Q61753 (SERA_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
D-3-phosphoglycerate dehydrogenase
Short name=3-PGDH
EC=1.1.1.95

Alternative name(s):
A10

Gene names

Name:

Phgdh

Organism

Mus musculus (Mouse)

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	533 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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 process	Amino-acid biosynthesis Serine biosynthesis
Ligand	NAD
Molecular function	Oxidoreductase
PTM	Acetylation Phosphoprotein
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	L-serine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW cell cycle 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 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 function	NAD binding Inferred from electronic annotation. Source: InterPro phosphoglycerate dehydrogenase activity Traceable author statement. Source: MGI
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed By similarity
	Chain	2 – 533	532	D-3-phosphoglycerate dehydrogenase		PRO_0000076014
Regions
	Nucleotide binding	155 – 156	2	NAD By similarity
	Nucleotide binding	234 – 236	3	NAD By similarity
	Nucleotide binding	283 – 286	4	NAD By similarity
Sites
	Active site	236	1	By similarity
	Active site	265	1	By similarity
	Active site	283	1	Proton donor By similarity
	Binding site	78	1	NAD By similarity
	Binding site	175	1	NAD By similarity
	Binding site	207	1	NAD; via carbonyl oxygen By similarity
	Binding site	260	1	NAD By similarity
Amino acid modifications
	Modified residue	2	1	N-acetylalanine By similarity
	Modified residue	371	1	Phosphoserine By similarity
Experimental info
	Sequence conflict	77	1	G → V in AAB67986. Ref.5
	Sequence conflict	87 – 88	2	AA → PP in AAB67986. Ref.5
	Sequence conflict	124	1	A → T in AAB67986. Ref.5
	Sequence conflict	369	1	C → W in AAB67986. Ref.5
	Sequence conflict	377	1	G → A in AAB67986. Ref.5
	Sequence conflict	447	1	M → K in BAC36494. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	Q61753 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 49CBF125AD6A12A5	FASTA	533	56,586
	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

References

	« Hide 'large scale' referencesShow '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: 14645240] [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(2005) [PubMed: 16141072] [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: 15489334] [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, 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: 19114063] [Abstract] Cited for: DISRUPTION PHENOTYPE.
+	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.
IPI	IPI00225961.
RefSeq	NP_058662.2. NM_016966.3.
UniGene	Mm.16898. Mm.371997.
3D structure databases
ProteinModelPortal	Q61753.
SMR	Q61753. Positions 6-517.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q61753. 2 interactions.
STRING	Q61753.
PTM databases
PhosphoSite	Q61753.
2D gel databases
SWISS-2DPAGE	Q61753.
COMPLUYEAST-2DPAGE	Q61753.
REPRODUCTION-2DPAGE	IPI00225961. Q61753.
Proteomic databases
PRIDE	Q61753.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000065793; ENSMUSP00000064755; ENSMUSG00000053398.
GeneID	236539.
KEGG	mmu:236539.
NMPDR	fig|10090.3.peg.26255.
UCSC	uc008qps.1. mouse.
Organism-specific databases
CTD	26227.
MGI	MGI:1355330. Phgdh.
Phylogenomic databases
eggNOG	roNOG06496.
GeneTree	ENSGT00530000063021.
HOGENOM	HBG731446.
HOVERGEN	HBG054241.
InParanoid	Q61753.
OMA	TGVFDGY.
OrthoDB	EOG4Q2DF9.
PhylomeDB	Q61753.
Gene expression databases
ArrayExpress	Q61753.
Bgee	Q61753.
CleanEx	MM_PHGDH.
Genevestigator	Q61753.
GermOnline	ENSMUSG00000053398. Mus musculus.
Family and domain databases
InterPro	IPR006236. D-3-Phosphoglycerate_DH. IPR006139. D-isomer_2_OHA_DH_cat_dom. IPR006140. D-isomer_2_OHA_DH_NAD-bd. IPR016040. NAD(P)-bd_dom. [Graphical view]
Gene3D	G3DSA:3.40.50.720. NAD(P)-bd. 2 hits.
KO	K00058.
PANTHER	PTHR10996:SF20. D3PG_Deh. 1 hit.
Pfam	PF00389. 2-Hacid_dh. 1 hit. PF02826. 2-Hacid_dh_C. 1 hit. [Graphical view]
TIGRFAMs	TIGR01327. PGDH. 1 hit.
PROSITE	PS00065. 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]
ProtoNet	Search...
Other
NextBio	382995.
SOURCE	Search...

Entry information

Entry name

SERA_MOUSE

Accession

Primary (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:	November 16, 2011
This is version 107 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program