Bacterial D-ribose uptake and entry

A reusable bacterial route in which an RbsABC complex imports D-ribose, RbsD accelerates interconversion of the beta-pyranose and beta-furanose forms, and RbsK phosphorylates ribose to D-ribose 5-phosphate for entry into central carbon and nucleotide metabolism. Transcriptional regulation and downstream pentose-phosphate reactions are outside the module boundary.

MODULE:bacterial_ribose_uptake_and_entryDRAFTCONCRETEBiological Processmodules/bacterial_ribose_uptake_and_entry.yaml
D-ribose catabolic processGO:0019303
GO:0015752
D-ribose transmembrane transport
Defines the substrate-specific import process represented by RbsABC.
GO:0019303
D-ribose catabolic process
Defines conversion of imported D-ribose into a metabolically usable form.
file:PSEPK/rbsB/rbsB-uniprot.txt
Grounds the KT2440 periplasmic substrate-binding exemplar.
file:PSEPK/rbsA-I/rbsA-I-uniprot.txt
Grounds the KT2440 ABC ATPase exemplar.
file:PSEPK/rbsC/rbsC-uniprot.txt
Grounds the KT2440 ribose-permease exemplar.
file:PSEPK/rbsD/rbsD-uniprot.txt
Grounds the KT2440 D-ribose pyranase exemplar and RHEA:25432 reaction.
file:PSEPK/rbsK/rbsK-uniprot.txt
Grounds the KT2440 ribokinase exemplar and RHEA:13697 reaction.
file:modules/bacterial_ribose_uptake_and_entry-deep-research-openscientist.md
Synthesizes experimental work on the assembled RbsABC importer, RbsD pyranase reaction, and RbsK mechanism while noting bacterial variation and the spontaneous background ring interconversion.
file:projects/P_PUTIDA/deep-research/PSEPK__bacterial_ribose_uptake_and_entry__rbs-locus-deep-research-openscientist.md
Supports satisfaction of all three operations by PP_2454-PP_2459 while documenting that direct KT2440 transport or pathway experiments were not found and that PP_2757-PP_2761 remains substrate-ambiguous.

The module is species-neutral and uses the contiguous KT2440 PP_2454-PP_2459 locus as an exact implementation. RbsR/PP_2457 regulates the locus but is not a transport or metabolic step. A second KT2440 pair, RbsA/PP_2759 and the permease PP_2760, lacks a neighboring substrate-binding protein and is not assigned to this module without substrate-specific evidence. PANTHER terms are omitted for RbsB and RbsA-I because their current UniProt selectors are labeled as D-allose-related families; exact UniProt exemplars retain the intended grounding without asserting unsupported family specificity.

4Nodes
3Parts
0Variant Sets
0Variants
3Annotons
2Connections

Derived QC

Recommended-field compliance

53.8% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)
  • module.knowledge_gaps[2] · status (0/1)
  • module.knowledge_gaps[2] · provenance (0/1)

Module deep research

✓ present

  • bacterial_ribose_uptake_and_entry-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (5/5 grounded genes reviewed)

5 complete review(s) · 5 with deep research · 0 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
rbsA-I Q88K37 ✓ ✓ ✓
rbsB Q88K38 ✓ ✓ ✓
rbsC Q88K36 ✓ ✓ ✓
rbsD Q88K33 ✓ ✓ ✓
rbsK Q88K34 ✓ ✓ ✓

Details

Context
bacteriaNCBITaxon:2
Bacterial D-ribose uptake and entryBiological Processbacterial_ribose_uptake_and_entry
D-ribose catabolic processGO:0019303
Context
bacteriaNCBITaxon:2

Connections

Imported cytoplasmic D-ribose is the substrate pool for RbsD.
RbsD accelerates formation of beta-D-ribofuranose for RbsK phosphorylation.
Part 1: ATP-dependent D-ribose import
RbsABC D-ribose importProtein Complexrbsabc_ribose_import

Annotons

RbsABC D-ribose transporter activity
rbsabc_transporter_activity
Participant: Protein Complex: bacterial RbsABC importer
Protein Complex:
bacterial RbsABC importer
Active units:
RbsB substrate-binding subunit
Participant: Family: bacterial RbsB D-ribose-binding protein family
Family:
bacterial RbsB D-ribose-binding protein family
Representative Members: RbsB (Pseudomonas putida KT2440)UniProtKB:Q88K38
Role: Captures D-ribose in the periplasm and presents it to RbsC.
RbsC permease subunit
Participant: Family: bacterial RbsC ribose-import permease family
Family:
bacterial RbsC ribose-import permease familyPANTHER:PTHR32196:SF72
Representative Members: RbsC (Pseudomonas putida KT2440)UniProtKB:Q88K36
Role: Forms the D-ribose-selective membrane pathway.
RbsA energy-coupling subunit
Participant: Family: bacterial RbsA ribose-import ATPase family
Family:
bacterial RbsA ribose-import ATPase family
Representative Members: RbsA-I (Pseudomonas putida KT2440)UniProtKB:Q88K37
Role: Hydrolyzes ATP to drive D-ribose import through RbsC.

Function

ABC-type D-ribose transporter activityGO:0015611
Substrates: extracellular D-ribose ATP water
Products: cytoplasmic D-ribose ADP phosphate

Processes

D-ribose transmembrane transportGO:0015752

The collective RbsB/RbsC/RbsA complex captures D-ribose and couples ATP hydrolysis to import across the inner membrane.

Part 2: D-ribose ring-form interconversion
RbsD D-ribose pyranase reactionReactionrbsd_ribose_pyranase

Annotons

RbsD D-ribose pyranase activity
rbsd_pyranase_activity
Participant: Family: bacterial D-ribose pyranase family
Family:
bacterial D-ribose pyranase familyPANTHER:PTHR37831:SF1
Representative Members: RbsD (Pseudomonas putida KT2440)UniProtKB:Q88K33

Function

D-ribose pyranase activityGO:0062193
Substrates: beta-D-ribopyranose
Products: beta-D-ribofuranose

Locations

cytosolGO:0005829

Accelerates equilibration of imported beta-D-ribopyranose with the beta-furanose form used by ribokinase; the reversible reaction is RHEA:25432.

Part 3: D-ribose phosphorylation
RbsK ribokinase reactionReactionrbsk_ribose_phosphorylation

Annotons

RbsK ribokinase activity
rbsk_ribokinase_activity
Participant: Family: bacterial ribokinase family
Family:
bacterial ribokinase familyPANTHER:PTHR10584:SF166
Representative Members: RbsK (Pseudomonas putida KT2440)UniProtKB:Q88K34

Function

ribokinase activityGO:0004747
Substrates: beta-D-ribofuranose ATP
Products: D-ribose 5-phosphate ADP proton

Locations

cytosolGO:0005829

Phosphorylates the furanose substrate at O-5 to form D-ribose 5-phosphate; the reaction is RHEA:13697.