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Protein

D-3-phosphoglycerate dehydrogenase

Gene

serA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.1 Publication

Catalytic activityi

3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH.1 Publication
(R)-2-hydroxyglutarate + NAD+ = 2-oxoglutarate + NADH.1 Publication

Enzyme regulationi

Displays feedback inhibition by L-serine. Inhibited by glycine.1 Publication

Kineticsi

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.1 Publication
  1. KM=1.2 mM for 3-phospho-D-glycerate1 Publication
  2. KM=3.2 µM for 3-phosphonooxypyruvate1 Publication
  3. KM=88 µM for 2-oxoglutarate1 Publication
  4. KM=0.37 mM for (R)-2-hydroxyglutarate1 Publication
  5. KM=2.9 mM for (S)-2-hydroxyglutarate1 Publication
  1. Vmax=183 nmol/min/mg enzyme for 3-phospho-D-glycerate oxidation1 Publication
  2. Vmax=9.27 µmol/min/mg enzyme for 3-phosphonooxypyruvate reduction1 Publication
  3. Vmax=11.1 µmol/min/mg enzyme for 2-oxoglutarate reduction1 Publication
  4. Vmax=237 nmol/min/mg enzyme for (R)-2-hydroxyglutarate oxidation1 Publication
  5. Vmax=83.3 nmol/min/mg enzyme for (S)-2-hydroxyglutarate oxidation1 Publication

pH dependencei

Optimum pH is 8.5 for the reductase activities and 9.0 for the dehydrogenase activities.1 Publication

Pathwayi: L-serine biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes L-serine from 3-phospho-D-glycerate.
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. D-3-phosphoglycerate dehydrogenase (serA)
  2. Phosphoserine aminotransferase (serC)
  3. Phosphoserine phosphatase (serB)
This subpathway is part of the pathway L-serine biosynthesis, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-serine from 3-phospho-D-glycerate, the pathway L-serine biosynthesis and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei181NAD1 Publication1
Active sitei2401
Binding sitei264NAD1 Publication1
Active sitei2691
Active sitei292Proton donor1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi161 – 162NAD1 Publication2
Nucleotide bindingi238 – 240NAD1 Publication3
Nucleotide bindingi292 – 295NAD1 Publication4

GO - Molecular functioni

  • 2-hydroxyglutarate dehydrogenase activity Source: EcoCyc
  • identical protein binding Source: EcoCyc
  • NAD binding Source: InterPro
  • phosphoglycerate dehydrogenase activity Source: EcoCyc
  • serine binding Source: EcoCyc

GO - Biological processi

  • L-serine biosynthetic process Source: EcoCyc

Keywordsi

Molecular functionOxidoreductase
Biological processAmino-acid biosynthesis, Serine biosynthesis
LigandNAD

Enzyme and pathway databases

BioCyciEcoCyc:PGLYCDEHYDROG-MONOMER.
MetaCyc:PGLYCDEHYDROG-MONOMER.
BRENDAi1.1.1.95. 2026.
SABIO-RKiP0A9T0.
UniPathwayiUPA00135; UER00196.

Names & Taxonomyi

Protein namesi
Recommended name:
D-3-phosphoglycerate dehydrogenase (EC:1.1.1.951 Publication)
Short name:
PGDH
Alternative name(s):
2-oxoglutarate reductaseCurated (EC:1.1.1.3991 Publication)
Gene namesi
Name:serA
Ordered Locus Names:b2913, JW2880
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10944. serA.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000759992 – 410D-3-phosphoglycerate dehydrogenaseAdd BLAST409

Proteomic databases

EPDiP0A9T0.
PaxDbiP0A9T0.
PRIDEiP0A9T0.

Interactioni

Subunit structurei

Homotetramer.

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4261173. 13 interactors.
DIPiDIP-10851N.
IntActiP0A9T0. 3 interactors.
STRINGi511145.b2913.

Structurei

Secondary structure

1410
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni6 – 8Combined sources3
Beta strandi9 – 11Combined sources3
Beta strandi13 – 15Combined sources3
Helixi21 – 29Combined sources9
Beta strandi35 – 37Combined sources3
Helixi44 – 50Combined sources7
Beta strandi55 – 59Combined sources5
Beta strandi61 – 63Combined sources3
Helixi67 – 72Combined sources6
Beta strandi78 – 81Combined sources4
Helixi91 – 96Combined sources6
Turni105 – 108Combined sources4
Helixi109 – 125Combined sources17
Helixi127 – 136Combined sources10
Helixi143 – 145Combined sources3
Beta strandi153 – 157Combined sources5
Helixi161 – 172Combined sources12
Beta strandi176 – 180Combined sources5
Helixi197 – 203Combined sources7
Beta strandi205 – 209Combined sources5
Turni215 – 219Combined sources5
Helixi223 – 228Combined sources6
Beta strandi233 – 237Combined sources5
Beta strandi241 – 244Combined sources4
Helixi246 – 254Combined sources9
Beta strandi257 – 264Combined sources8
Turni276 – 278Combined sources3
Helixi279 – 281Combined sources3
Beta strandi287 – 290Combined sources4
Helixi298 – 318Combined sources21
Beta strandi324 – 327Combined sources4
Beta strandi336 – 346Combined sources11
Helixi350 – 360Combined sources11
Beta strandi364 – 372Combined sources9
Beta strandi374 – 384Combined sources11
Helixi387 – 398Combined sources12
Beta strandi403 – 410Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1PSDX-ray2.75A/B2-410[»]
1SC6X-ray2.09A/B/C/D7-410[»]
1YBAX-ray2.24A/B/C/D1-410[»]
2P9CX-ray2.46A/B1-410[»]
2P9EX-ray2.60A/B/C/D1-410[»]
2P9GX-ray2.80A/B1-410[»]
2PA3X-ray2.74A1-410[»]
ProteinModelPortaliP0A9T0.
SMRiP0A9T0.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A9T0.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini339 – 410ACTPROSITE-ProRule annotationAdd BLAST72

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108JQ1. Bacteria.
COG0111. LUCA.
HOGENOMiHOG000136696.
InParanoidiP0A9T0.
KOiK00058.
OMAiKFVKYSD.
PhylomeDBiP0A9T0.

Family and domain databases

InterProiView protein in InterPro
IPR002912. ACT_dom.
IPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR029753. D-isomer_DH_CS.
IPR029752. D-isomer_DH_CS1.
IPR006140. D-isomer_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
PfamiView protein in Pfam
PF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
PF01842. ACT. 1 hit.
SUPFAMiSSF51735. SSF51735. 1 hit.
PROSITEiView protein in PROSITE
PS51671. ACT. 1 hit.
PS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A9T0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKVSLEKDK IKFLLVEGVH QKALESLRAA GYTNIEFHKG ALDDEQLKES
60 70 80 90 100
IRDAHFIGLR SRTHLTEDVI NAAEKLVAIG CFCIGTNQVD LDAAAKRGIP
110 120 130 140 150
VFNAPFSNTR SVAELVIGEL LLLLRGVPEA NAKAHRGVWN KLAAGSFEAR
160 170 180 190 200
GKKLGIIGYG HIGTQLGILA ESLGMYVYFY DIENKLPLGN ATQVQHLSDL
210 220 230 240 250
LNMSDVVSLH VPENPSTKNM MGAKEISLMK PGSLLINASR GTVVDIPALC
260 270 280 290 300
DALASKHLAG AAIDVFPTEP ATNSDPFTSP LCEFDNVLLT PHIGGSTQEA
310 320 330 340 350
QENIGLEVAG KLIKYSDNGS TLSAVNFPEV SLPLHGGRRL MHIHENRPGV
360 370 380 390 400
LTALNKIFAE QGVNIAAQYL QTSAQMGYVV IDIEADEDVA EKALQAMKAI
410
PGTIRARLLY
Length:410
Mass (Da):44,176
Last modified:January 23, 2007 - v2
Checksum:i61EF5EFC304DF6F0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L29397 Genomic DNA. Translation: AAA24625.1.
U28377 Genomic DNA. Translation: AAA69080.1.
U00096 Genomic DNA. Translation: AAC75950.1.
AP009048 Genomic DNA. Translation: BAE76977.1.
X66836 Genomic DNA. Translation: CAA47308.1.
M64630 Genomic DNA. Translation: AAA73016.1.
PIRiA25200. DEECPG.
RefSeqiNP_417388.1. NC_000913.3.
WP_001151604.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75950; AAC75950; b2913.
BAE76977; BAE76977; BAE76977.
GeneIDi945258.
KEGGiecj:JW2880.
eco:b2913.
PATRICi32121238. VBIEscCol129921_3007.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L29397 Genomic DNA. Translation: AAA24625.1.
U28377 Genomic DNA. Translation: AAA69080.1.
U00096 Genomic DNA. Translation: AAC75950.1.
AP009048 Genomic DNA. Translation: BAE76977.1.
X66836 Genomic DNA. Translation: CAA47308.1.
M64630 Genomic DNA. Translation: AAA73016.1.
PIRiA25200. DEECPG.
RefSeqiNP_417388.1. NC_000913.3.
WP_001151604.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1PSDX-ray2.75A/B2-410[»]
1SC6X-ray2.09A/B/C/D7-410[»]
1YBAX-ray2.24A/B/C/D1-410[»]
2P9CX-ray2.46A/B1-410[»]
2P9EX-ray2.60A/B/C/D1-410[»]
2P9GX-ray2.80A/B1-410[»]
2PA3X-ray2.74A1-410[»]
ProteinModelPortaliP0A9T0.
SMRiP0A9T0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261173. 13 interactors.
DIPiDIP-10851N.
IntActiP0A9T0. 3 interactors.
STRINGi511145.b2913.

Proteomic databases

EPDiP0A9T0.
PaxDbiP0A9T0.
PRIDEiP0A9T0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75950; AAC75950; b2913.
BAE76977; BAE76977; BAE76977.
GeneIDi945258.
KEGGiecj:JW2880.
eco:b2913.
PATRICi32121238. VBIEscCol129921_3007.

Organism-specific databases

EchoBASEiEB0937.
EcoGeneiEG10944. serA.

Phylogenomic databases

eggNOGiENOG4108JQ1. Bacteria.
COG0111. LUCA.
HOGENOMiHOG000136696.
InParanoidiP0A9T0.
KOiK00058.
OMAiKFVKYSD.
PhylomeDBiP0A9T0.

Enzyme and pathway databases

UniPathwayiUPA00135; UER00196.
BioCyciEcoCyc:PGLYCDEHYDROG-MONOMER.
MetaCyc:PGLYCDEHYDROG-MONOMER.
BRENDAi1.1.1.95. 2026.
SABIO-RKiP0A9T0.

Miscellaneous databases

EvolutionaryTraceiP0A9T0.
PROiPR:P0A9T0.

Family and domain databases

InterProiView protein in InterPro
IPR002912. ACT_dom.
IPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR029753. D-isomer_DH_CS.
IPR029752. D-isomer_DH_CS1.
IPR006140. D-isomer_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
PfamiView protein in Pfam
PF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
PF01842. ACT. 1 hit.
SUPFAMiSSF51735. SSF51735. 1 hit.
PROSITEiView protein in PROSITE
PS51671. ACT. 1 hit.
PS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiSERA_ECOLI
AccessioniPrimary (citable) accession number: P0A9T0
Secondary accession number(s): P08328, Q2M9S9, Q47633
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: January 23, 2007
Last modified: May 10, 2017
This is version 111 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.