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Protein

Pyridoxal phosphate phosphatase

Gene

PDXP

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

Functioni

Protein serine phosphatase that dephosphorylates 'Ser-3' in cofilin and probably also dephosphorylates phospho-serine residues in DSTN. Regulates cofilin-dependent actin cytoskeleton reorganization. Required for normal progress through mitosis and normal cytokinesis. Does not dephosphorylate phospho-threonines in LIMK1. Does not dephosphorylate peptides containing phospho-tyrosine. Pyridoxal phosphate phosphatase. Has some activity towards pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PMP) and pyridoxine 5'-phosphate (PNP), with a highest activity with PLP followed by PNP.2 Publications

Catalytic activityi

Pyridoxal 5'-phosphate + H2O = pyridoxal + phosphate.By similarity
O-phospho-L(or D)-serine + H2O = L(or D)-serine + phosphate.1 Publication

Cofactori

Mg2+2 PublicationsNote: Divalent metal ions. Mg2+ is the most effective.2 Publications

Enzyme regulationi

Inhibited by NaF, Zn2+, Ca2+, Mn2+ and EDTA.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei25 – 251Nucleophile1 Publication
Metal bindingi25 – 251Magnesium
Active sitei27 – 271Proton donor1 Publication
Metal bindingi27 – 271Magnesium; via carbonyl oxygen
Binding sitei182 – 1821Substrate
Binding sitei213 – 2131Substrate
Metal bindingi238 – 2381Magnesium

GO - Molecular functioni

  • heat shock protein binding Source: MGI
  • magnesium ion binding Source: UniProtKB
  • phosphoprotein phosphatase activity Source: UniProtKB
  • phosphoserine phosphatase activity Source: UniProtKB-EC
  • pyridoxal phosphatase activity Source: UniProtKB

GO - Biological processi

  • actin rod assembly Source: MGI
  • cellular response to ATP Source: MGI
  • positive regulation of actin filament depolymerization Source: UniProtKB
  • protein dephosphorylation Source: UniProtKB
  • pyridoxal phosphate catabolic process Source: UniProtKB
  • regulation of cytokinesis Source: UniProtKB
  • regulation of mitotic nuclear division Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium, Metal-binding, Pyridoxal phosphate

Enzyme and pathway databases

BRENDAi3.1.3.74. 2681.
SABIO-RKQ96GD0.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxal phosphate phosphatase (EC:3.1.3.31 Publication, EC:3.1.3.74By similarity)
Short name:
PLP phosphatase
Alternative name(s):
Chronophin
Gene namesi
Name:PDXP
Synonyms:CIN, PLP, PLPP
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 22

Organism-specific databases

HGNCiHGNC:30259. PDXP.

Subcellular locationi

  • Cytoplasmcytosol 1 Publication
  • Cytoplasmcytoskeleton 1 Publication
  • Cell projectionruffle membrane 1 Publication; Peripheral membrane protein 1 Publication; Cytoplasmic side 1 Publication
  • Cell projectionlamellipodium membrane 1 Publication; Peripheral membrane protein 1 Publication; Cytoplasmic side 1 Publication
  • Cell membrane 1 Publication; Peripheral membrane protein 1 Publication; Cytoplasmic side 1 Publication

  • Note: Colocalizes with the actin cytoskeleton in membrane ruffles and lamellipodia. Diffusely distributed throughout the cytosol during pro-metaphase and metaphase. Detected at the dynamic cell poles during telophase. Detected at the cleavage furrow and contractile ring during cytokinesis. Transiently detected at the plasma membrane in late stages of cytokinesis. Detected at the midbody.1 Publication

GO - Cellular componenti

  • cytoskeleton Source: UniProtKB-SubCell
  • cytosol Source: UniProtKB
  • extracellular exosome Source: UniProtKB
  • lamellipodium membrane Source: UniProtKB-SubCell
  • ruffle membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cell projection, Cytoplasm, Cytoskeleton, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi25 – 251D → N: Abolishes phosphatase activity. 1 Publication

Organism-specific databases

PharmGKBiPA134882132.

Polymorphism and mutation databases

BioMutaiPDXP.
DMDMi44888310.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 296296Pyridoxal phosphate phosphatasePRO_0000068837Add
BLAST

Proteomic databases

EPDiQ96GD0.
MaxQBiQ96GD0.
PaxDbiQ96GD0.
PeptideAtlasiQ96GD0.
PRIDEiQ96GD0.

2D gel databases

REPRODUCTION-2DPAGEIPI00025340.
UCD-2DPAGEQ96GD0.

PTM databases

DEPODiQ96GD0.
iPTMnetiQ96GD0.
PhosphoSiteiQ96GD0.

Expressioni

Tissue specificityi

Ubiquitous. Highly expressed in all the regions of central nerve system except the spinal cord. Also expressed at high level in liver and testis. In fetus, it is weakly expressed in all organs except brain.2 Publications

Gene expression databases

BgeeiENSG00000241360.
CleanExiHS_PDXP.
ExpressionAtlasiQ96GD0. baseline and differential.
GenevisibleiQ96GD0. HS.

Organism-specific databases

HPAiHPA000531.

Interactioni

Subunit structurei

Homodimer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
Arrb1P290662EBI-4303060,EBI-4303019From a different organism.

GO - Molecular functioni

  • heat shock protein binding Source: MGI

Protein-protein interaction databases

BioGridi121330. 6 interactions.
IntActiQ96GD0. 2 interactions.
STRINGi9606.ENSP00000215904.

Structurei

Secondary structure

1
296
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi9 – 1810Combined sources
Beta strandi20 – 245Combined sources
Turni27 – 293Combined sources
Beta strandi30 – 323Combined sources
Helixi40 – 4910Combined sources
Beta strandi53 – 586Combined sources
Helixi65 – 7410Combined sources
Helixi82 – 843Combined sources
Beta strandi85 – 873Combined sources
Helixi88 – 9912Combined sources
Beta strandi104 – 1063Combined sources
Beta strandi109 – 1146Combined sources
Helixi116 – 1249Combined sources
Beta strandi143 – 1486Combined sources
Helixi156 – 16611Combined sources
Beta strandi171 – 1766Combined sources
Beta strandi181 – 1833Combined sources
Beta strandi189 – 1913Combined sources
Helixi193 – 20412Combined sources
Helixi217 – 2259Combined sources
Helixi230 – 2323Combined sources
Beta strandi233 – 2386Combined sources
Turni240 – 2423Combined sources
Helixi243 – 2508Combined sources
Beta strandi253 – 2619Combined sources
Helixi264 – 2729Combined sources
Helixi276 – 2783Combined sources
Beta strandi281 – 2866Combined sources
Helixi287 – 2937Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CFRX-ray2.40A1-296[»]
2CFSX-ray2.40A1-296[»]
2CFTX-ray1.80A1-296[»]
2OYCX-ray1.72A2-296[»]
2P27X-ray1.90A2-296[»]
2P69X-ray2.25A2-296[»]
ProteinModelPortaliQ96GD0.
SMRiQ96GD0. Positions 1-294.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ96GD0.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni58 – 625Substrate binding

Sequence similaritiesi

Belongs to the HAD-like hydrolase superfamily.Curated

Phylogenomic databases

eggNOGiKOG2882. Eukaryota.
COG0647. LUCA.
GeneTreeiENSGT00510000047020.
HOGENOMiHOG000068104.
HOVERGENiHBG049429.
InParanoidiQ96GD0.
KOiK07758.
OMAiMIGDRLY.
OrthoDBiEOG091G0I92.
PhylomeDBiQ96GD0.
TreeFamiTF314344.

Family and domain databases

Gene3Di3.40.50.1000. 2 hits.
3.40.50.10410. 1 hit.
InterProiIPR023214. HAD-like_dom.
IPR006357. HAD-SF_hydro_IIA.
IPR023215. NPhePase-like_dom.
IPR006349. PGP_euk.
[Graphical view]
PfamiPF13344. Hydrolase_6. 1 hit.
[Graphical view]
PIRSFiPIRSF000915. PGP-type_phosphatase. 1 hit.
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR01460. HAD-SF-IIA. 1 hit.
TIGR01452. PGP_euk. 1 hit.

Sequencei

Sequence statusi: Complete.

Q96GD0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARCERLRGA ALRDVLGRAQ GVLFDCDGVL WNGERAVPGA PELLERLARA
60 70 80 90 100
GKAALFVSNN SRRARPELAL RFARLGFGGL RAEQLFSSAL CAARLLRQRL
110 120 130 140 150
PGPPDAPGAV FVLGGEGLRA ELRAAGLRLA GDPSAGDGAA PRVRAVLVGY
160 170 180 190 200
DEHFSFAKLR EACAHLRDPE CLLVATDRDP WHPLSDGSRT PGTGSLAAAV
210 220 230 240 250
ETASGRQALV VGKPSPYMFE CITENFSIDP ARTLMVGDRL ETDILFGHRC
260 270 280 290
GMTTVLTLTG VSRLEEAQAY LAAGQHDLVP HYYVESIADL TEGLED
Length:296
Mass (Da):31,698
Last modified:March 1, 2004 - v2
Checksum:i33466C35A76B458C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY125047 mRNA. Translation: AAM94358.1.
Z83844 Genomic DNA. Translation: CAB63038.1.
BC000320 mRNA. Translation: AAH00320.1.
BC009756 mRNA. Translation: AAH09756.2.
BC064922 mRNA. Translation: AAH64922.1.
CCDSiCCDS13953.1.
RefSeqiNP_064711.1. NM_020315.4.
UniGeneiHs.632762.

Genome annotation databases

EnsembliENST00000215904; ENSP00000215904; ENSG00000241360.
GeneIDi57026.
KEGGihsa:57026.
UCSCiuc003atm.2. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY125047 mRNA. Translation: AAM94358.1.
Z83844 Genomic DNA. Translation: CAB63038.1.
BC000320 mRNA. Translation: AAH00320.1.
BC009756 mRNA. Translation: AAH09756.2.
BC064922 mRNA. Translation: AAH64922.1.
CCDSiCCDS13953.1.
RefSeqiNP_064711.1. NM_020315.4.
UniGeneiHs.632762.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CFRX-ray2.40A1-296[»]
2CFSX-ray2.40A1-296[»]
2CFTX-ray1.80A1-296[»]
2OYCX-ray1.72A2-296[»]
2P27X-ray1.90A2-296[»]
2P69X-ray2.25A2-296[»]
ProteinModelPortaliQ96GD0.
SMRiQ96GD0. Positions 1-294.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121330. 6 interactions.
IntActiQ96GD0. 2 interactions.
STRINGi9606.ENSP00000215904.

PTM databases

DEPODiQ96GD0.
iPTMnetiQ96GD0.
PhosphoSiteiQ96GD0.

Polymorphism and mutation databases

BioMutaiPDXP.
DMDMi44888310.

2D gel databases

REPRODUCTION-2DPAGEIPI00025340.
UCD-2DPAGEQ96GD0.

Proteomic databases

EPDiQ96GD0.
MaxQBiQ96GD0.
PaxDbiQ96GD0.
PeptideAtlasiQ96GD0.
PRIDEiQ96GD0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000215904; ENSP00000215904; ENSG00000241360.
GeneIDi57026.
KEGGihsa:57026.
UCSCiuc003atm.2. human.

Organism-specific databases

CTDi57026.
GeneCardsiPDXP.
HGNCiHGNC:30259. PDXP.
HPAiHPA000531.
MIMi609246. gene.
neXtProtiNX_Q96GD0.
PharmGKBiPA134882132.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2882. Eukaryota.
COG0647. LUCA.
GeneTreeiENSGT00510000047020.
HOGENOMiHOG000068104.
HOVERGENiHBG049429.
InParanoidiQ96GD0.
KOiK07758.
OMAiMIGDRLY.
OrthoDBiEOG091G0I92.
PhylomeDBiQ96GD0.
TreeFamiTF314344.

Enzyme and pathway databases

BRENDAi3.1.3.74. 2681.
SABIO-RKQ96GD0.

Miscellaneous databases

EvolutionaryTraceiQ96GD0.
GenomeRNAii57026.
PROiQ96GD0.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000241360.
CleanExiHS_PDXP.
ExpressionAtlasiQ96GD0. baseline and differential.
GenevisibleiQ96GD0. HS.

Family and domain databases

Gene3Di3.40.50.1000. 2 hits.
3.40.50.10410. 1 hit.
InterProiIPR023214. HAD-like_dom.
IPR006357. HAD-SF_hydro_IIA.
IPR023215. NPhePase-like_dom.
IPR006349. PGP_euk.
[Graphical view]
PfamiPF13344. Hydrolase_6. 1 hit.
[Graphical view]
PIRSFiPIRSF000915. PGP-type_phosphatase. 1 hit.
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR01460. HAD-SF-IIA. 1 hit.
TIGR01452. PGP_euk. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPLPP_HUMAN
AccessioniPrimary (citable) accession number: Q96GD0
Secondary accession number(s): Q9UGY2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 2004
Last sequence update: March 1, 2004
Last modified: September 7, 2016
This is version 133 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 22
    Human chromosome 22: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.