ExPASy logo ExPASy Home page Site Map Search ExPASy Contact us Swiss-Prot
Notice: This page will be replaced with www.uniprot.org. Please send us your feedback!
Search for

UniProtKB/Swiss-Prot entry O43175


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

Note: most headings are clickable, even if they don't appear as links. They link to the user manual or other documents.
Entry information
Entry name SERA_HUMAN
Primary accession number O43175
Secondary accession numbers Q5SZU3 Q9BQ01
Integrated into Swiss-Prot on July 15, 1999
Sequence was last modified on January 23, 2007 (Sequence version 4)
Annotations were last modified on    June 16, 2009 (Entry version 96)
Name and origin of the protein
Protein name D-3-phosphoglycerate dehydrogenase
Synonyms 3-PGDH
EC 1.1.1.95
Gene name
Name: PHGDH
Synonyms: PGDH3
From
Homo sapiens (Human) [TaxID: 9606] 
Taxonomy Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo.
Protein existence 1: Evidence at protein level;
References
[1]
NUCLEOTIDE SEQUENCE [MRNA].
DOI=10.1016/S0378-1119(00)00009-3; PubMed=10713460 [NCBI, ExPASy, EBI, Israel, Japan]
Cho H.M., Jun D.Y., Bae M.A., Ahn J.D., Kim Y.H.;
"Nucleotide sequence and differential expression of the human 3-phosphoglycerate dehydrogenase gene.";
Gene 245:193-201(2000).
[2]
NUCLEOTIDE SEQUENCE [MRNA], AND VARIANTS PHGDH DEFICIENCY MET-425 AND MET-490.
DOI=10.1086/316886; PubMed=11055895 [NCBI, ExPASy, EBI, Israel, Japan]
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.;
"Molecular characterization of 3-phosphoglycerate dehydrogenase deficiency -- a neurometabolic disorder associated with reduced L-serine biosynthesis.";
Am. J. Hum. Genet. 67:1389-1399(2000).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.;
"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201).";
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
DOI=10.1038/nature04727; PubMed=16710414 [NCBI, ExPASy, EBI, Israel, Japan]
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., 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.;
"The DNA sequence and biological annotation of human chromosome 1.";
Nature 441:315-321(2006).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Brain, Lung, and Muscle;
DOI=10.1101/gr.2596504; PubMed=15489334 [NCBI, ExPASy, EBI, Israel, Japan]
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[6]
PROTEIN SEQUENCE OF 2-8, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT ALA-2, AND MASS SPECTROMETRY.
TISSUE=B-cell lymphoma;
Bienvenut W.V.;
Submitted (OCT-2004) to UniProtKB.
[7]
PROTEIN SEQUENCE OF 9-20; 22-33; 76-90; 248-268 AND 271-289.
TISSUE=Fetal brain cortex;
Lubec G., Chen W.-Q., Sun Y.;
Submitted (DEC-2008) to UniProtKB.
[8]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-371, AND MASS SPECTROMETRY.
DOI=10.1073/pnas.0805139105; PubMed=18669648 [NCBI, ExPASy, EBI, Israel, Japan]
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.;
"A quantitative atlas of mitotic phosphorylation.";
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
[9]
IDENTIFICATION [LARGE SCALE ANALYSIS], AND MASS SPECTROMETRY.
Colinge J., Superti-Furga G., Bennett K.L.;
Submitted (OCT-2008) to UniProtKB.
Comments
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
AF006043; AAB88664.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AF171237; AAD51415.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
CR456795; CAG33076.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AL589734; CAI22407.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AL139251; CAI22407.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AL139251; CAI22212.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AL589734; CAI22212.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
BC000303; AAH00303.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
BC001349; AAH01349.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
BC011262; AAH11262.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
IPI IPI00011200; -.
RefSeq NP_006614.2; -.
UniGene Hs.487296
3D structure databases
PDB
2G76; X-ray; 1.70 A; A/B=4-314.[ExPASy / RCSB / EBI]
PDBsum 2G76; -.
ModBase O43175.
Protein-protein interaction databases
IntAct O43175; 4.
PTM databases
PhosphoSite O43175; -.
Enzyme and pathway databases
BRENDA 1.1.1.95; 247.
Organism-specific databases
GeneCards GC01P119966; -.
H-InvDB HIX0000952; -.
HGNC HGNC:8923; PHGDH.
GenAtlas PHGDH.
HPA CAB003681; -.
MIM 601815; phenotype. [NCBI / EBI]
606879; gene. [NCBI / EBI]
Orphanet 79351; 3-Phosphoglycerate dehydrogenase deficiency.
35705; Neurometabolic disorder due to serine deficiency.
PharmGKB PA33264; -.
Gene expression databases
ArrayExpress O43175; -.
Bgee O43175; -.
CleanEx HS_PHGDH; -.
GermOnline ENSG00000092621; Homo sapiens.
Ontologies
GO
GO:0009055; Molecular function: electron carrier activity (traceable author statement from UniProtKB).
GO:0051287; Molecular function: NAD or NADH binding (inferred from electronic annotation from InterPro).
GO:0004617; Molecular function: phosphoglycerate dehydrogenase activity (traceable author statement from ProtInc).
GO:0007420; Biological process: brain development (traceable author statement from ProtInc).
GO:0006564; Biological process: L-serine biosynthetic process (inferred from electronic annotation from UniProtKB-KW).
GO:0055114; Biological process: oxidation reduction (inferred from electronic annotation from UniProtKB-KW).
QuickGo view.
Family and domain databases
InterPro IPR006236; D-3-Phosphoglycerate_DH.
IPR006139; D-isomer_2_OHA_DH.
IPR006140; D-isomer_2_OHA_DH_NAD-bd.
IPR015508; D3PG_DH.
IPR016040; NAD(P)-bd_dom.
Graphical view of domain structure.
Gene3D G3DSA:3.40.50.720; NAD(P)-bd; 1.
PANTHER PTHR10996:SF20; D3PG_Deh; 1.
Pfam PF00389; 2-Hacid_dh; 1.
PF02826; 2-Hacid_dh_C; 1.
Pfam graphical view of domain structure.
TIGRFAMs TIGR01327; PGDH; 1.
PROSITE PS00065; D_2_HYDROXYACID_DH_1; 1.
PS00670; D_2_HYDROXYACID_DH_2; 1.
PS00671; D_2_HYDROXYACID_DH_3; 1.
Proteomic databases
PeptideAtlas O43175; -.
PRIDE O43175; -.
Genome annotation databases
Ensembl ENSG00000092621; Homo sapiens. [Contig view]
GeneID 26227; -.
KEGG hsa:26227; -.
NMPDR fig|9606.3.peg.1817; -.
Phylogenomic databases
HOGENOM O43175; -.
HOVERGEN O43175; -.
OMA O43175; GTIQVIT.
Other
DrugBank DB00157; NADH.
NextBio 48383; -.
SOURCE PHGDH; Homo sapiens.
ProtoNet O43175.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
3D-structure; Acetylation; Amino-acid biosynthesis; Direct protein sequencing; Disease mutation; NAD; Oxidoreductase; Phosphoprotein; Serine biosynthesis.
Features
SEVIEWER logo Feature table viewer
KeyFrom   To Length Description FTId
INIT_MET   1     1        Removed. 
CHAIN   2   533  532     D-3-phosphoglycerate dehydrogenase. PRO_0000076012
ACT_SITE   236   236        By similarity. 
ACT_SITE   265   265        By similarity. 
ACT_SITE   283   283        Proton donor (By similarity). 
MOD_RES   2     2        N-acetylalanine. 
MOD_RES   371   371        Phosphoserine. 
VARIANT   425   425  1     V -> M (in PHGDH deficiency). VAR_013461 
VARIANT   490   490  1     V -> M (in PHGDH deficiency). VAR_013462 
CONFLICT   25    25        D -> E (in Ref. 1; AAB88664/AAD51415). 
STRAND   8    11  4      
HELIX   18    26  9      
STRAND   29    32  4      
HELIX   38    44  7      
HELIX   45    47  3      
STRAND   49    53  5      
STRAND   55    57  3      
HELIX   61    66  6      
STRAND   72    79  8      
HELIX   85    91  7      
STRAND   94    96  3      
HELIX   103   119  17      
HELIX   121   129  9      
HELIX   136   138  3      
STRAND   147   151  5      
HELIX   155   165  11      
TURN   166   168  3      
STRAND   170   174  5      
STRAND   176   178  3      
HELIX   180   185  6      
HELIX   193   196  4      
HELIX   197   199  3      
STRAND   201   205  5      
TURN   211   215  5      
HELIX   219   222  4      
STRAND   229   233  5      
HELIX   242   251  10      
STRAND   252   260  9      
STRAND   263   266  4      
HELIX   271   274  4      
STRAND   278   280  3      
HELIX   289   306  18      
Sequence information
Length: 533 AA [This is the length of the unprocessed precursor] Molecular weight: 56651 Da [This is the MW of the unprocessed precursor] CRC64: C58EB72275C45B35 [This is a checksum on the sequence]
        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 

O43175 in FASTA format

View entry in raw text format (no links)
Report form for errors/updates in this UniProtKB/Swiss-Prot entry

BLAST logo BLAST submission on ExPASy/SIB
or at NCBI (USA)
Tools Sequence analysis tools: ProtParam, ProtScale, Compute pI/Mw, PeptideMass, PeptideCutter, Dotlet (Java)
PROSITE logo ScanProsite, MotifScan SWISS-MODEL Submit a homology modeling request to SWISS-MODEL
NPSA logo NPSA Sequence analysis tools

ExPASy logo ExPASy Home page Site Map Search ExPASy Contact us Swiss-Prot
 Hosted by ch flag SIB Switzerland Mirror sites: Australia  Brazil  Canada  China  Korea
Notice: This page will be replaced with www.uniprot.org. Please send us your feedback!