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Protein

D-3-phosphoglycerate dehydrogenase

Gene

Phgdh

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -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. Does not catalyze the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate and the reversible oxidation of (S)-malate to oxaloacetate.1 Publication

Catalytic activityi

3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH.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.1 Publication
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. D-3-phosphoglycerate dehydrogenase (Phgdh)
  2. Phosphoserine aminotransferase (Psat1), Phosphoserine aminotransferase (Psat1), Phosphoserine aminotransferase (Psat1), Phosphoserine aminotransferase
  3. Phosphoserine phosphatase (Psph)
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 sitei78NADBy similarity1
Binding sitei175NADBy similarity1
Binding sitei207NAD; via carbonyl oxygenBy similarity1
Active sitei236By similarity1
Binding sitei260NADBy similarity1
Active sitei265By similarity1
Active sitei283Proton donorBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi155 – 156NADBy similarity2
Nucleotide bindingi234 – 236NADBy similarity3
Nucleotide bindingi283 – 286NADBy similarity4

GO - Molecular functioni

  • NAD binding Source: InterPro
  • phosphoglycerate dehydrogenase activity Source: RGD

GO - Biological processi

Keywordsi

Molecular functionOxidoreductase
Biological processAmino-acid biosynthesis, Serine biosynthesis
LigandNAD

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-10261
ReactomeiR-RNO-977347 Serine biosynthesis
UniPathwayiUPA00135; UER00196

Names & Taxonomyi

Protein namesi
Recommended name:
D-3-phosphoglycerate dehydrogenase (EC:1.1.1.951 Publication)
Short name:
3-PGDH
Gene namesi
Name:Phgdh
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 2

Organism-specific databases

RGDi61987 Phgdh

Subcellular locationi

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00000760162 – 533D-3-phosphoglycerate dehydrogenaseAdd BLAST532

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineBy similarity1
Modified residuei14PhosphoserineBy similarity1
Modified residuei21N6-acetyllysine; alternateBy similarity1
Cross-linki21Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1); alternateBy similarity
Cross-linki21Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Modified residuei58N6-acetyllysineBy similarity1
Modified residuei78PhosphothreonineBy similarity1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiO08651
PRIDEiO08651

2D gel databases

World-2DPAGE0004:O08651

PTM databases

iPTMnetiO08651
PhosphoSitePlusiO08651
SwissPalmiO08651

Expressioni

Tissue specificityi

Liver, kidney, brain, testis.1 Publication

Gene expression databases

BgeeiENSRNOG00000019328
GenevisibleiO08651 RN

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

BioGridi248638, 1 interactor
IntActiO08651, 1 interactor
STRINGi10116.ENSRNOP00000053019

Structurei

3D structure databases

ProteinModelPortaliO08651
SMRiO08651
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG0068 Eukaryota
COG0111 LUCA
GeneTreeiENSGT00530000063021
HOGENOMiHOG000136693
HOVERGENiHBG054241
InParanoidiO08651
KOiK00058
OMAiNIAGMQV
OrthoDBiEOG091G0C5D
PhylomeDBiO08651
TreeFamiTF314548

Family and domain databases

Gene3Di3.30.1330.90, 1 hit
InterProiView protein in InterPro
IPR029009 ASB_dom_sf
IPR006139 D-isomer_2_OHA_DH_cat_dom
IPR029753 D-isomer_DH_CS
IPR029752 D-isomer_DH_CS1
IPR006140 D-isomer_DH_NAD-bd
IPR036291 NAD(P)-bd_dom_sf
IPR006236 PGDH
PfamiView protein in Pfam
PF00389 2-Hacid_dh, 1 hit
PF02826 2-Hacid_dh_C, 1 hit
SUPFAMiSSF143548 SSF143548, 1 hit
SSF51735 SSF51735, 1 hit
TIGRFAMsiTIGR01327 PGDH, 1 hit
PROSITEiView protein in PROSITE
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.

O08651-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAFANLRKIL ISDSLDPCCR KILQDGGLQV VEKQNLSKEE LIAELQDCEG
60 70 80 90 100
LIVRSATKVT ADVINAAEKL QVVGRAGTGV DNVDLEAATR KGVLVMNTPN
110 120 130 140 150
GNSLSAAELT CGMLMCLARQ IPQATASMKD GKWDRKKFMG TELNGKTLGI
160 170 180 190 200
LGLGRIGREV AARMQAFGMK TVGYDPIISP EVAASFGVQQ LPLEEIWPLC
210 220 230 240 250
DFITVHTPLL PSTTGLLNDS TFAQCKKGVR VVNCARGGIV DEGALLRALQ
260 270 280 290 300
SGQCAGAALD VFTEEPPRDR ALVDHENVIS CPHLGASTKE AQSRCGEEIA
310 320 330 340 350
VQFVDMVKGK SLTGVVNAQA LTSAFSPHTK PWIGLAEALG TLMHAWAGSP
360 370 380 390 400
KGTIQVVTQG TSLKNAGTCL SPAVIVGLLR EASKQADVNL VNAKLLVKEA
410 420 430 440 450
GLNVTTSHSP GVPGEQGIGE CLLTVALAGA PYQAVGLVQG TTPMLQMLNG
460 470 480 490 500
AVFRPEVPLR RGQPLLLFRA QPSDPVMLPT MIGLLAEAGV QLLSYQTSKV
510 520 530
SDGDTWHVMG LSSLLPSLDA WKQHVSEAFQ FCF
Length:533
Mass (Da):56,493
Last modified:January 23, 2007 - v3
Checksum:i7273DAC3349E95EF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X97772 mRNA Translation: CAA66374.1
AJ271975 Genomic DNA Translation: CAB89828.1
BC086327 mRNA Translation: AAH86327.1
RefSeqiNP_113808.1, NM_031620.1
XP_006233072.1, XM_006233010.1
UniGeneiRn.6872

Genome annotation databases

EnsembliENSRNOT00000056173; ENSRNOP00000053019; ENSRNOG00000019328
GeneIDi58835
KEGGirno:58835
UCSCiRGD:61987 rat

Similar proteinsi

Entry informationi

Entry nameiSERA_RAT
AccessioniPrimary (citable) accession number: O08651
Secondary accession number(s): Q546Q9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: January 23, 2007
Last modified: May 23, 2018
This is version 150 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome
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Main funding by: National Institutes of Health