P0A9T0 · SERA_ECOLI
- ProteinD-3-phosphoglycerate dehydrogenase
- GeneserA
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids410 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L-serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate.
Catalytic activity
- (2R)-3-phosphoglycerate + NAD+ = 3-phosphooxypyruvate + H+ + NADH
Activity regulation
Displays feedback inhibition by L-serine. Inhibited by glycine.
Kinetics
KM | SUBSTRATE | pH | TEMPERATURE[C] | NOTES | EVIDENCE | |
---|---|---|---|---|---|---|
1.2 mM | 3-phospho-D-glycerate | |||||
3.2 μM | 3-phosphonooxypyruvate | |||||
88 μM | 2-oxoglutarate | |||||
0.37 mM | (R)-2-hydroxyglutarate | |||||
2.9 mM | (S)-2-hydroxyglutarate |
Vmax | pH | TEMPERATURE[C] | NOTES | EVIDENCE | |
---|---|---|---|---|---|
183 nmol/min/mg | for 3-phospho-D-glycerate oxidation | ||||
9.27 μmol/min/mg | for 3-phosphonooxypyruvate reduction | ||||
11.1 μmol/min/mg | for 2-oxoglutarate reduction | ||||
237 nmol/min/mg | for (R)-2-hydroxyglutarate oxidation | ||||
83.3 nmol/min/mg | for (S)-2-hydroxyglutarate oxidation |
kcat is 0.55 sec-1 for 3-phospho-D-glycerate oxidation. kcat is 27.8 sec-1 for 3-phosphonooxypyruvate reduction. kcat is 33.3 sec-1 for 2-oxoglutarate reduction. kcat is 0.71 sec-1 for (R)-2-hydroxyglutarate oxidation. kcat is 0.25 sec-1 for (S)-2-hydroxyglutarate oxidation.
pH Dependence
Optimum pH is 8.5 for the reductase activities and 9.0 for the dehydrogenase activities.
Pathway
Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 1/3.
Features
Showing features for binding site, active site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 161-162 | NAD+ (UniProtKB | ChEBI) | ||||
Sequence: HI | ||||||
Binding site | 181 | NAD+ (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 238-240 | NAD+ (UniProtKB | ChEBI) | ||||
Sequence: ASR | ||||||
Active site | 240 | |||||
Sequence: R | ||||||
Binding site | 264 | NAD+ (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Active site | 269 | |||||
Sequence: E | ||||||
Active site | 292 | Proton donor | ||||
Sequence: H | ||||||
Binding site | 292-295 | NAD+ (UniProtKB | ChEBI) | ||||
Sequence: HIGG |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytosol | |
Molecular Function | 2-hydroxyglutarate dehydrogenase activity | |
Molecular Function | identical protein binding | |
Molecular Function | NAD+ binding | |
Molecular Function | NADH binding | |
Molecular Function | phosphoglycerate dehydrogenase activity | |
Molecular Function | serine binding | |
Biological Process | L-serine biosynthetic process |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameD-3-phosphoglycerate dehydrogenase
- EC number
- Short namesPGDH
- Alternative names
Gene names
Organism names
- Organism
- Strains
- Taxonomic lineageBacteria > Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Escherichia
Accessions
- Primary accessionP0A9T0
- Secondary accessions
Proteomes
Subcellular Location
UniProt Annotation
GO Annotation
PTM/Processing
Features
Showing features for initiator methionine, chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Initiator methionine | 1 | Removed | ||||
Sequence: M | ||||||
Chain | PRO_0000075999 | 2-410 | D-3-phosphoglycerate dehydrogenase | |||
Sequence: AKVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGRRLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY |
Proteomic databases
Structure
Family & Domains
Features
Showing features for domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 339-410 | ACT | ||||
Sequence: RLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY |
Sequence similarities
Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length410
- Mass (Da)44,176
- Last updated2007-01-23 v2
- Checksum61EF5EFC304DF6F0
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
L29397 EMBL· GenBank· DDBJ | AAA24625.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
U28377 EMBL· GenBank· DDBJ | AAA69080.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
U00096 EMBL· GenBank· DDBJ | AAC75950.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AP009048 EMBL· GenBank· DDBJ | BAE76977.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
X66836 EMBL· GenBank· DDBJ | CAA47308.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
M64630 EMBL· GenBank· DDBJ | AAA73016.1 EMBL· GenBank· DDBJ | Genomic DNA |