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Identification
HMDB Protein ID HMDBP00922
Secondary Accession Numbers
  • 6210
  • HMDBP04975
Name D-3-phosphoglycerate dehydrogenase
Synonyms
  1. 3-PGDH
Gene Name PHGDH
Protein Type Unknown
Biological Properties
General Function Involved in phosphoglycerate dehydrogenase activity
Specific Function Not Available
Pathways
  • 3-Phosphoglycerate dehydrogenase deficiency
  • Dihydropyrimidine Dehydrogenase Deficiency (DHPD)
  • Dimethylglycine Dehydrogenase Deficiency
  • Dimethylglycine Dehydrogenase Deficiency
  • Glycine, serine and threonine metabolism
  • Glycine, serine and threonine metabolism
  • Hyperglycinemia, non-ketotic
  • L-serine biosynthesis
  • Non Ketotic Hyperglycinemia
  • Sarcosinemia
Reactions
3-Phosphoglyceric acid + NAD → Phosphohydroxypyruvic acid + NADH details
2-Hydroxyglutarate + NAD → Oxoglutaric acid + NADH details
3-Phosphoglyceric acid + NAD → Phosphohydroxypyruvic acid + NADH + Hydrogen Ion details
GO Classification
Biological Process
cellular nitrogen compound metabolic process
brain development
L-serine biosynthetic process
Cellular Component
cytosol
Function
binding
nucleotide binding
catalytic activity
nad or nadh binding
phosphoglycerate dehydrogenase activity
oxidoreductase activity, acting on the ch-oh group of donors, nad or nadp as acceptor
cofactor binding
oxidoreductase activity, acting on ch-oh group of donors
oxidoreductase activity
Molecular Function
electron carrier activity
NAD binding
phosphoglycerate dehydrogenase activity
Process
metabolic process
cellular metabolic process
serine family amino acid metabolic process
oxidation reduction
l-serine metabolic process
cellular amino acid and derivative metabolic process
cellular amino acid metabolic process
l-serine biosynthetic process
Cellular Location Not Available
Gene Properties
Chromosome Location 1
Locus 1p12
SNPs PHGDH
Gene Sequence
>1602 bp
ATGGCTTTTGCAAATCTGCGGAAAGTGCTCATCAGTGACAGCCTGGACCCTTGCTGCCGG
AAGATCTTGCAAGAGGGAGGGCTGCAGGTGGTGGAAAAGCAGAACCTTAGCAAAGAGGAG
CTGATAGCGGAGCTGCAGGACTGTGAAGGCCTTATTGTTCGCTCTGCCACCAAGGTGACC
GCTGATGTCATCAACGCAGCTGAGAAACTCCAGGTGGTGGGCAGGGCTGGCACAGGTGTG
GACAATGTGGATCTGGAGGCCGCAACAAGGAAGGGCATCTTGGTTATGAACACCCCCAAT
GGGAACAGCCTCAGTGCCGCAGAACTCACTTGTGGAATGATCATGTGCCTGGCCAGGCAG
ATTCCCCAGGCGACGGCTTCGATGAAGGACGGCAAATGGGAGCGGAAGAAGTTCATGGGA
ACAGAGCTGAATGGAAAGACCCTGGGAATTCTTGGCCTGGGCAGGATTGGGAGAGAGGTA
GCTACCCGGATGCAGTCCTTTGGGATGAAGACTATAGGGTATGACCCCATCATTTCCCCA
GAGGTCTCGGCCTCCTTTGGTGTTCAGCAGCTGCCCCTGGAGGAGATCTGGCCTCTCTGT
GATTTCATCACTGTGCACACTCCTCTCCTGCCCTCCACGACAGGCTTGCTGAATGACAAC
ACCTTTGCCCAGTGCAAGAAGGGGGTGCGTGTGGTGAACTGTGCCCGTGGAGGGATCGTG
GACGAAGGCGCCCTGCTCCGGGCCCTGCAGTCTGGCCAGTGTGCCGGGGCTGCACTGGAC
GTGTTTACGGAAGAGCCGCCACGGGACCGGGCCTTGGTGGACCATGAGAATGTCATCAGC
TGTCCCCACCTGGGTGCCAGCACCAAGGAGGCTCAGAGCCGCTGTGGGGAGGAAATTGCT
GTTCAGTTCGTGGACATGGTGAAGGGGAAATCTCTCACGGGGGTTGTGAATGCCCAGGCC
CTTACCAGTGCCTTCTCTCCACACACCAAGCCTTGGATTGGTCTGGCAGAAGCTCTGGGG
ACACTGATGCGAGCCTGGGCTGGGTCCCCCAAAGGGACCATCCAGGTGATAACACAGGGA
ACATCCCTGAAGAATGCTGGGAACTGCCTAAGCCCCGCAGTCATTGTCGGCCTCCTGAAA
GAGGCTTCCAAGCAGGCGGATGTGAACTTGGTGAACGCTAAGCTGCTGGTGAAAGAGGCT
GGCCTCAATGTCACCACCTCCCACAGCCCTGCTGCACCAGGGGAGCAAGGCTTCGGGGAA
TGCCTCCTGGCCGTGGCCCTGGCAGGCGCCCCTTACCAGGCTGTGGGCTTGGTCCAAGGC
ACTACACCTGTACTGCAGGGGCTCAATGGAGCTGTCTTCAGGCCAGAAGTGCCTCTCCGC
AGGGACCTGCCCCTGCTCCTATTCCGGACTCAGACCTCTGACCCTGCAATGCTGCCTACC
ATGATTGGCCTCCTGGCAGAGGCAGGCGTGCGGCTGCTGTCCTACCAGACTTCACTGGTG
TCAGATGGGGAGACCTGGCACGTCATGGGCATCTCCTCCTTGCTGCCCAGCCTGGAAGCG
TGGAAGCAGCATGTGACTGAAGCCTTCCAGTTCCACTTCTAA
Protein Properties
Number of Residues 533
Molecular Weight 56650.03
Theoretical pI 6.715
Pfam Domain Function
Signals Not Available
Transmembrane Regions Not Available
Protein Sequence
>D-3-phosphoglycerate dehydrogenase
MAFANLRKVLISDSLDPCCRKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKVT
ADVINAAEKLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCGMIMCLARQ
IPQATASMKDGKWERKKFMGTELNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISP
EVSASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIV
DEGALLRALQSGQCAGAALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSRCGEEIA
VQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEALGTLMRAWAGSPKGTIQVITQG
TSLKNAGNCLSPAVIVGLLKEASKQADVNLVNAKLLVKEAGLNVTTSHSPAAPGEQGFGE
CLLAVALAGAPYQAVGLVQGTTPVLQGLNGAVFRPEVPLRRDLPLLLFRTQTSDPAMLPT
MIGLLAEAGVRLLSYQTSLVSDGETWHVMGISSLLPSLEAWKQHVTEAFQFHF
GenBank ID Protein 2674062
UniProtKB/Swiss-Prot ID O43175
UniProtKB/Swiss-Prot Entry Name SERA_HUMAN
PDB IDs
GenBank Gene ID AF006043
GeneCard ID PHGDH
GenAtlas ID PHGDH
HGNC ID HGNC:8923
References
General References
  1. 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, 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 TO, 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: Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet. 2004 Jan;36(1):40-5. Epub 2003 Dec 21. [PubMed:14702039 ]
  2. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7. [PubMed:15489334 ]
  3. Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D, Dunham A, Scott CE, Howe KL, Woodfine K, Spencer CC, Jones MC, Gillson C, Searle S, Zhou Y, Kokocinski F, McDonald L, Evans R, Phillips K, Atkinson A, Cooper R, Jones C, Hall RE, Andrews TD, Lloyd C, Ainscough R, Almeida JP, Ambrose KD, Anderson F, Andrew RW, Ashwell RI, Aubin K, Babbage AK, Bagguley CL, Bailey J, Beasley H, Bethel G, Bird CP, Bray-Allen S, Brown JY, Brown AJ, Buckley D, Burton J, Bye J, Carder C, Chapman JC, Clark SY, Clarke G, Clee C, Cobley V, Collier RE, Corby N, Coville GJ, Davies J, Deadman R, Dunn M, Earthrowl M, Ellington AG, Errington H, Frankish A, Frankland J, French L, Garner P, Garnett J, Gay L, Ghori MR, Gibson R, Gilby LM, Gillett W, Glithero RJ, Grafham DV, Griffiths C, Griffiths-Jones S, Grocock R, Hammond S, Harrison ES, Hart E, Haugen E, Heath PD, Holmes S, Holt K, Howden PJ, Hunt AR, Hunt SE, Hunter G, Isherwood J, James R, Johnson C, Johnson D, Joy A, Kay M, Kershaw JK, Kibukawa M, Kimberley AM, King A, Knights AJ, Lad H, Laird G, Lawlor S, Leongamornlert DA, Lloyd DM, Loveland J, Lovell J, Lush MJ, Lyne R, Martin S, Mashreghi-Mohammadi M, Matthews L, Matthews NS, McLaren S, Milne S, Mistry S, Moore MJ, Nickerson T, O'Dell CN, Oliver K, Palmeiri A, Palmer SA, Parker A, Patel D, Pearce AV, Peck AI, Pelan S, Phelps K, Phillimore BJ, Plumb R, Rajan J, Raymond C, Rouse G, Saenphimmachak C, Sehra HK, Sheridan E, Shownkeen R, Sims S, Skuce CD, Smith M, Steward C, Subramanian S, Sycamore N, Tracey A, Tromans A, Van Helmond Z, Wall M, Wallis JM, White S, Whitehead SL, Wilkinson JE, Willey DL, Williams H, Wilming L, Wray PW, Wu Z, Coulson A, Vaudin M, Sulston JE, Durbin R, Hubbard T, Wooster R, Dunham I, Carter NP, McVean G, Ross MT, Harrow J, Olson MV, Beck S, Rogers J, Bentley DR, Banerjee R, Bryant SP, Burford DC, Burrill WD, Clegg SM, Dhami P, Dovey O, Faulkner LM, Gribble SM, Langford CF, Pandian RD, Porter KM, Prigmore E: The DNA sequence and biological annotation of human chromosome 1. Nature. 2006 May 18;441(7091):315-21. [PubMed:16710414 ]
  4. Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP: A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi: 10.1073/pnas.0805139105. Epub 2008 Jul 31. [PubMed:18669648 ]
  5. Cho HM, Jun DY, Bae MA, Ahn JD, Kim YH: Nucleotide sequence and differential expression of the human 3-phosphoglycerate dehydrogenase gene. Gene. 2000 Mar 7;245(1):193-201. [PubMed:10713460 ]
  6. Klomp LW, de Koning TJ, Malingre HE, van Beurden EA, Brink M, Opdam FL, Duran M, Jaeken J, Pineda M, Van Maldergem L, Poll-The BT, van den Berg IE, Berger R: Molecular characterization of 3-phosphoglycerate dehydrogenase deficiency--a neurometabolic disorder associated with reduced L-serine biosynthesis. Am J Hum Genet. 2000 Dec;67(6):1389-99. Epub 2000 Oct 27. [PubMed:11055895 ]
  7. Pind S, Slominski E, Mauthe J, Pearlman K, Swoboda KJ, Wilkins JA, Sauder P, Natowicz MR: V490M, a common mutation in 3-phosphoglycerate dehydrogenase deficiency, causes enzyme deficiency by decreasing the yield of mature enzyme. J Biol Chem. 2002 Mar 1;277(9):7136-43. Epub 2001 Dec 20. [PubMed:11751922 ]
  8. Al-Dhaheri MH, Shah YM, Basrur V, Pind S, Rowan BG: Identification of novel proteins induced by estradiol, 4-hydroxytamoxifen and acolbifene in T47D breast cancer cells. Steroids. 2006 Nov;71(11-12):966-78. Epub 2006 Sep 1. [PubMed:16949628 ]
  9. Jun DY, Park HS, Lee JY, Baek JY, Park HK, Fukui K, Kim YH: Positive regulation of promoter activity of human 3-phosphoglycerate dehydrogenase (PHGDH) gene is mediated by transcription factors Sp1 and NF-Y. Gene. 2008 May 15;414(1-2):106-14. doi: 10.1016/j.gene.2008.02.018. Epub 2008 Mar 4. [PubMed:18378410 ]
  10. Tabatabaie L, de Koning TJ, Geboers AJ, van den Berg IE, Berger R, Klomp LW: Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics. Hum Mutat. 2009 May;30(5):749-56. doi: 10.1002/humu.20934. [PubMed:19235232 ]