significance of the secondary allose pyranase activity (conversion between beta-allofuranose and beta-allopyranose)?
Suggested experts: Ryu KS, Park C
Q: Is the homodecameric assembly required for catalytic activity, or can smaller oligomeric forms retain pyranase function?
Suggested experts: Kim MS, Oh BH
Experiment: Generate point mutations that disrupt decamer formation without affecting the active site residues (His-20, His-106). Test whether dimers or other intermediate oligomeric forms retain catalytic activity using NMR-based pyranase assays.
Hypothesis: The decameric assembly is required for proper active site formation
Type: Site-directed mutagenesis with oligomerization and activity assays
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