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Protein

D-3-phosphoglycerate dehydrogenase

Gene

Phgdh

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH.1 Publication
2-hydroxyglutarate + NAD+ = 2-oxoglutarate + 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 (Psat1)
  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

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Amino-acid biosynthesis, Serine biosynthesis

Keywords - Ligandi

NAD

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:1.1.1.95)
Short name:
3-PGDH
Gene namesi
Name:Phgdh
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 2

Organism-specific databases

RGDi61987. Phgdh.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

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.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG0068. Eukaryota.
COG0111. LUCA.
GeneTreeiENSGT00840000129939.
HOGENOMiHOG000136693.
HOVERGENiHBG054241.
InParanoidiO08651.
KOiK00058.
OMAiDNTFAQC.
OrthoDBiEOG091G0C5D.
PhylomeDBiO08651.
TreeFamiTF314548.

Family and domain databases

Gene3Di3.30.1330.90. 1 hit.
3.40.50.720. 2 hits.
InterProiIPR029009. ASB_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.
IPR006236. PGDH.
[Graphical view]
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]
SUPFAMiSSF143548. SSF143548. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01327. PGDH. 1 hit.
PROSITEiPS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
[Graphical view]

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.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliO08651.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi248638. 1 interactor.
IntActiO08651. 1 interactor.
STRINGi10116.ENSRNOP00000053019.

PTM databases

iPTMnetiO08651.
PhosphoSitePlusiO08651.
SwissPalmiO08651.

2D gel databases

World-2DPAGE0004:O08651.

Proteomic databases

PaxDbiO08651.
PRIDEiO08651.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi26227.
RGDi61987. Phgdh.

Phylogenomic databases

eggNOGiKOG0068. Eukaryota.
COG0111. LUCA.
GeneTreeiENSGT00840000129939.
HOGENOMiHOG000136693.
HOVERGENiHBG054241.
InParanoidiO08651.
KOiK00058.
OMAiDNTFAQC.
OrthoDBiEOG091G0C5D.
PhylomeDBiO08651.
TreeFamiTF314548.

Enzyme and pathway databases

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

Miscellaneous databases

PROiO08651.

Gene expression databases

BgeeiENSRNOG00000019328.
GenevisibleiO08651. RN.

Family and domain databases

Gene3Di3.30.1330.90. 1 hit.
3.40.50.720. 2 hits.
InterProiIPR029009. ASB_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.
IPR006236. PGDH.
[Graphical view]
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]
SUPFAMiSSF143548. SSF143548. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01327. PGDH. 1 hit.
PROSITEiPS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSERA_RAT
AccessioniPrimary (citable) accession number: O08651
Secondary accession number(s): Q546Q9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 140 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.