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Protein

Pyridoxal phosphate phosphatase

Gene

Pdxp

Organism
Mus musculus (Mouse)
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 (By similarity). 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.By similarity2 Publications

Catalytic activityi

Pyridoxal 5'-phosphate + H2O = pyridoxal + phosphate.2 Publications
O-phospho-L(or D)-serine + H2O = L(or D)-serine + phosphate.1 Publication

Cofactori

Mg2+1 PublicationNote: Divalent metal ions. Mg2+ is the most effective.1 Publication

Enzyme regulationi

Inhibited by beryllium trifluoride.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei25NucleophileBy similarity1
Metal bindingi25Magnesium2 Publications1
Active sitei27Proton donorBy similarity1
Metal bindingi27Magnesium; via carbonyl oxygen2 Publications1
Binding sitei178SubstrateBy similarity1
Binding sitei209SubstrateBy similarity1
Metal bindingi234Magnesium2 Publications1

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
  • protein homodimerization activity Source: UniProtKB
  • pyridoxal phosphatase activity Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium, Metal-binding, Pyridoxal phosphate

Enzyme and pathway databases

BRENDAi3.1.3.74. 3474.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxal phosphate phosphatase (EC:3.1.3.31 Publication, EC:3.1.3.742 Publications)
Short name:
PLP phosphatase
Alternative name(s):
Chronophin1 Publication
Gene namesi
Name:Pdxp
Synonyms:Cin, Plp, Plpp
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 15

Organism-specific databases

MGIiMGI:1919282. Pdxp.

Subcellular locationi

  • Cytoplasmcytosol By similarity
  • Cytoplasmcytoskeleton By similarity
  • Cell projectionruffle membrane By similarity; Peripheral membrane protein By similarity; Cytoplasmic side By similarity
  • Cell projectionlamellipodium membrane By similarity; Peripheral membrane protein By similarity; Cytoplasmic side By similarity
  • Cell membrane By similarity; Peripheral membrane protein By similarity; Cytoplasmic side By similarity

  • 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.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cell projection, Cytoplasm, Cytoskeleton, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi194 – 195AA → KK: Abolishes homodimerization. Strongly decreases affinity for pyridoxal phosphate. 1 Publication2

Chemistry databases

ChEMBLiCHEMBL3425392.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000688381 – 292Pyridoxal phosphate phosphataseAdd BLAST292

Proteomic databases

EPDiP60487.
MaxQBiP60487.
PaxDbiP60487.
PeptideAtlasiP60487.
PRIDEiP60487.

2D gel databases

REPRODUCTION-2DPAGEP60487.

PTM databases

iPTMnetiP60487.
PhosphoSitePlusiP60487.

Expressioni

Tissue specificityi

Ubiquitous. highly expressed in brain (at protein level).1 Publication

Gene expression databases

BgeeiENSMUSG00000068221.
CleanExiMM_PDXP.
ExpressionAtlasiP60487. baseline and differential.
GenevisibleiP60487. MM.

Interactioni

Subunit structurei

Homodimer.2 Publications

GO - Molecular functioni

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

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000086796.

Chemistry databases

BindingDBiP60487.

Structurei

Secondary structure

1292
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi9 – 18Combined sources10
Beta strandi20 – 25Combined sources6
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
Turni104 – 106Combined sources3
Beta strandi109 – 114Combined sources6
Helixi116 – 124Combined sources9
Beta strandi132 – 134Combined sources3
Beta strandi139 – 144Combined sources6
Helixi152 – 161Combined sources10
Beta strandi167 – 172Combined sources6
Beta strandi176 – 179Combined sources4
Beta strandi185 – 187Combined sources3
Helixi189 – 200Combined sources12
Helixi213 – 221Combined sources9
Helixi226 – 228Combined sources3
Beta strandi229 – 234Combined sources6
Turni236 – 238Combined sources3
Helixi239 – 246Combined sources8
Beta strandi249 – 257Combined sources9
Helixi260 – 268Combined sources9
Helixi272 – 274Combined sources3
Beta strandi277 – 282Combined sources6
Helixi283 – 289Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4BKMX-ray2.65A/B/C/D1-100[»]
A/B/C/D208-292[»]
4BX0X-ray1.75A1-292[»]
4BX2X-ray2.19A/B1-292[»]
4BX3X-ray2.19A/B1-292[»]
5AESX-ray2.75A/B1-292[»]
ProteinModelPortaliP60487.
SMRiP60487.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni58 – 62Substrate bindingBy similarity5

Sequence similaritiesi

Belongs to the HAD-like hydrolase superfamily.Curated

Phylogenomic databases

eggNOGiKOG2882. Eukaryota.
COG0647. LUCA.
GeneTreeiENSGT00760000118863.
HOGENOMiHOG000068104.
HOVERGENiHBG049429.
InParanoidiP60487.
KOiK07758.
OMAiMIGDRLY.
PhylomeDBiP60487.
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.

P60487-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARCERLRGA ALRDVLGQAQ GVLFDCDGVL WNGERIVPGA PELLQRLARA
60 70 80 90 100
GKNTLFVSNN SRRARPELAL RFARLGFAGL RAEQLFSSAL CAARLLRQRL
110 120 130 140 150
SGPPDASGAV FVLGGEGLRA ELRAAGLRLA GDPGEDPRVR AVLVGYDEQF
160 170 180 190 200
SFSRLTEACA HLRDPDCLLV ATDRDPWHPL SDGSRTPGTG SLAAAVETAS
210 220 230 240 250
GRQALVVGKP SPYMFQCITE DFSVDPARTL MVGDRLETDI LFGHRCGMTT
260 270 280 290
VLTLTGVSSL EEAQAYLTAG QRDLVPHYYV ESIADLMEGL ED
Length:292
Mass (Da):31,512
Last modified:March 1, 2004 - v1
Checksum:iB5F1B2C7E71A585D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY366300 mRNA. Translation: AAR12209.1.
BC058388 mRNA. Translation: AAH58388.1.
CCDSiCCDS27627.1.
RefSeqiNP_064667.2. NM_020271.3.
UniGeneiMm.263169.

Genome annotation databases

EnsembliENSMUST00000089378; ENSMUSP00000086796; ENSMUSG00000022436.
GeneIDi57028.
KEGGimmu:57028.
UCSCiuc007wru.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY366300 mRNA. Translation: AAR12209.1.
BC058388 mRNA. Translation: AAH58388.1.
CCDSiCCDS27627.1.
RefSeqiNP_064667.2. NM_020271.3.
UniGeneiMm.263169.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4BKMX-ray2.65A/B/C/D1-100[»]
A/B/C/D208-292[»]
4BX0X-ray1.75A1-292[»]
4BX2X-ray2.19A/B1-292[»]
4BX3X-ray2.19A/B1-292[»]
5AESX-ray2.75A/B1-292[»]
ProteinModelPortaliP60487.
SMRiP60487.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000086796.

Chemistry databases

BindingDBiP60487.
ChEMBLiCHEMBL3425392.

PTM databases

iPTMnetiP60487.
PhosphoSitePlusiP60487.

2D gel databases

REPRODUCTION-2DPAGEP60487.

Proteomic databases

EPDiP60487.
MaxQBiP60487.
PaxDbiP60487.
PeptideAtlasiP60487.
PRIDEiP60487.

Protocols and materials databases

DNASUi57028.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000089378; ENSMUSP00000086796; ENSMUSG00000022436.
GeneIDi57028.
KEGGimmu:57028.
UCSCiuc007wru.1. mouse.

Organism-specific databases

CTDi57026.
MGIiMGI:1919282. Pdxp.

Phylogenomic databases

eggNOGiKOG2882. Eukaryota.
COG0647. LUCA.
GeneTreeiENSGT00760000118863.
HOGENOMiHOG000068104.
HOVERGENiHBG049429.
InParanoidiP60487.
KOiK07758.
OMAiMIGDRLY.
PhylomeDBiP60487.
TreeFamiTF314344.

Enzyme and pathway databases

BRENDAi3.1.3.74. 3474.

Miscellaneous databases

PROiP60487.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000068221.
CleanExiMM_PDXP.
ExpressionAtlasiP60487. baseline and differential.
GenevisibleiP60487. MM.

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_MOUSE
AccessioniPrimary (citable) accession number: P60487
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 2004
Last sequence update: March 1, 2004
Last modified: November 2, 2016
This is version 114 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.