CMP-KDO biosynthesis

A four-reaction bacterial pathway that converts D-ribulose-5-phosphate to CMP-3-deoxy-D-manno-octulosonate (CMP-KDO). An arabinose-5-phosphate isomerase supplies D-arabinose-5-phosphate, KdsA forms KDO-8-phosphate, KdsC removes the phosphate, and KdsB activates KDO with CTP. Alternative paralogs may implement the first two reactions. Transfer of CMP-KDO to lipid A by WaaA and the separate ADP-heptose pathway are outside the module boundary.

MODULE:kdo_biosynthesisDRAFTCONCRETEMetabolic Pathwaymodules/kdo_biosynthesis.yaml
KDO biosynthetic processGO:0019294 CMP-KDO biosynthetic processGO:0033468
GO:0019294
keto-3-deoxy-D-manno-octulosonic acid biosynthetic process
Defines biosynthesis of the KDO sugar used in bacterial lipopolysaccharide.
GO:0033468
CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process
Defines activation of KDO to CMP-KDO.
KEGG:M00063
CMP-KDO biosynthesis
Defines the four committed reaction classes represented here.
PMID:16199563
Identification of GutQ from Escherichia coli as a D-arabinose 5-phosphate isomerase.
Comparative E. coli biochemistry and genetics establish that a second API can substitute for KdsD in KDO/LPS synthesis.
Recombinant GutQ was shown to indeed be a second copy of API from the E. coli K-12 genome
PMID:16765569
Non-essential KDO biosynthesis and new essential cell envelope biogenesis genes in the Escherichia coli yrbG-yhbG locus.
Comparative E. coli genetics demonstrates redundancy in early KDO biosynthetic functions.
were shown to be non-essential, indicating genetic redundancy for these two functions
file:projects/P_PUTIDA/deep-research/PSEPK__kdo-biosynthesis__ppu00541-deep-research-openscientist.md
OpenScientist PSEPK KDO-biosynthesis synthesis
Species-aware retrieval used to separate M00063 from the broad ppu00541 map and to identify paralog alternatives at the first two reactions.
RHEA:23104
arabinose-5-phosphate isomerase reaction
Defines reversible interconversion of ribulose-5-phosphate and arabinose-5-phosphate.
RHEA:14053
KDO-8-phosphate synthase reaction
Defines condensation of arabinose-5-phosphate with phosphoenolpyruvate.
RHEA:11500
KDO-8-phosphate phosphatase reaction
Defines hydrolysis of KDO-8-phosphate to KDO.
RHEA:23448
CMP-KDO synthetase reaction
Defines CTP-dependent activation of KDO.

The broad KEGG ppu00541 map also contains ADP-heptose, dTDP-rhamnose, GDP-mannose, and UDP-sugar enzymes; these are not parts of CMP-KDO synthesis. KT2440 has two API candidates and two KdsA paralogs, represented as ONE_OR_MORE alternatives rather than serial steps. All target assignments are based on reviewed or rule-based database evidence and pathway continuity; no direct KT2440 biochemical assay was found. No generic cytoplasm/cytosol term is asserted at module level.

9Nodes
4Parts
2Variant Sets
4Variants
6Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:kdo_biosynthesis deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • api_step → kdsA_step [NOT_CHECKED]
    API produces D-arabinose-5-phosphate consumed by KdsA.
  • kdsA_step → kdsC_step [NOT_CHECKED]
    KdsA produces KDO-8-phosphate consumed by KdsC.
  • kdsC_step → kdsB_step [NOT_CHECKED]
    KdsC produces KDO consumed by KdsB.

Gene-review completeness (6/9 grounded genes reviewed)

6 complete review(s) · 0 with deep research · 3 missing review · 6 reviewed but lacking deep research

Gene Review Complete Deep research
kdsA1 Q88MG0 ✓ ✓ ✗
kdsA2 Q88LX0 ✓ ✓ ✗
kdsB Q88LM7 ✓ ✓ ✗
kdsC Q88P96 ✓ ✓ ✗
kdsD Q88P95 ✓ ✓ ✗
Escherichia coli KdsA P0A715 ✗ — —
Escherichia coli GutQ P17115 ✗ — —
Escherichia coli KdsD P45395 ✗ — —
PP_1806 Q88LX1 ✓ ✓ ✗

Details

CMP-KDO biosynthesisMetabolic Pathwaykdo_biosynthesis
KDO biosynthetic processGO:0019294 CMP-KDO biosynthetic processGO:0033468

Connections

api_step -> kdsA_step Precedes
kdsA_step -> kdsC_step Precedes
kdsC_step -> kdsB_step Precedes
Part 1: D-arabinose-5-phosphate supply
D-ribulose-5-phosphate isomerizationReactionapi_step
Variant set: Arabinose-5-phosphate isomerase alternatives by paralog (One Or More)
KdsD-family APIReactionkdsD_api_variant

Annotons

KdsD arabinose-5-phosphate isomerase
kdsD_api_activity
Participant: Family: KdsD API subfamily
Family:
KdsD API subfamilyPANTHER:PTHR42745:SF1
Representative Members: PSEPK KdsDUniProtKB:Q88P95 Escherichia coli KdsDUniProtKB:P45395

Function

arabinose-5-phosphate isomerase activityGO:0019146
Substrates: D-ribulose 5-phosphate
Products: D-arabinose 5-phosphate

Processes

KDO biosynthetic processGO:0019294

Housekeeping API candidate for KDO synthesis.

Candidate secondary GutQ/KpsF-family APIReactionsecondary_api_variant

Annotons

Secondary arabinose-5-phosphate isomerase
secondary_api_activity
Participant: Family: GutQ/KpsF API family
Family:
GutQ/KpsF API familyInterPro:IPR050986
Representative Members: PSEPK PP_1806 candidateUniProtKB:Q88LX1 Escherichia coli GutQUniProtKB:P17115

Function

arabinose-5-phosphate isomerase activityGO:0019146
Substrates: D-ribulose 5-phosphate
Products: D-arabinose 5-phosphate

Processes

KDO biosynthetic processGO:0019294

Alternative API implementation exemplified by E. coli GutQ; target-genome paralogs require physiological disambiguation.

Part 2: KDO-8-phosphate formation
KDO-8-phosphate synthesisReactionkdsA_step
Variant set: KdsA paralog alternatives by paralog (One Or More)
KdsA1 implementationReactionkdsA1_variant

Annotons

KdsA1 KDO-8-phosphate synthase
kdsA1_activity
Participant: Family: KDO-8-phosphate synthase family
Family:
KDO-8-phosphate synthase familyInterPro:IPR006269
Representative Members: PSEPK KdsA1UniProtKB:Q88MG0 Escherichia coli KdsAUniProtKB:P0A715

Function

KDO-8-phosphate synthase activityGO:0008676
Substrates: D-arabinose 5-phosphate phosphoenolpyruvate water
Products: KDO 8-phosphate phosphate

Processes

KDO biosynthetic processGO:0019294

One of two KT2440 KdsA implementations.

KdsA2 implementationReactionkdsA2_variant

Annotons

KdsA2 KDO-8-phosphate synthase
kdsA2_activity
Participant: Family: KDO-8-phosphate synthase family
Family:
KDO-8-phosphate synthase familyInterPro:IPR006269
Representative Members: PSEPK KdsA2UniProtKB:Q88LX0

Function

KDO-8-phosphate synthase activityGO:0008676
Substrates: D-arabinose 5-phosphate phosphoenolpyruvate water
Products: KDO 8-phosphate phosphate

Processes

KDO biosynthetic processGO:0019294

Second KT2440 KdsA implementation adjacent to PP_1806.

Part 3: KDO-8-phosphate dephosphorylation
KDO formationReactionkdsC_step

Annotons

KDO-8-phosphate phosphatase
kdsC_activity
Participant: Family: KdsC family
Family:
KdsC familyInterPro:IPR010023
Representative Members: PSEPK KdsCUniProtKB:Q88P96

Function

KDO-8-phosphate phosphatase activityGO:0019143
Substrates: KDO 8-phosphate water
Products: KDO phosphate

Processes

KDO biosynthetic processGO:0019294

Produces free KDO for nucleotide activation.

Part 4: CMP-KDO formation
CTP-dependent KDO activationReactionkdsB_step

Annotons

CMP-KDO synthetase
kdsB_activity
Participant: Family: KdsB family
Family:
KdsB familyInterPro:IPR004528
Representative Members: PSEPK KdsBUniProtKB:Q88LM7

Function

CMP-KDO synthetase activityGO:0008690
Substrates: KDO CTP
Products: CMP-KDO diphosphate

Processes

CMP-KDO biosynthetic processGO:0033468 lipopolysaccharide biosynthetic processGO:0009103

Produces the activated KDO donor consumed downstream by WaaA.