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Protein

D-3-phosphoglycerate dehydrogenase

Gene

Phgdh

Organism
Mus musculus (Mouse)
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.
2-hydroxyglutarate + NAD+ = 2-oxoglutarate + NADH.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei78 – 781NADBy similarity
Binding sitei175 – 1751NADBy similarity
Binding sitei207 – 2071NAD; via carbonyl oxygenBy similarity
Active sitei236 – 2361By similarity
Binding sitei260 – 2601NADBy similarity
Active sitei265 – 2651By similarity
Active sitei283 – 2831Proton donorBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi155 – 1562NADBy similarity
Nucleotide bindingi234 – 2363NADBy similarity
Nucleotide bindingi283 – 2864NADBy similarity

GO - Molecular functioni

  1. NAD binding Source: InterPro
  2. phosphoglycerate dehydrogenase activity Source: MGI

GO - Biological processi

  1. G1 to G0 transition Source: MGI
  2. gamma-aminobutyric acid metabolic process Source: MGI
  3. glial cell development Source: MGI
  4. glutamine metabolic process Source: MGI
  5. glycine metabolic process Source: MGI
  6. L-serine biosynthetic process Source: UniProtKB-KW
  7. L-serine metabolic process Source: MGI
  8. neural tube development Source: MGI
  9. neurogenesis Source: MGI
  10. neuron projection development Source: MGI
  11. regulation of gene expression Source: MGI
  12. spinal cord development Source: MGI
  13. taurine metabolic process Source: MGI
  14. threonine metabolic process Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Amino-acid biosynthesis, Serine biosynthesis

Keywords - Ligandi

NAD

Enzyme and pathway databases

BRENDAi1.1.1.95. 3474.
ReactomeiREACT_306239. Serine biosynthesis.
UniPathwayiUPA00135; UER00196.

Names & Taxonomyi

Protein namesi
Recommended name:
D-3-phosphoglycerate dehydrogenase (EC:1.1.1.95)
Short name:
3-PGDH
Alternative name(s):
A10
Gene namesi
Name:Phgdh
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 3

Organism-specific databases

MGIiMGI:1355330. Phgdh.

Subcellular locationi

GO - Cellular componenti

  1. extracellular vesicular exosome Source: MGI
  2. myelin sheath Source: UniProtKB
Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

Decreased level of free serine, glycine, taurine, GABA, glutamine, and threonine in spinal cord and head. Impaired central nervous system (CNS) with shorter neural tube length and overall growth retardation. Severe atrophy at the thoracic level, particularly in the dorsal spinal cord. Poorly developed dorsal horn and adjacent mantle zone. Neurons fail to develop neurites, particularly commissural axonal fibers.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 533532D-3-phosphoglycerate dehydrogenasePRO_0000076014Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity
Modified residuei14 – 141PhosphoserineBy similarity
Modified residuei21 – 211N6-acetyllysine1 Publication
Modified residuei58 – 581N6-acetyllysine1 Publication
Modified residuei78 – 781PhosphothreonineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ61753.
PaxDbiQ61753.
PRIDEiQ61753.

2D gel databases

COMPLUYEAST-2DPAGEQ61753.
REPRODUCTION-2DPAGEIPI00225961.
Q61753.
SWISS-2DPAGEQ61753.

PTM databases

PhosphoSiteiQ61753.

Expressioni

Gene expression databases

BgeeiQ61753.
CleanExiMM_PHGDH.
GenevestigatoriQ61753.

Interactioni

Subunit structurei

Homotetramer.By similarity

Protein-protein interaction databases

BioGridi231770. 3 interactions.
IntActiQ61753. 4 interactions.
MINTiMINT-4114515.

Structurei

3D structure databases

ProteinModelPortaliQ61753.
SMRiQ61753. Positions 5-503.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0111.
GeneTreeiENSGT00530000063021.
HOGENOMiHOG000136693.
HOVERGENiHBG054241.
InParanoidiQ61753.
KOiK00058.
OMAiDNTFAQC.
OrthoDBiEOG7JT6WT.
PhylomeDBiQ61753.
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.
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.

Q61753-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAFANLRKVL ISDSLDPCCR KILQDGGLQV VEKQNLSKEE LIAELQDCEG
60 70 80 90 100
LIVRSATKVT ADVINAAEKL QVVGRAGTGV DNVDLEAATR KGILVMNTPN
110 120 130 140 150
GNSLSAAELT CGMIMCLARQ IPQATASMKD GKWDRKKFMG TELNGKTLGI
160 170 180 190 200
LGLGRIGREV ATRMQSFGMK 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 PWIGLAEAMG TLMHAWAGSP
360 370 380 390 400
KGTIQVVTQG TSLKNAGTCL SPAVIVGLLR EASKQADVNL VNAKLLVKEA
410 420 430 440 450
GLNVTTSHNP GVPGEQGSGE CLLTVALAGA PYQAVGLVQG TTPMLQMLNG
460 470 480 490 500
AVFRPEVPLR RGQPLLVFRA QPSDPGMLPT MIGLLAEAGV QLLSYQTSMV
510 520 530
SDGEPWHVMG LSSLLPSLET WKQHVLEAFQ FCF
Length:533
Mass (Da):56,586
Last modified:January 22, 2007 - v3
Checksum:i49CBF125AD6A12A5
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti77 – 771G → V in AAB67986 (Ref. 5) Curated
Sequence conflicti87 – 882AA → PP in AAB67986 (Ref. 5) Curated
Sequence conflicti124 – 1241A → T in AAB67986 (Ref. 5) Curated
Sequence conflicti369 – 3691C → W in AAB67986 (Ref. 5) Curated
Sequence conflicti377 – 3771G → A in AAB67986 (Ref. 5) Curated
Sequence conflicti447 – 4471M → K in BAC36494 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB128936 Genomic DNA. Translation: BAD08449.1.
AK076815 mRNA. Translation: BAC36494.1.
AK169684 mRNA. Translation: BAE41303.1.
BC086668 mRNA. Translation: AAH86668.1.
BC110673 mRNA. Translation: AAI10674.1.
L21027 mRNA. Translation: AAB67986.1.
CCDSiCCDS17663.1.
RefSeqiNP_058662.2. NM_016966.3.
UniGeneiMm.16898.
Mm.371997.

Genome annotation databases

EnsembliENSMUST00000065793; ENSMUSP00000064755; ENSMUSG00000053398.
GeneIDi236539.
KEGGimmu:236539.
UCSCiuc008qps.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB128936 Genomic DNA. Translation: BAD08449.1.
AK076815 mRNA. Translation: BAC36494.1.
AK169684 mRNA. Translation: BAE41303.1.
BC086668 mRNA. Translation: AAH86668.1.
BC110673 mRNA. Translation: AAI10674.1.
L21027 mRNA. Translation: AAB67986.1.
CCDSiCCDS17663.1.
RefSeqiNP_058662.2. NM_016966.3.
UniGeneiMm.16898.
Mm.371997.

3D structure databases

ProteinModelPortaliQ61753.
SMRiQ61753. Positions 5-503.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi231770. 3 interactions.
IntActiQ61753. 4 interactions.
MINTiMINT-4114515.

PTM databases

PhosphoSiteiQ61753.

2D gel databases

COMPLUYEAST-2DPAGEQ61753.
REPRODUCTION-2DPAGEIPI00225961.
Q61753.
SWISS-2DPAGEQ61753.

Proteomic databases

MaxQBiQ61753.
PaxDbiQ61753.
PRIDEiQ61753.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000065793; ENSMUSP00000064755; ENSMUSG00000053398.
GeneIDi236539.
KEGGimmu:236539.
UCSCiuc008qps.1. mouse.

Organism-specific databases

CTDi26227.
MGIiMGI:1355330. Phgdh.

Phylogenomic databases

eggNOGiCOG0111.
GeneTreeiENSGT00530000063021.
HOGENOMiHOG000136693.
HOVERGENiHBG054241.
InParanoidiQ61753.
KOiK00058.
OMAiDNTFAQC.
OrthoDBiEOG7JT6WT.
PhylomeDBiQ61753.
TreeFamiTF314548.

Enzyme and pathway databases

UniPathwayiUPA00135; UER00196.
BRENDAi1.1.1.95. 3474.
ReactomeiREACT_306239. Serine biosynthesis.

Miscellaneous databases

NextBioi382995.
PROiQ61753.
SOURCEiSearch...

Gene expression databases

BgeeiQ61753.
CleanExiMM_PHGDH.
GenevestigatoriQ61753.

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.
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...

Publicationsi

« Hide 'large scale' publications
  1. "Targeted disruption of the mouse 3-phosphoglycerate dehydrogenase gene causes severe neurodevelopmental defects and results in embryonic lethality."
    Yoshida K., Furuya S., Osuka S., Mitoma J., Shinoda Y., Watanabe M., Azuma N., Tanaka H., Hashikawa T., Itohara S., Hirabayashi Y.
    J. Biol. Chem. 279:3573-3577(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 129/SvJ.
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J and NOD.
    Tissue: Testis and Thymus.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6.
    Tissue: Brain and Olfactory epithelium.
  4. Lubec G., Klug S., Yang J.W., Zigmond M.
    Submitted (JUN-2007) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 39-54; 248-268; 365-380 AND 523-533, IDENTIFICATION BY MASS SPECTROMETRY.
    Tissue: Brain and Hippocampus.
  5. "Sequences and expression patterns of murine erythroleukemia cDNAs isolated by subtractive cloning."
    Miller I.J., Bieker J.J.
    Submitted (AUG-1993) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 49-533.
  6. "Impaired neurogenesis in embryonic spinal cord of Phgdh knockout mice, a serine deficiency disorder model."
    Kawakami Y., Yoshida K., Yang J.H., Suzuki T., Azuma N., Sakai K., Hashikawa T., Watanabe M., Yasuda K., Kuhara S., Hirabayashi Y., Furuya S.
    Neurosci. Res. 63:184-193(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
  7. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
    Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
    Mol. Cell 50:919-930(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-21 AND LYS-58, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic fibroblast.

Entry informationi

Entry nameiSERA_MOUSE
AccessioniPrimary (citable) accession number: Q61753
Secondary accession number(s): Q3TEE5, Q75SV9, Q8C603
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 14, 1998
Last sequence update: January 22, 2007
Last modified: March 31, 2015
This is version 135 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. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.