Phosphorylated L-serine biosynthesis

A reusable three-reaction pathway that converts the glycolytic intermediate 3-phospho-D-glycerate to L-serine through 3-phosphooxypyruvate and O-phospho-L-serine. The module represents the conserved SerA, SerC, and SerB reaction roles independently of their genomic arrangement. Additional activities of individual enzymes, including 2-hydroxyglutarate oxidation by some SerA proteins and vitamin B6 precursor transamination by some SerC proteins, are outside this pathway boundary.

MODULE:phosphorylated_serine_biosynthesisDRAFTMetabolic Pathwaymodules/phosphorylated_serine_biosynthesis.yaml
L-serine biosynthetic processGO:0006564
GO:0006564
L-serine biosynthetic process
GO:0006564 provides the biological-process context for synthesis of L-serine.
PMID:14154
Transient kinetic and deuterium isotope effect studies on the catalytic mechanism of phosphoglycerate dehydrogenase
Characterized phosphoglycerate dehydrogenase is a V-type allosteric enzyme inhibited by serine; this grounds the regulatory context without making feedback control a required pathway part.
Phosphoglycerate dehydrogenase corresponds to a V-type allosteric enzyme.
file:modules/phosphorylated_serine_biosynthesis-deep-research-openscientist.md
OpenScientist research for phosphorylated L-serine biosynthesis
The generic pathway review evaluates the three conserved reaction roles, their chemistry, and lineage-dependent enzyme architectures.
file:PSEPK/serA/serA-ai-review.yaml
PSEPK serA gene review
Q88CM5 supplies the phosphoglycerate dehydrogenase step.
file:PSEPK/serC/serC-ai-review.yaml
PSEPK serC gene review
Q88M07 supplies the phosphoserine aminotransferase step.
file:PSEPK/serB/serB-ai-review.yaml
PSEPK serB gene review
Q88DB8 supplies the phosphoserine phosphatase step.
4Nodes
3Parts
0Variant Sets
0Variants
3Annotons
2Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • phosphorylated_serine_biosynthesis-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 (3/6 grounded genes reviewed)

3 complete review(s) · 1 with deep research · 3 missing review · 2 reviewed but lacking deep research

Gene Review Complete Deep research
Escherichia coli SerB P0AGB0 ✗ — —
Escherichia coli SerC P23721 ✗ — —
Haemophilus influenzae SerA P43885 ✗ — —
serA Q88CM5 ✓ ✓ ✗
serB Q88DB8 ✓ ✓ ✗
serC Q88M07 ✓ ✓ ✓

Details

Phosphorylated L-serine biosynthesisMetabolic Pathwayphosphorylated_serine_biosynthesis
L-serine biosynthetic processGO:0006564

Exact UniProt exemplars delimit the three reaction roles without restricting the module taxonomically. No cellular location or molecular function is repeated at module level. SerC can also catalyze phosphohydroxythreonine transamination in DXP-dependent vitamin B6 biosynthesis, but that separate reaction is not a fourth part of this module. Some bacterial SerA proteins use an ACT domain for L-serine feedback, but effector sensitivity is a lineage- and sequence-dependent regulatory property rather than an additional pathway part. No ancestral PTN node is asserted without verified PAINT IBD evidence.

Connections

SerA supplies 3-phosphooxypyruvate to SerC.
SerC supplies O-phospho-L-serine to SerB.
Part 1: 3-phosphooxypyruvate formation
Phosphoglycerate dehydrogenaseReactionphosphoglycerate_dehydrogenase_step

Annotons

Phosphoglycerate dehydrogenase
serA_activity
Participant: Family: D-isomer-specific 2-hydroxyacid dehydrogenases
Family:
D-isomer-specific 2-hydroxyacid dehydrogenasesPANTHER:PTHR43761
Representative Members: PSEPK SerAUniProtKB:Q88CM5 Haemophilus influenzae SerAUniProtKB:P43885
Required Function:
phosphoglycerate dehydrogenase activityGO:0004617

Function

phosphoglycerate dehydrogenase activityGO:0004617
Substrates: 3-phospho-D-glycerate NAD+
Products: 3-phosphooxypyruvate NADH proton

Oxidizes a glycolytic intermediate to the first committed phosphorylated-serine precursor.

Part 2: O-phospho-L-serine formation
Phosphoserine aminotransferaseReactionphosphoserine_aminotransferase_step

Annotons

Phosphoserine aminotransferase
serC_activity
Participant: Family: SerC phosphoserine aminotransferases
Family:
SerC phosphoserine aminotransferasesPANTHER:PTHR43247
Representative Members: PSEPK SerCUniProtKB:Q88M07 Escherichia coli SerCUniProtKB:P23721
Required Function:
O-phospho-L-serine:2-oxoglutarate aminotransferase activityGO:0004648

Function

O-phospho-L-serine:2-oxoglutarate aminotransferase activityGO:0004648
Substrates: 3-phosphooxypyruvate L-glutamate
Products: O-phospho-L-serine 2-oxoglutarate

Transfers an amino group from glutamate to 3-phosphooxypyruvate.

Part 3: L-serine formation
Phosphoserine phosphataseReactionphosphoserine_phosphatase_step

Annotons

Phosphoserine phosphatase
serB_activity
Participant: Family: SerB phosphoserine phosphatases
Family:
SerB phosphoserine phosphatasesPANTHER:PTHR43344
Representative Members: PSEPK SerBUniProtKB:Q88DB8 Escherichia coli SerBUniProtKB:P0AGB0
Required Function:
L-phosphoserine phosphatase activityGO:0036424

Function

L-phosphoserine phosphatase activityGO:0036424
Substrates: O-phospho-L-serine water
Products: L-serine phosphate

Hydrolyzes O-phospho-L-serine to free L-serine.