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Protein

Pyridoxal phosphate phosphatase

Gene

PDXP

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 (PubMed:15580268). Pyridoxal phosphate (PLP) phosphatase, which also catalyzes the dephosphorylation of pyridoxine 5'-phosphate (PNP) and pyridoxamine 5'-phosphate (PMP), with order of substrate preference PLP > PNP > PMP (PubMed:14522954).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)DescriptionActionsGraphical viewLength
Active sitei25Nucleophile1 Publication1
Metal bindingi25Magnesium1
Active sitei27Proton donor1 Publication1
Metal bindingi27Magnesium; via carbonyl oxygen1
Binding sitei182Substrate1
Binding sitei213Substrate1
Metal bindingi238Magnesium1

GO - Molecular functioni

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

Keywordsi

Molecular functionHydrolase
LigandMagnesium, Metal-binding, Pyridoxal phosphate

Enzyme and pathway databases

BRENDAi3.1.3.74 2681
SABIO-RKiQ96GD0
SIGNORiQ96GD0

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

EuPathDBiHostDB:ENSG00000241360.1
HGNCiHGNC:30259 PDXP
MIMi609246 gene
neXtProtiNX_Q96GD0

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cell membrane, Cell projection, Cytoplasm, Cytoskeleton, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi25D → N: Abolishes phosphatase activity. 1 Publication1

Organism-specific databases

DisGeNETi57026
OpenTargetsiENSG00000241360
PharmGKBiPA134882132

Chemistry databases

DrugBankiDB00114 Pyridoxal Phosphate

Polymorphism and mutation databases

BioMutaiPDXP
DMDMi44888310

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000688371 – 296Pyridoxal phosphate phosphataseAdd BLAST296

Proteomic databases

EPDiQ96GD0
MaxQBiQ96GD0
PaxDbiQ96GD0
PeptideAtlasiQ96GD0
PRIDEiQ96GD0
ProteomicsDBi76616

2D gel databases

REPRODUCTION-2DPAGEiIPI00025340
UCD-2DPAGEiQ96GD0

PTM databases

DEPODiQ96GD0
iPTMnetiQ96GD0
PhosphoSitePlusiQ96GD0

Expressioni

Tissue specificityi

Ubiquitously expressed (at protein level) (PubMed:23223568). 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 (PubMed:14522954, PubMed:15580268).3 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 Rattus norvegicus.

GO - Molecular functioni

  • heat shock protein binding Source: MGI
  • protein homodimerization activity Source: Ensembl

Protein-protein interaction databases

BioGridi121330, 12 interactors
IntActiQ96GD0, 2 interactors
MINTiQ96GD0
STRINGi9606.ENSP00000215904

Structurei

Secondary structure

1296
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi9 – 18Combined sources10
Beta strandi20 – 24Combined sources5
Turni27 – 29Combined sources3
Beta strandi30 – 32Combined sources3
Helixi40 – 49Combined sources10
Beta strandi53 – 58Combined sources6
Helixi65 – 74Combined sources10
Helixi82 – 84Combined sources3
Beta strandi85 – 87Combined sources3
Helixi88 – 99Combined sources12
Beta strandi104 – 106Combined sources3
Beta strandi109 – 114Combined sources6
Helixi116 – 124Combined sources9
Beta strandi143 – 148Combined sources6
Helixi156 – 166Combined sources11
Beta strandi171 – 176Combined sources6
Beta strandi181 – 183Combined sources3
Beta strandi189 – 191Combined sources3
Helixi193 – 204Combined sources12
Helixi217 – 225Combined sources9
Helixi230 – 232Combined sources3
Beta strandi233 – 238Combined sources6
Turni240 – 242Combined sources3
Helixi243 – 250Combined sources8
Beta strandi253 – 261Combined sources9
Helixi264 – 272Combined sources9
Helixi276 – 278Combined sources3
Beta strandi281 – 286Combined sources6
Helixi287 – 293Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5GYNX-ray2.00A1-296[»]
ProteinModelPortaliQ96GD0
SMRiQ96GD0
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ96GD0

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni58 – 62Substrate binding5

Sequence similaritiesi

Belongs to the HAD-like hydrolase superfamily.Curated

Phylogenomic databases

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

Family and domain databases

Gene3Di3.40.50.1000, 3 hits
InterProiView protein in InterPro
IPR036412 HAD-like_sf
IPR006357 HAD-SF_hydro_IIA
IPR023214 HAD_sf
IPR006349 PGP_euk
PfamiView protein in Pfam
PF13344 Hydrolase_6, 1 hit
PIRSFiPIRSF000915 PGP-type_phosphatase, 1 hit
SUPFAMiSSF56784 SSF56784, 1 hit
TIGRFAMsiTIGR01460 HAD-SF-IIA, 1 hit
TIGR01452 PGP_euk, 1 hit

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing and alternative initiation. AlignAdd to basket

Isoform CIN1 Publication (identifier: Q96GD0-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« 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
Isoform Long BGIN1 Publication (identifier: Q6ZT62-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry Q6ZT62.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Based on a naturally occurring readthrough transcript which produces a SH3BP1-PDXP fusion protein. Translation initiation occurs at a non-canonical CUG codon.1 Publication
Length:677
Mass (Da):73,599
GO
Isoform Short BGIN1 Publication (identifier: Q6ZT62-2) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry Q6ZT62.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by alternative initiation at Met-73 of isoform long BGIN.1 Publication
Length:605
Mass (Da):66,180
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY125047 mRNA Translation: AAM94358.1
Z83844 Genomic DNA No translation available.
BC000320 mRNA Translation: AAH00320.1
BC009756 mRNA Translation: AAH09756.2
BC064922 mRNA Translation: AAH64922.1
CCDSiCCDS13953.1 [Q96GD0-1]
RefSeqiNP_064711.1, NM_020315.4 [Q96GD0-1]
UniGeneiHs.632762

Genome annotation databases

EnsembliENST00000215904; ENSP00000215904; ENSG00000241360 [Q96GD0-1]
GeneIDi57026
KEGGihsa:57026
UCSCiuc003atm.2 human [Q96GD0-1]

Keywords - Coding sequence diversityi

Alternative initiation, Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiPLPP_HUMAN
AccessioniPrimary (citable) accession number: Q96GD0
Secondary accession number(s): Q9UGY2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 1, 2004
Last sequence update: March 1, 2004
Last modified: June 20, 2018
This is version 149 of the entry and version 2 of the sequence. See 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

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