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Protein

Phosphoserine phosphatase

Gene

PSPH

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: 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 Mg2+ ion per subunit.1 Publication

Enzyme regulationi

Inhibited by calcium ions.1 Publication

Pathwayi: L-serine biosynthesis

This protein is involved in step 3 of the subpathway that synthesizes L-serine from 3-phospho-D-glycerate.
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. D-3-phosphoglycerate dehydrogenase (PHGDH), D-3-phosphoglycerate dehydrogenase (HEL-S-113), D-3-phosphoglycerate dehydrogenase (PHGDH)
  2. Phosphoserine aminotransferase, Phosphoserine aminotransferase (PSAT1), Phosphoserine aminotransferase (PSAT1)
  3. Phosphoserine phosphatase (PSPH)
This subpathway is part of the pathway L-serine biosynthesis, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-serine from 3-phospho-D-glycerate, the pathway L-serine biosynthesis and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei20Nucleophile1
Metal bindingi20Magnesium1
Active sitei22Proton donor1
Metal bindingi22Magnesium; via carbonyl oxygen1
Binding sitei29Substrate1
Binding sitei65Substrate1
Binding sitei158Substrate1
Metal bindingi179Magnesium1

GO - Molecular functioni

  • calcium ion binding Source: UniProtKB
  • magnesium ion binding Source: UniProtKB
  • phosphoserine phosphatase activity Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB

GO - Biological processi

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.
ZFISH:HS07370-MONOMER.
ReactomeiR-HSA-977347. 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
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:9577. PSPH.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Involvement in diseasei

Phosphoserine phosphatase deficiency (PSPHD)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder that results in pre- and postnatal growth retardation, moderate psychomotor retardation and facial features suggestive of Williams syndrome.
See also OMIM:614023
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_02237832D → N in PSPHD. 1 PublicationCorresponds to variant rs28933976dbSNPEnsembl.1
Natural variantiVAR_02237952M → T in PSPHD. 1 PublicationCorresponds to variant rs104894036dbSNPEnsembl.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi23S → A: Reduces activity by about 50%. 1 Publication1
Mutagenesisi23S → T: Reduces activity by about 80%. 1 Publication1
Mutagenesisi29E → D: Reduces activity by about 95%. 1 Publication1
Mutagenesisi29E → Q: Loss of activity. 1 Publication1
Mutagenesisi65R → A or K: Loss of activity. 1 Publication1
Mutagenesisi133N → A: Reduces activity by about 75%. 1 Publication1
Mutagenesisi182T → S: Reduces activity by about 99%. 1 Publication1
Mutagenesisi182T → V: Reduces activity by about 25%. 1 Publication1
Mutagenesisi202R → A: Reduces activity by about 99%. 1 Publication1
Mutagenesisi202R → K: Reduces activity by about 95%. 1 Publication1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi5723.
MalaCardsiPSPH.
MIMi614023. phenotype.
OpenTargetsiENSG00000146733.
Orphaneti79350. 3-phosphoserine phosphatase deficiency.
PharmGKBiPA33928.

Polymorphism and mutation databases

BioMutaiPSPH.
DMDMi62906870.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001568791 – 225Phosphoserine phosphataseAdd BLAST225

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP78330.
MaxQBiP78330.
PaxDbiP78330.
PeptideAtlasiP78330.
PRIDEiP78330.

PTM databases

DEPODiP78330.
iPTMnetiP78330.
PhosphoSitePlusiP78330.

Expressioni

Gene expression databases

BgeeiENSG00000146733.
CleanExiHS_PSPH.
ExpressionAtlasiP78330. baseline and differential.
GenevisibleiP78330. HS.

Organism-specific databases

HPAiHPA020376.
HPA029515.

Interactioni

Subunit structurei

Homodimer.3 Publications

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi111695. 10 interactors.
IntActiP78330. 1 interactor.
STRINGi9606.ENSP00000275605.

Structurei

Secondary structure

1225
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 13Combined sources8
Beta strandi15 – 20Combined sources6
Turni23 – 25Combined sources3
Beta strandi26 – 28Combined sources3
Helixi30 – 37Combined sources8
Turni41 – 43Combined sources3
Turni45 – 47Combined sources3
Turni49 – 52Combined sources4
Helixi58 – 69Combined sources12
Helixi73 – 82Combined sources10
Helixi91 – 100Combined sources10
Beta strandi104 – 112Combined sources9
Helixi113 – 122Combined sources10
Helixi127 – 129Combined sources3
Beta strandi130 – 133Combined sources4
Beta strandi135 – 137Combined sources3
Beta strandi143 – 146Combined sources4
Beta strandi148 – 150Combined sources3
Helixi151 – 153Combined sources3
Helixi157 – 169Combined sources13
Beta strandi174 – 180Combined sources7
Helixi181 – 184Combined sources4
Turni185 – 189Combined sources5
Beta strandi190 – 196Combined sources7
Helixi203 – 208Combined sources6
Beta strandi210 – 214Combined sources5
Helixi216 – 219Combined sources4
Helixi221 – 224Combined sources4

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP78330.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni109 – 110Substrate binding2

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1615. Eukaryota.
COG0560. LUCA.
GeneTreeiENSGT00390000003115.
HOGENOMiHOG000231116.
HOVERGENiHBG057486.
InParanoidiP78330.
KOiK01079.
OMAiRAQYYVT.
OrthoDBiEOG091G0JBZ.
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.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR01488. HAD-SF-IB. 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)DescriptionActionsGraphical viewLength
Sequence conflicti2V → I in CAA71318 (PubMed:9188776).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_02237832D → N in PSPHD. 1 PublicationCorresponds to variant rs28933976dbSNPEnsembl.1
Natural variantiVAR_02237952M → T in PSPHD. 1 PublicationCorresponds to variant rs104894036dbSNPEnsembl.1

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_006715823.1. XM_006715760.1.
XP_011513763.1. XM_011515461.1.
XP_016867955.1. XM_017012466.1.
XP_016867956.1. XM_017012467.1.
UniGeneiHs.512656.

Genome annotation databases

EnsembliENST00000275605; ENSP00000275605; ENSG00000146733.
ENST00000395471; ENSP00000378854; ENSG00000146733.
ENST00000437355; ENSP00000401639; ENSG00000146733.
GeneIDi5723.
KEGGihsa:5723.
UCSCiuc003trh.4. human.

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.
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_006715823.1. XM_006715760.1.
XP_011513763.1. XM_011515461.1.
XP_016867955.1. XM_017012466.1.
XP_016867956.1. XM_017012467.1.
UniGeneiHs.512656.

3D structure databases

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

Protein-protein interaction databases

BioGridi111695. 10 interactors.
IntActiP78330. 1 interactor.
STRINGi9606.ENSP00000275605.

PTM databases

DEPODiP78330.
iPTMnetiP78330.
PhosphoSitePlusiP78330.

Polymorphism and mutation databases

BioMutaiPSPH.
DMDMi62906870.

Proteomic databases

EPDiP78330.
MaxQBiP78330.
PaxDbiP78330.
PeptideAtlasiP78330.
PRIDEiP78330.

Protocols and materials databases

DNASUi5723.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000275605; ENSP00000275605; ENSG00000146733.
ENST00000395471; ENSP00000378854; ENSG00000146733.
ENST00000437355; ENSP00000401639; ENSG00000146733.
GeneIDi5723.
KEGGihsa:5723.
UCSCiuc003trh.4. human.

Organism-specific databases

CTDi5723.
DisGeNETi5723.
GeneCardsiPSPH.
HGNCiHGNC:9577. PSPH.
HPAiHPA020376.
HPA029515.
MalaCardsiPSPH.
MIMi172480. gene.
614023. phenotype.
neXtProtiNX_P78330.
OpenTargetsiENSG00000146733.
Orphaneti79350. 3-phosphoserine phosphatase deficiency.
PharmGKBiPA33928.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1615. Eukaryota.
COG0560. LUCA.
GeneTreeiENSGT00390000003115.
HOGENOMiHOG000231116.
HOVERGENiHBG057486.
InParanoidiP78330.
KOiK01079.
OMAiRAQYYVT.
OrthoDBiEOG091G0JBZ.
PhylomeDBiP78330.
TreeFamiTF315024.

Enzyme and pathway databases

UniPathwayiUPA00135; UER00198.
BioCyciMetaCyc:HS07370-MONOMER.
ZFISH:HS07370-MONOMER.
ReactomeiR-HSA-977347. Serine biosynthesis.

Miscellaneous databases

ChiTaRSiPSPH. human.
EvolutionaryTraceiP78330.
GeneWikiiPSPH.
GenomeRNAii5723.
PROiP78330.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000146733.
CleanExiHS_PSPH.
ExpressionAtlasiP78330. baseline and differential.
GenevisibleiP78330. HS.

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.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR01488. HAD-SF-IB. 1 hit.
ProtoNetiSearch...

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 2, 2016
This is version 159 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.