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Reviewed, UniProtKB/Swiss-Prot O43175 (SERA_HUMAN)

Last modified February 9, 2010. Version 106. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (7) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

Names and origin

Protein namesRecommended name:
    D-3-phosphoglycerate dehydrogenase
      Short name=3-PGDH
    EC=1.1.1.95
Gene names
Name: PHGDH
Synonyms: PGDH3
OrganismHomo sapiens (Human) [Complete proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

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. Ref.10

2-hydroxyglutarate + NAD+ = 2-oxoglutarate + NADH. Ref.10

Pathway

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

Subunit structure

Homotetramer By similarity.

Induction

Induced by 17-beta-estradiol (estrogenic ligand) and 4-hydroxytamoxifen (agonist/antagonist ligand). Positively regulated by the transcription factors SP1 and NF-Y. Ref.11 Ref.12

Involvement in disease

Defects in PHGDH are the cause of phosphoglycerate dehydrogenase deficiency (PHGDH deficiency) [MIM:601815]. It is characterized by congenital microcephaly, psychomotor retardation, and seizures.

Sequence similarities

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

Biophysicochemical properties

Kinetic parameters:

KM=21.6 µM for 3-phosphohydroxypyruvate

Vmax=35 nmol/min/mg enzyme with 3-phosphohydroxypyruvate as substrate (in patient-derived fibroblasts)

Vmax=168 nmol/min/mg enzyme with 3-phosphohydroxypyruvate as substrate (in 3-PGDH overexpressed cells)

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.8
Chain2 – 533532D-3-phosphoglycerate dehydrogenase
PRO_0000076012

Regions

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

Sites

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

Amino acid modifications

Modified residue21N-acetylalanine Ref.8
Modified residue3711Phosphoserine Ref.13

Natural variations

Natural variant1351R → W in PHGDH deficiency; results in a 2-fold decrease in enzyme activity with 3-phosphohydroxypyruvate, but no change in substrate affinity. Ref.16
VAR_059026
Natural variant2611V → M in PHGDH deficiency; results in a four-fold decrease in substrate affinity and a slight increase in maximal enzyme activity with 3-phosphohydroxypyruvate. Ref.16
VAR_059027
Natural variant3731A → T in PHGDH deficiency; results in almost undetectable enzyme activity with 3-phosphohydroxypyruvate. Ref.16
VAR_059028
Natural variant3771G → S in PHGDH deficiency; results in a 2-fold decrease in enzyme activity with 3-phosphohydroxypyruvate, but no change in substrate affinity. Ref.16
VAR_059029
Natural variant4251V → M in PHGDH deficiency; results in almost undetectable enzyme activity with 3-phosphohydroxypyruvate. Ref.16 Ref.2
VAR_013461
Natural variant4901V → M in PHGDH deficiency; results in almost undetectable enzyme activity with 3-phosphohydroxypyruvate. Ref.10 Ref.16 Ref.2
VAR_059030

Experimental info

Sequence conflict251D → E in AAB88664. Ref.1
Sequence conflict251D → E in AAD51415. Ref.1

Secondary structure

............................................................. 533
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O43175-1 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: C58EB72275C45B35

FASTA53356,651
        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 GKWERKKFMG TELNGKTLGI LGLGRIGREV ATRMQSFGMK TIGYDPIISP 

       190        200        210        220        230        240 
EVSASFGVQQ LPLEEIWPLC DFITVHTPLL PSTTGLLNDN TFAQCKKGVR VVNCARGGIV 

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

       310        320        330        340        350        360 
VQFVDMVKGK SLTGVVNAQA LTSAFSPHTK PWIGLAEALG TLMRAWAGSP KGTIQVITQG 

       370        380        390        400        410        420 
TSLKNAGNCL SPAVIVGLLK EASKQADVNL VNAKLLVKEA GLNVTTSHSP AAPGEQGFGE 

       430        440        450        460        470        480 
CLLAVALAGA PYQAVGLVQG TTPVLQGLNG AVFRPEVPLR RDLPLLLFRT QTSDPAMLPT 

       490        500        510        520        530 
MIGLLAEAGV RLLSYQTSLV SDGETWHVMG ISSLLPSLEA WKQHVTEAFQ FHF 

« Hide

References

« Hide 'large scale' references
[1]"Nucleotide sequence and differential expression of the human 3-phosphoglycerate dehydrogenase gene."
Cho H.M., Jun D.Y., Bae M.A., Ahn J.D., Kim Y.H.
Gene 245:193-201(2000) [PubMed: 10713460] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"Molecular characterization of 3-phosphoglycerate dehydrogenase deficiency -- a neurometabolic disorder associated with reduced L-serine biosynthesis."
Klomp L.W.J., de Koning T.J., Malingre H.E.M., van Beurden E.A.C.M., Brink M., Opdam F.L., Duran M., Jaeken J., Pineda M., van Maldergem L., Poll-The B.T., van den Berg I.E.T., Berger R.
Am. J. Hum. Genet. 67:1389-1399(2000) [PubMed: 11055895] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANTS PHGDH DEFICIENCY MET-425 AND MET-490.
[3]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[4]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[5]"The DNA sequence and biological annotation of human chromosome 1."
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. expand/collapse author list , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
Nature 441:315-321(2006) [PubMed: 16710414] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]"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: 15489334] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Brain, Lung and Muscle.
[8]Bienvenut W.V.
Submitted (JAN-2010) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 2-54; 59-69; 76-119; 138-155; 237-289; 295-308; 352-380; 385-394; 462-491 AND 523-533, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT ALA-2, MASS SPECTROMETRY.
Tissue: B-cell lymphoma and Ovarian carcinoma.
[9]Lubec G., Chen W.-Q., Sun Y.
Submitted (DEC-2008) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 9-20; 22-33; 76-90; 248-268 AND 271-289.
Tissue: Fetal brain cortex.
[10]"V490M, a common mutation in 3-phosphoglycerate dehydrogenase deficiency, causes enzyme deficiency by decreasing the yield of mature enzyme."
Pind S., Slominski E., Mauthe J., Pearlman K., Swoboda K.J., Wilkins J.A., Sauder P., Natowicz M.R.
J. Biol. Chem. 277:7136-7143(2002) [PubMed: 11751922] [Abstract]
Cited for: CATALYTIC ACTIVITY, VARIANT MET-490.
[11]"Identification of novel proteins induced by estradiol, 4-hydroxytamoxifen and acolbifene in T47D breast cancer cells."
Al-Dhaheri M.H., Shah Y.M., Basrur V., Pind S., Rowan B.G.
Steroids 71:966-978(2006) [PubMed: 16949628] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, INDUCTION BY 17-BETA-ESTRADIOL AND 4-HYDROXYTAMOXIFEN.
[12]"Positive regulation of promoter activity of human 3-phosphoglycerate dehydrogenase (PHGDH) gene is mediated by transcription factors Sp1 and NF-Y."
Jun D.Y., Park H.S., Lee J.Y., Baek J.Y., Park H.-K., Fukui K., Kim Y.H.
Gene 414:106-114(2008) [PubMed: 18378410] [Abstract]
Cited for: INDUCTION BY SP1 AND NF-Y.
[13]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-371, MASS SPECTROMETRY.
[14]Colinge J., Superti-Furga G., Bennett K.L.
Submitted (OCT-2008) to UniProtKB
Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[15]"Crystal structure of human 3-phosphoglycerate dehydrogenase."
Structural genomics consortium (SGC)
Submitted (FEB-2009) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 4-314 IN COMPLEX WITH NAD AND SUBSTRATE.
[16]"Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics."
Tabatabaie L., de Koning T.J., Geboers A.J.J.M., van den Berg I.E.T., Berger R., Klomp L.W.J.
Hum. Mutat. 30:749-756(2009) [PubMed: 19235232] [Abstract]
Cited for: VARIANTS PHGDH DEFICIENCY TRP-135; MET-261; THR-373 AND SER-377, CHARACTERIZATION OF VARIANTS PHGDH DEFICIENCY TRP-135; MET-261; THR-373; SER-377; MET-425 AND MET-490, BIOPHYSICOCHEMICAL PROPERTIES.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF006043 mRNA. Translation: AAB88664.1.
AF171237 mRNA. Translation: AAD51415.1.
CR456795 mRNA. Translation: CAG33076.1.
AK315360 mRNA. Translation: BAG37755.1.
AL589734, AL139251 Genomic DNA. Translation: CAI22407.1.
AL139251, AL589734 Genomic DNA. Translation: CAI22212.1.
CH471122 Genomic DNA. Translation: EAW56708.1.
BC000303 mRNA. Translation: AAH00303.1.
BC001349 mRNA. Translation: AAH01349.1.
BC011262 mRNA. Translation: AAH11262.1.
IPIIPI00011200.
RefSeqNP_006614.2.
UniGeneHs.487296

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2G76X-ray1.70A/B4-314[»]
SMRO43175. Positions 7-516.
ModBaseSearch...

Protein-protein interaction databases

IntActO43175. 5 interactions.
STRINGO43175.

PTM databases

PhosphoSiteO43175.

Proteomic databases

PeptideAtlasO43175.
PRIDEO43175.

Genome annotation databases

EnsemblENST00000369409; ENSP00000358417; ENSG00000092621; Homo sapiens. [Genome view]
GeneID26227.
KEGGhsa:26227.
NMPDRfig|9606.3.peg.1817.
UCSCuc001ehz.1. human.

Organism-specific databases

CTD26227.
GeneCardsGC01P119966.
H-InvDBHIX0000952.
HGNCHGNC:8923. PHGDH.
HPACAB003681.
HPA021241.
HPA024031.
MIM601815. phenotype.
606879. gene.
Orphanet79351. 3-Phosphoglycerate dehydrogenase deficiency.
35705. Neurometabolic disorder due to serine deficiency.
PharmGKBPA33264.
GenAtlasSearch...

Phylogenomic databases

eggNOGprNOG13949.
HOGENOMHBG731446.
HOVERGENO43175.
InParanoidO43175.
OMANDNTFAQ.
OrthoDBEOG93N9ZD.
PhylomeDBO43175.

Enzyme and pathway databases

BRENDA1.1.1.95. 247.

Gene expression databases

ArrayExpressO43175.
BgeeO43175.
CleanExHS_PHGDH.
GenevestigatorO43175.
GermOnlineENSG00000092621. Homo sapiens.

Family and domain databases

InterProIPR006236. D-3-Phosphoglycerate_DH.
IPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR006140. D-isomer_2_OHA_DH_NAD-bd.
IPR015508. D3PG_DH.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
Gene3DG3DSA:3.40.50.720. NAD(P)-bd. 1 hit.
PANTHERPTHR10996:SF20. D3PG_Deh. 1 hit.
PfamPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]
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 Resources

DrugBankDB00157. NADH.
NextBio48383.
SOURCESearch...

Entry information

Entry nameSERA_HUMAN
AccessionPrimary (citable) accession number: O43175
Secondary accession number(s): B2RD08, Q5SZU3, Q9BQ01
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: January 23, 2007
Last modified: February 9, 2010
This is version 106 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHPI (Human Proteome Initiative)
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents