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P78330 (SERB_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 133. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (7) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Phosphoserine phosphatase

Short name=PSP
Short name=PSPase
EC=3.1.3.3
Alternative name(s):
L-3-phosphoserine phosphatase
O-phosphoserine phosphohydrolase
Gene names
Name:PSPH
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length225 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the last step in the biosynthesis of serine from carbohydrates. The reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediates. Ref.9

Catalytic activity

O-phospho-L(or D)-serine + H2O = L(or D)-serine + phosphate. Ref.8 Ref.9 Ref.10

Cofactor

Binds 1 magnesium ion per subunit. Ref.10

Enzyme regulation

Inhibited by calcium ions. Ref.10

Pathway

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

Subunit structure

Homodimer. Ref.8 Ref.9

Involvement in disease

Phosphoserine phosphatase deficiency (PSPHD) [MIM:614023]: A disorder that results in pre- and postnatal growth retardation, moderate psychomotor retardation and facial features suggestive of Williams syndrome.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.11

Sequence similarities

Belongs to the SerB family.

Ontologies

Keywords
   Biological processAmino-acid biosynthesis
Serine biosynthesis
   DiseaseDisease mutation
   LigandMagnesium
Metal-binding
   Molecular functionHydrolase
   PTMAcetylation
Phosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processL-serine biosynthetic process

Inferred from Biological aspect of Ancestor. Source: RefGenome

L-serine metabolic process

Inferred from direct assay Ref.10. Source: UniProtKB

cellular amino acid biosynthetic process

Traceable author statement. Source: Reactome

cellular nitrogen compound metabolic process

Traceable author statement. Source: Reactome

dephosphorylation

Inferred from direct assay Ref.11Ref.10. Source: GOC

response to mechanical stimulus

Inferred from electronic annotation. Source: Ensembl

response to nutrient levels

Inferred from electronic annotation. Source: Ensembl

response to testosterone

Inferred from electronic annotation. Source: Ensembl

small molecule metabolic process

Traceable author statement. Source: Reactome

   Cellular_componentcytoplasm

Inferred from Biological aspect of Ancestor. Source: RefGenome

cytosol

Traceable author statement. Source: Reactome

neuron projection

Inferred from electronic annotation. Source: Ensembl

   Molecular_functioncalcium ion binding

Inferred from direct assay Ref.9Ref.10. Source: UniProtKB

magnesium ion binding

Inferred from direct assay Ref.10. Source: UniProtKB

phosphoserine phosphatase activity

Inferred from direct assay Ref.11Ref.10. Source: UniProtKB

protein homodimerization activity

Inferred from physical interaction Ref.9. Source: UniProtKB

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 225225Phosphoserine phosphatase
PRO_0000156879

Regions

Region109 – 1102Substrate binding

Sites

Active site201Nucleophile Ref.8 Ref.9
Active site221Proton donor Ref.8 Ref.9
Metal binding201Magnesium
Metal binding221Magnesium; via carbonyl oxygen
Metal binding1791Magnesium
Binding site291Substrate
Binding site651Substrate
Binding site1581Substrate

Amino acid modifications

Modified residue11N-acetylmethionine Ref.6

Natural variations

Natural variant321D → N in PSPHD. Ref.11
Corresponds to variant rs28933976 [ dbSNP | Ensembl ].
VAR_022378
Natural variant521M → T in PSPHD. Ref.11
VAR_022379

Experimental info

Mutagenesis231S → A: Reduces activity by about 50%. Ref.8
Mutagenesis231S → T: Reduces activity by about 80%. Ref.8
Mutagenesis291E → D: Reduces activity by about 95%. Ref.8
Mutagenesis291E → Q: Loss of activity. Ref.8
Mutagenesis651R → A or K: Loss of activity. Ref.8
Mutagenesis1331N → A: Reduces activity by about 75%. Ref.8
Mutagenesis1821T → S: Reduces activity by about 99%. Ref.8
Mutagenesis1821T → V: Reduces activity by about 25%. Ref.8
Mutagenesis2021R → A: Reduces activity by about 99%. Ref.8
Mutagenesis2021R → K: Reduces activity by about 95%. Ref.8
Sequence conflict21V → I in CAA71318. Ref.1

Secondary structure

.................................................. 225
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P78330 [UniParc].

Last modified April 26, 2005. Version 2.
Checksum: BD5D72697747FA30

FASTA22525,008
        10         20         30         40         50         60 
MVSHSELRKL FYSADAVCFD VDSTVIREEG IDELAKICGV EDAVSEMTRR AMGGAVPFKA 

        70         80         90        100        110        120 
ALTERLALIQ PSREQVQRLI AEQPPHLTPG IRELVSRLQE RNVQVFLISG GFRSIVEHVA 

       130        140        150        160        170        180 
SKLNIPATNV FANRLKFYFN GEYAGFDETQ PTAESGGKGK VIKLLKEKFH FKKIIMIGDG 

       190        200        210        220 
ATDMEACPPA DAFIGFGGNV IRQQVKDNAK WYITDFVELL GELEE 

« Hide

References

« Hide 'large scale' references
[1]"Human L-3-phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate."
Collet J.-F., Gerin I., Rider M.H., Veiga-Da-Cunha M., Van Schaftingen E.
FEBS Lett. 408:281-284(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Kidney.
[3]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Endometrial tumor.
[4]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].
[5]"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].
[6]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[7]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]"Molecular basis for the local conformational rearrangement of human phosphoserine phosphatase."
Kim H.Y., Heo Y.S., Kim J.H., Park M.H., Moon J., Kim E., Kwon D., Yoon J., Shin D., Jeong E.J., Park S.Y., Lee T.G., Jeon Y.H., Ro S., Cho J.M., Hwang K.Y.
J. Biol. Chem. 277:46651-46658(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.51 ANGSTROMS) OF 3-225 IN COMPLEXES WITH INHIBITOR 2-AMINO-3-PHOSPHONOPROPIONIC ACID; SERINE AND PHOSPHATE ION, SUBUNIT, CATALYTIC ACTIVITY, ACTIVE SITE, MUTAGENESIS OF SER-23; GLU-29; ARG-65; ASN-133; THR-182 AND ARG-202.
[9]"High-resolution structure of human phosphoserine phosphatase in open conformation."
Peeraer Y., Rabijns A., Verboven C., Collet J.F., Van Schaftingen E., De Ranter C.
Acta Crystallogr. D 59:971-977(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.53 ANGSTROMS) OF 3-225 IN COMPLEX WITH CALCIUM IONS, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, SUBUNIT.
[10]"How calcium inhibits the magnesium-dependent enzyme human phosphoserine phosphatase."
Peeraer Y., Rabijns A., Collet J.F., Van Schaftingen E., De Ranter C.
Eur. J. Biochem. 271:3421-3427(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.53 ANGSTROMS) OF 3-225 IN COMPLEX WITH CALCIUM IONS, COFACTOR, CATALYTIC ACTIVITY, ENZYME REGULATION.
[11]"Mutations responsible for 3-phosphoserine phosphatase deficiency."
Veiga-da-Cunha M., Collet J.F., Prieur B., Jaeken J., Peeraer Y., Rabbijns A., Van Schaftingen E.
Eur. J. Hum. Genet. 12:163-166(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS PSPHD ASN-32 AND THR-52.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Y10275 mRNA. Translation: CAA71318.1.
AK315235 mRNA. Translation: BAG37662.1.
BX537439 mRNA. Translation: CAD97681.1.
CH471140 Genomic DNA. Translation: EAX07968.1.
BC063614 mRNA. Translation: AAH63614.1.
RefSeqNP_004568.2. NM_004577.3.
XP_005271830.1. XM_005271773.1.
XP_005271831.1. XM_005271774.1.
XP_005271832.1. XM_005271775.1.
XP_005271833.1. XM_005271776.1.
XP_005271834.1. XM_005271777.2.
UniGeneHs.512656.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1L8LX-ray2.51A/B3-225[»]
1L8OX-ray2.80A/B3-225[»]
1NNLX-ray1.53A/B3-225[»]
ProteinModelPortalP78330.
SMRP78330. Positions 4-225.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid111695. 6 interactions.
IntActP78330. 1 interaction.
STRING9606.ENSP00000275605.

PTM databases

PhosphoSiteP78330.

Polymorphism databases

DMDM62906870.

Proteomic databases

PaxDbP78330.
PeptideAtlasP78330.
PRIDEP78330.

Protocols and materials databases

DNASU5723.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000275605; ENSP00000275605; ENSG00000146733.
ENST00000395471; ENSP00000378854; ENSG00000146733.
ENST00000437355; ENSP00000401639; ENSG00000146733.
GeneID5723.
KEGGhsa:5723.
UCSCuc003trh.3. human.

Organism-specific databases

CTD5723.
GeneCardsGC07M056046.
HGNCHGNC:9577. PSPH.
HPAHPA020376.
HPA029515.
MIM172480. gene.
614023. phenotype.
neXtProtNX_P78330.
Orphanet79350. 3-phosphoserine phosphatase deficiency.
PharmGKBPA33928.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0560.
HOGENOMHOG000231116.
HOVERGENHBG057486.
InParanoidP78330.
KOK01079.
OMAYAGFDES.
OrthoDBEOG7CRTQD.
PhylomeDBP78330.
TreeFamTF315024.

Enzyme and pathway databases

BioCycMetaCyc:HS07370-MONOMER.
ReactomeREACT_111217. Metabolism.
UniPathwayUPA00135; UER00198.

Gene expression databases

ArrayExpressP78330.
BgeeP78330.
CleanExHS_PSPH.
GenevestigatorP78330.

Family and domain databases

Gene3D1.10.150.210. 1 hit.
3.40.50.1000. 2 hits.
InterProIPR023214. HAD-like_dom.
IPR006383. HAD-SF_hydro_IB_PSP-like.
IPR023190. Pser_Pase_dom_2.
IPR004469. SerB.
[Graphical view]
PfamPF00702. Hydrolase. 1 hit.
[Graphical view]
SUPFAMSSF56784. SSF56784. 1 hit.
TIGRFAMsTIGR01488. HAD-SF-IB. 1 hit.
TIGR00338. serB. 1 hit.
ProtoNetSearch...

Other

ChiTaRSPSPH. human.
EvolutionaryTraceP78330.
GeneWikiPSPH.
GenomeRNAi5723.
NextBio22244.
PROP78330.
SOURCESearch...

Entry information

Entry nameSERB_HUMAN
AccessionPrimary (citable) accession number: P78330
Secondary accession number(s): B2RCR5, Q7Z3S5
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: April 26, 2005
Last modified: April 16, 2014
This is version 133 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
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

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

MIM cross-references

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

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 7

Human chromosome 7: entries, gene names and cross-references to MIM