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Q61753 (SERA_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 128. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
D-3-phosphoglycerate dehydrogenase

Short name=3-PGDH
EC=1.1.1.95
Alternative name(s):
A10
Gene names
Name:Phgdh
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length533 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH.

2-hydroxyglutarate + NAD+ = 2-oxoglutarate + NADH.

Pathway

Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 1/3.

Subunit structure

Homotetramer By similarity.

Disruption phenotype

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. Ref.6

Sequence similarities

Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family.

Ontologies

Keywords
   Biological processAmino-acid biosynthesis
Serine biosynthesis
   LigandNAD
   Molecular functionOxidoreductase
   PTMAcetylation
   Technical termComplete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processG1 to G0 transition

Inferred from mutant phenotype Ref.6. Source: MGI

L-serine biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-KW

L-serine metabolic process

Inferred from mutant phenotype Ref.6. Source: MGI

gamma-aminobutyric acid metabolic process

Inferred from mutant phenotype Ref.6. Source: MGI

glial cell development

Inferred from mutant phenotype Ref.6. Source: MGI

glutamine metabolic process

Inferred from mutant phenotype Ref.6. Source: MGI

glycine metabolic process

Inferred from mutant phenotype Ref.6. Source: MGI

neural tube development

Inferred from mutant phenotype Ref.6. Source: MGI

neurogenesis

Inferred from mutant phenotype Ref.6. Source: MGI

neuron projection development

Inferred from mutant phenotype Ref.6. Source: MGI

regulation of gene expression

Inferred from mutant phenotype Ref.6. Source: MGI

spinal cord development

Inferred from mutant phenotype Ref.6. Source: MGI

taurine metabolic process

Inferred from mutant phenotype Ref.6. Source: MGI

threonine metabolic process

Inferred from mutant phenotype Ref.6. Source: MGI

   Molecular_functionNAD binding

Inferred from electronic annotation. Source: InterPro

phosphoglycerate dehydrogenase activity

Traceable author statement PubMed 11567059. Source: MGI

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 533532D-3-phosphoglycerate dehydrogenase
PRO_0000076014

Regions

Nucleotide binding155 – 1562NAD By similarity
Nucleotide binding234 – 2363NAD By similarity
Nucleotide binding283 – 2864NAD By similarity

Sites

Active site2361 By similarity
Active site2651 By similarity
Active site2831Proton donor By similarity
Binding site781NAD By similarity
Binding site1751NAD By similarity
Binding site2071NAD; via carbonyl oxygen By similarity
Binding site2601NAD By similarity

Amino acid modifications

Modified residue21N-acetylalanine By similarity
Modified residue211N6-acetyllysine Ref.7
Modified residue581N6-acetyllysine Ref.7

Experimental info

Sequence conflict771G → V in AAB67986. Ref.5
Sequence conflict87 – 882AA → PP in AAB67986. Ref.5
Sequence conflict1241A → T in AAB67986. Ref.5
Sequence conflict3691C → W in AAB67986. Ref.5
Sequence conflict3771G → A in AAB67986. Ref.5
Sequence conflict4471M → K in BAC36494. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Q61753 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 49CBF125AD6A12A5

FASTA53356,586
        10         20         30         40         50         60 
MAFANLRKVL ISDSLDPCCR KILQDGGLQV VEKQNLSKEE LIAELQDCEG LIVRSATKVT 

        70         80         90        100        110        120 
ADVINAAEKL QVVGRAGTGV DNVDLEAATR KGILVMNTPN GNSLSAAELT CGMIMCLARQ 

       130        140        150        160        170        180 
IPQATASMKD GKWDRKKFMG TELNGKTLGI LGLGRIGREV ATRMQSFGMK TVGYDPIISP 

       190        200        210        220        230        240 
EVAASFGVQQ LPLEEIWPLC DFITVHTPLL PSTTGLLNDS TFAQCKKGVR VVNCARGGIV 

       250        260        270        280        290        300 
DEGALLRALQ SGQCAGAALD VFTEEPPRDR ALVDHENVIS CPHLGASTKE AQSRCGEEIA 

       310        320        330        340        350        360 
VQFVDMVKGK SLTGVVNAQA LTSAFSPHTK PWIGLAEAMG TLMHAWAGSP KGTIQVVTQG 

       370        380        390        400        410        420 
TSLKNAGTCL SPAVIVGLLR EASKQADVNL VNAKLLVKEA GLNVTTSHNP GVPGEQGSGE 

       430        440        450        460        470        480 
CLLTVALAGA PYQAVGLVQG TTPMLQMLNG AVFRPEVPLR RGQPLLVFRA QPSDPGMLPT 

       490        500        510        520        530 
MIGLLAEAGV QLLSYQTSMV SDGEPWHVMG LSSLLPSLET WKQHVLEAFQ FCF 

« Hide

References

« Hide 'large scale' references
[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(2004) [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. expand/collapse author list , 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(2005) [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(2004) [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 (JUL-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 (SEP-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(2009) [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(2013) [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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS17663.1.
RefSeqNP_058662.2. NM_016966.3.
UniGeneMm.16898.
Mm.371997.

3D structure databases

ProteinModelPortalQ61753.
SMRQ61753. Positions 5-503.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid231770. 2 interactions.
IntActQ61753. 4 interactions.
MINTMINT-4114515.

PTM databases

PhosphoSiteQ61753.

2D gel databases

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

Proteomic databases

MaxQBQ61753.
PaxDbQ61753.
PRIDEQ61753.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000065793; ENSMUSP00000064755; ENSMUSG00000053398.
GeneID236539.
KEGGmmu:236539.
UCSCuc008qps.1. mouse.

Organism-specific databases

CTD26227.
MGIMGI:1355330. Phgdh.

Phylogenomic databases

eggNOGCOG0111.
GeneTreeENSGT00530000063021.
HOGENOMHOG000136693.
HOVERGENHBG054241.
InParanoidQ61753.
KOK00058.
OMADNTFAQC.
OrthoDBEOG7JT6WT.
PhylomeDBQ61753.
TreeFamTF314548.

Enzyme and pathway databases

UniPathwayUPA00135; UER00196.

Gene expression databases

BgeeQ61753.
CleanExMM_PHGDH.
GenevestigatorQ61753.

Family and domain databases

Gene3D3.30.1330.90. 1 hit.
3.40.50.720. 2 hits.
InterProIPR029009. ASB_dom.
IPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR006140. D-isomer_2_OHA_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
IPR006236. PGDH_1.
[Graphical view]
PfamPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]
SUPFAMSSF143548. SSF143548. 1 hit.
TIGRFAMsTIGR01327. PGDH. 1 hit.
PROSITEPS00065. 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]
ProtoNetSearch...

Other

NextBio382995.
PROQ61753.
SOURCESearch...

Entry information

Entry nameSERA_MOUSE
AccessionPrimary (citable) accession number: Q61753
Secondary accession number(s): Q3TEE5, Q75SV9, Q8C603
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 128 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot