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P78330

- SERB_HUMAN

UniProt

P78330 - SERB_HUMAN

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Protein

Phosphoserine phosphatase

Gene

PSPH

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalyzes the last step in the biosynthesis of serine from carbohydrates. The reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediates.1 Publication

Catalytic activityi

O-phospho-L(or D)-serine + H2O = L(or D)-serine + phosphate.3 Publications

Cofactori

Mg2+1 PublicationNote: Binds 1 Mg(2+) ion per subunit.1 Publication

Enzyme regulationi

Inhibited by calcium ions.1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei20 – 201Nucleophile
Metal bindingi20 – 201Magnesium
Active sitei22 – 221Proton donor
Metal bindingi22 – 221Magnesium; via carbonyl oxygen
Binding sitei29 – 291Substrate
Binding sitei65 – 651Substrate
Binding sitei158 – 1581Substrate
Metal bindingi179 – 1791Magnesium

GO - Molecular functioni

  1. calcium ion binding Source: UniProtKB
  2. magnesium ion binding Source: UniProtKB
  3. phosphoserine phosphatase activity Source: UniProtKB
  4. protein homodimerization activity Source: UniProtKB

GO - Biological processi

  1. cellular amino acid biosynthetic process Source: Reactome
  2. cellular nitrogen compound metabolic process Source: Reactome
  3. dephosphorylation Source: GOC
  4. L-serine biosynthetic process Source: RefGenome
  5. L-serine metabolic process Source: UniProtKB
  6. response to mechanical stimulus Source: Ensembl
  7. response to nutrient levels Source: Ensembl
  8. response to testosterone Source: Ensembl
  9. small molecule metabolic process Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Amino-acid biosynthesis, Serine biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciMetaCyc:HS07370-MONOMER.
ReactomeiREACT_115789. Serine biosynthesis.
UniPathwayiUPA00135; UER00198.

Names & Taxonomyi

Protein namesi
Recommended name:
Phosphoserine phosphatase (EC:3.1.3.3)
Short name:
PSP
Short name:
PSPase
Alternative name(s):
L-3-phosphoserine phosphatase
O-phosphoserine phosphohydrolase
Gene namesi
Name:PSPH
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 7

Organism-specific databases

HGNCiHGNC:9577. PSPH.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: RefGenome
  2. cytosol Source: Reactome
  3. neuron projection Source: Ensembl
Complete GO annotation...

Pathology & Biotechi

Involvement in diseasei

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.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti32 – 321D → N in PSPHD. 1 Publication
Corresponds to variant rs28933976 [ dbSNP | Ensembl ].
VAR_022378
Natural varianti52 – 521M → T in PSPHD. 1 Publication
VAR_022379

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi23 – 231S → A: Reduces activity by about 50%. 1 Publication
Mutagenesisi23 – 231S → T: Reduces activity by about 80%. 1 Publication
Mutagenesisi29 – 291E → D: Reduces activity by about 95%. 1 Publication
Mutagenesisi29 – 291E → Q: Loss of activity. 1 Publication
Mutagenesisi65 – 651R → A or K: Loss of activity. 1 Publication
Mutagenesisi133 – 1331N → A: Reduces activity by about 75%. 1 Publication
Mutagenesisi182 – 1821T → S: Reduces activity by about 99%. 1 Publication
Mutagenesisi182 – 1821T → V: Reduces activity by about 25%. 1 Publication
Mutagenesisi202 – 2021R → A: Reduces activity by about 99%. 1 Publication
Mutagenesisi202 – 2021R → K: Reduces activity by about 95%. 1 Publication

Keywords - Diseasei

Disease mutation

Organism-specific databases

MIMi614023. phenotype.
Orphaneti79350. 3-phosphoserine phosphatase deficiency.
PharmGKBiPA33928.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 225225Phosphoserine phosphatasePRO_0000156879Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionine1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP78330.
PaxDbiP78330.
PeptideAtlasiP78330.
PRIDEiP78330.

PTM databases

PhosphoSiteiP78330.

Expressioni

Gene expression databases

BgeeiP78330.
CleanExiHS_PSPH.
ExpressionAtlasiP78330. baseline and differential.
GenevestigatoriP78330.

Organism-specific databases

HPAiHPA020376.
HPA029515.

Interactioni

Subunit structurei

Homodimer.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ASF1BQ9NVP21EBI-1042956,EBI-1055650
PRPSAP1Q145581EBI-1042956,EBI-724449
STYXL1Q9Y6J81EBI-1042956,EBI-1044511

Protein-protein interaction databases

BioGridi111695. 6 interactions.
IntActiP78330. 1 interaction.
STRINGi9606.ENSP00000275605.

Structurei

Secondary structure

1
225
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 138Combined sources
Beta strandi15 – 206Combined sources
Turni23 – 253Combined sources
Beta strandi26 – 283Combined sources
Helixi30 – 378Combined sources
Turni41 – 433Combined sources
Turni45 – 473Combined sources
Turni49 – 524Combined sources
Helixi58 – 6912Combined sources
Helixi73 – 8210Combined sources
Helixi91 – 10010Combined sources
Beta strandi104 – 1129Combined sources
Helixi113 – 12210Combined sources
Helixi127 – 1293Combined sources
Beta strandi130 – 1334Combined sources
Beta strandi135 – 1373Combined sources
Beta strandi143 – 1464Combined sources
Beta strandi148 – 1503Combined sources
Helixi151 – 1533Combined sources
Helixi157 – 16913Combined sources
Beta strandi174 – 1807Combined sources
Helixi181 – 1844Combined sources
Turni185 – 1895Combined sources
Beta strandi190 – 1967Combined sources
Helixi203 – 2086Combined sources
Beta strandi210 – 2145Combined sources
Helixi216 – 2194Combined sources
Helixi221 – 2244Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1L8LX-ray2.51A/B1-225[»]
1L8OX-ray2.80A/B1-225[»]
1NNLX-ray1.53A/B1-225[»]
ProteinModelPortaliP78330.
SMRiP78330. Positions 4-225.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP78330.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni109 – 1102Substrate binding

Sequence similaritiesi

Belongs to the SerB family.Curated

Phylogenomic databases

eggNOGiCOG0560.
GeneTreeiENSGT00390000003115.
HOGENOMiHOG000231116.
HOVERGENiHBG057486.
InParanoidiP78330.
KOiK01079.
OMAiYAGFDES.
OrthoDBiEOG7CRTQD.
PhylomeDBiP78330.
TreeFamiTF315024.

Family and domain databases

Gene3Di1.10.150.210. 1 hit.
3.40.50.1000. 2 hits.
InterProiIPR023214. HAD-like_dom.
IPR006383. HAD-SF_hydro_IB_PSP-like.
IPR023190. Pser_Pase_dom_2.
IPR004469. SerB.
[Graphical view]
PfamiPF00702. Hydrolase. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR01488. HAD-SF-IB. 1 hit.
TIGR00338. serB. 1 hit.

Sequencei

Sequence statusi: Complete.

P78330-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MVSHSELRKL FYSADAVCFD VDSTVIREEG IDELAKICGV EDAVSEMTRR
60 70 80 90 100
AMGGAVPFKA ALTERLALIQ PSREQVQRLI AEQPPHLTPG IRELVSRLQE
110 120 130 140 150
RNVQVFLISG GFRSIVEHVA SKLNIPATNV FANRLKFYFN GEYAGFDETQ
160 170 180 190 200
PTAESGGKGK VIKLLKEKFH FKKIIMIGDG ATDMEACPPA DAFIGFGGNV
210 220
IRQQVKDNAK WYITDFVELL GELEE
Length:225
Mass (Da):25,008
Last modified:April 26, 2005 - v2
Checksum:iBD5D72697747FA30
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti2 – 21V → I in CAA71318. (PubMed:9188776)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti32 – 321D → N in PSPHD. 1 Publication
Corresponds to variant rs28933976 [ dbSNP | Ensembl ].
VAR_022378
Natural varianti52 – 521M → T in PSPHD. 1 Publication
VAR_022379

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS5522.1.
RefSeqiNP_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.
XP_006715823.1. XM_006715760.1.
UniGeneiHs.512656.

Genome annotation databases

EnsembliENST00000275605; ENSP00000275605; ENSG00000146733.
ENST00000395471; ENSP00000378854; ENSG00000146733.
ENST00000437355; ENSP00000401639; ENSG00000146733.
GeneIDi5723.
KEGGihsa:5723.
UCSCiuc003trh.3. human.

Polymorphism databases

DMDMi62906870.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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 .
CCDSi CCDS5522.1.
RefSeqi NP_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.
XP_006715823.1. XM_006715760.1.
UniGenei Hs.512656.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1L8L X-ray 2.51 A/B 1-225 [» ]
1L8O X-ray 2.80 A/B 1-225 [» ]
1NNL X-ray 1.53 A/B 1-225 [» ]
ProteinModelPortali P78330.
SMRi P78330. Positions 4-225.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 111695. 6 interactions.
IntActi P78330. 1 interaction.
STRINGi 9606.ENSP00000275605.

PTM databases

PhosphoSitei P78330.

Polymorphism databases

DMDMi 62906870.

Proteomic databases

MaxQBi P78330.
PaxDbi P78330.
PeptideAtlasi P78330.
PRIDEi P78330.

Protocols and materials databases

DNASUi 5723.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000275605 ; ENSP00000275605 ; ENSG00000146733 .
ENST00000395471 ; ENSP00000378854 ; ENSG00000146733 .
ENST00000437355 ; ENSP00000401639 ; ENSG00000146733 .
GeneIDi 5723.
KEGGi hsa:5723.
UCSCi uc003trh.3. human.

Organism-specific databases

CTDi 5723.
GeneCardsi GC07M056046.
HGNCi HGNC:9577. PSPH.
HPAi HPA020376.
HPA029515.
MIMi 172480. gene.
614023. phenotype.
neXtProti NX_P78330.
Orphaneti 79350. 3-phosphoserine phosphatase deficiency.
PharmGKBi PA33928.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0560.
GeneTreei ENSGT00390000003115.
HOGENOMi HOG000231116.
HOVERGENi HBG057486.
InParanoidi P78330.
KOi K01079.
OMAi YAGFDES.
OrthoDBi EOG7CRTQD.
PhylomeDBi P78330.
TreeFami TF315024.

Enzyme and pathway databases

UniPathwayi UPA00135 ; UER00198 .
BioCyci MetaCyc:HS07370-MONOMER.
Reactomei REACT_115789. Serine biosynthesis.

Miscellaneous databases

ChiTaRSi PSPH. human.
EvolutionaryTracei P78330.
GeneWikii PSPH.
GenomeRNAii 5723.
NextBioi 22244.
PROi P78330.
SOURCEi Search...

Gene expression databases

Bgeei P78330.
CleanExi HS_PSPH.
ExpressionAtlasi P78330. baseline and differential.
Genevestigatori P78330.

Family and domain databases

Gene3Di 1.10.150.210. 1 hit.
3.40.50.1000. 2 hits.
InterProi IPR023214. HAD-like_dom.
IPR006383. HAD-SF_hydro_IB_PSP-like.
IPR023190. Pser_Pase_dom_2.
IPR004469. SerB.
[Graphical view ]
Pfami PF00702. Hydrolase. 1 hit.
[Graphical view ]
SUPFAMi SSF56784. SSF56784. 1 hit.
TIGRFAMsi TIGR01488. HAD-SF-IB. 1 hit.
TIGR00338. serB. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Endometrial tumor.
  4. 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. 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. Cited for: VARIANTS PSPHD ASN-32 AND THR-52.

Entry informationi

Entry nameiSERB_HUMAN
AccessioniPrimary (citable) accession number: P78330
Secondary accession number(s): B2RCR5, Q7Z3S5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: April 26, 2005
Last modified: November 26, 2014
This is version 139 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3