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Pyridoxal phosphate phosphatase (PLP phosphatase) (EC 3.1.3.3) (EC 3.1.3.74) (Chronophin)

 PLPP_HUMAN              Reviewed;         296 AA.
Q96GD0; Q9UGY2;
01-MAR-2004, integrated into UniProtKB/Swiss-Prot.
01-MAR-2004, sequence version 2.
12-SEP-2018, entry version 150.
RecName: Full=Pyridoxal phosphate phosphatase;
Short=PLP phosphatase;
EC=3.1.3.3 {ECO:0000269|PubMed:15580268};
EC=3.1.3.74 {ECO:0000250|UniProtKB:P60487};
AltName: Full=Chronophin;
Name=PDXP; Synonyms=CIN, PLP, PLPP;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM CIN), FUNCTION, HOMODIMERIZATION,
COFACTOR, SUBUNIT, AND TISSUE SPECIFICITY.
TISSUE=Brain;
PubMed=14522954; DOI=10.1074/jbc.M309619200;
Jang Y.M., Kim D.W., Kang T.-C., Won M.H., Baek N.-I., Moon B.J.,
Choi S.Y., Kwon O.-S.;
"Human pyridoxal phosphatase. Molecular cloning, functional
expression, and tissue distribution.";
J. Biol. Chem. 278:50040-50046(2003).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=10591208; DOI=10.1038/990031;
Dunham I., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M.,
Clamp M., Smink L.J., Ainscough R., Almeida J.P., Babbage A.K.,
Bagguley C., Bailey J., Barlow K.F., Bates K.N., Beasley O.P.,
Bird C.P., Blakey S.E., Bridgeman A.M., Buck D., Burgess J.,
Burrill W.D., Burton J., Carder C., Carter N.P., Chen Y., Clark G.,
Clegg S.M., Cobley V.E., Cole C.G., Collier R.E., Connor R.,
Conroy D., Corby N.R., Coville G.J., Cox A.V., Davis J., Dawson E.,
Dhami P.D., Dockree C., Dodsworth S.J., Durbin R.M., Ellington A.G.,
Evans K.L., Fey J.M., Fleming K., French L., Garner A.A.,
Gilbert J.G.R., Goward M.E., Grafham D.V., Griffiths M.N.D., Hall C.,
Hall R.E., Hall-Tamlyn G., Heathcott R.W., Ho S., Holmes S.,
Hunt S.E., Jones M.C., Kershaw J., Kimberley A.M., King A.,
Laird G.K., Langford C.F., Leversha M.A., Lloyd C., Lloyd D.M.,
Martyn I.D., Mashreghi-Mohammadi M., Matthews L.H., Mccann O.T.,
Mcclay J., Mclaren S., McMurray A.A., Milne S.A., Mortimore B.J.,
Odell C.N., Pavitt R., Pearce A.V., Pearson D., Phillimore B.J.C.T.,
Phillips S.H., Plumb R.W., Ramsay H., Ramsey Y., Rogers L., Ross M.T.,
Scott C.E., Sehra H.K., Skuce C.D., Smalley S., Smith M.L.,
Soderlund C., Spragon L., Steward C.A., Sulston J.E., Swann R.M.,
Vaudin M., Wall M., Wallis J.M., Whiteley M.N., Willey D.L.,
Williams L., Williams S.A., Williamson H., Wilmer T.E., Wilming L.,
Wright C.L., Hubbard T., Bentley D.R., Beck S., Rogers J., Shimizu N.,
Minoshima S., Kawasaki K., Sasaki T., Asakawa S., Kudoh J.,
Shintani A., Shibuya K., Yoshizaki Y., Aoki N., Mitsuyama S.,
Roe B.A., Chen F., Chu L., Crabtree J., Deschamps S., Do A., Do T.,
Dorman A., Fang F., Fu Y., Hu P., Hua A., Kenton S., Lai H., Lao H.I.,
Lewis J., Lewis S., Lin S.-P., Loh P., Malaj E., Nguyen T., Pan H.,
Phan S., Qi S., Qian Y., Ray L., Ren Q., Shaull S., Sloan D., Song L.,
Wang Q., Wang Y., Wang Z., White J., Willingham D., Wu H., Yao Z.,
Zhan M., Zhang G., Chissoe S., Murray J., Miller N., Minx P.,
Fulton R., Johnson D., Bemis G., Bentley D., Bradshaw H., Bourne S.,
Cordes M., Du Z., Fulton L., Goela D., Graves T., Hawkins J.,
Hinds K., Kemp K., Latreille P., Layman D., Ozersky P., Rohlfing T.,
Scheet P., Walker C., Wamsley A., Wohldmann P., Pepin K., Nelson J.,
Korf I., Bedell J.A., Hillier L.W., Mardis E., Waterston R.,
Wilson R., Emanuel B.S., Shaikh T., Kurahashi H., Saitta S.,
Budarf M.L., McDermid H.E., Johnson A., Wong A.C.C., Morrow B.E.,
Edelmann L., Kim U.J., Shizuya H., Simon M.I., Dumanski J.P.,
Peyrard M., Kedra D., Seroussi E., Fransson I., Tapia I., Bruder C.E.,
O'Brien K.P., Wilkinson P., Bodenteich A., Hartman K., Hu X.,
Khan A.S., Lane L., Tilahun Y., Wright H.;
"The DNA sequence of human chromosome 22.";
Nature 402:489-495(1999).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM CIN).
TISSUE=Eye, Lung, and Placenta;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[4]
PROTEIN SEQUENCE OF 19-35; 100-119 AND 145-158 (ISOFORM CIN), AND
IDENTIFICATION BY MASS SPECTROMETRY.
TISSUE=Brain, Cajal-Retzius cell, and Fetal brain cortex;
Lubec G., Afjehi-Sadat L., Chen W.-Q., Sun Y.;
Submitted (DEC-2008) to UniProtKB.
[5]
PROTEIN SEQUENCE OF 19-30 AND 145-158 (ISOFORM CIN), AND ENZYME
ACTIVITY.
PubMed=8132548;
Gao G.-J., Fonda M.L.;
"Identification of an essential cysteine residue in pyridoxal
phosphatase from human erythrocytes.";
J. Biol. Chem. 269:8234-8239(1994).
[6]
FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, COFACTOR, ACTIVE
SITE, SUBCELLULAR LOCATION, MUTAGENESIS OF ASP-25, AND TISSUE
SPECIFICITY.
PubMed=15580268; DOI=10.1038/ncb1201;
Gohla A., Birkenfeld J., Bokoch G.M.;
"Chronophin, a novel HAD-type serine protein phosphatase, regulates
cofilin-dependent actin dynamics.";
Nat. Cell Biol. 7:21-29(2005).
[7]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21269460; DOI=10.1186/1752-0509-5-17;
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
"Initial characterization of the human central proteome.";
BMC Syst. Biol. 5:17-17(2011).
[8]
ALTERNATIVE SPLICING (ISOFORMS CIN; LONG BGIN AND SHORT BGIN), AND
TISSUE SPECIFICITY.
PubMed=23223568; DOI=10.1091/mbc.E12-07-0565;
Huang T.Y., Michael S., Xu T., Sarkeshik A., Moresco J.J.,
Yates J.R. III, Masliah E., Bokoch G.M., DerMardirossian C.;
"A novel Rac1 GAP splice variant relays poly-Ub accumulation signals
to mediate Rac1 inactivation.";
Mol. Biol. Cell 24:194-209(2013).
[9]
X-RAY CRYSTALLOGRAPHY (1.72 ANGSTROMS) OF 2-296 IN COMPLEXES WITH
PYRODOXAL PHOSPHATE; CALCIUM AND MAGNESIUM IONS.
PubMed=18058037; DOI=10.1007/s10969-007-9036-1;
Almo S.C., Bonanno J.B., Sauder J.M., Emtage S., Dilorenzo T.P.,
Malashkevich V., Wasserman S.R., Swaminathan S., Eswaramoorthy S.,
Agarwal R., Kumaran D., Madegowda M., Ragumani S., Patskovsky Y.,
Alvarado J., Ramagopal U.A., Faber-Barata J., Chance M.R., Sali A.,
Fiser A., Zhang Z.Y., Lawrence D.S., Burley S.K.;
"Structural genomics of protein phosphatases.";
J. Struct. Funct. Genomics 8:121-140(2007).
-!- FUNCTION: 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).
{ECO:0000269|PubMed:14522954, ECO:0000269|PubMed:15580268}.
-!- CATALYTIC ACTIVITY: Pyridoxal 5'-phosphate + H(2)O = pyridoxal +
phosphate. {ECO:0000250|UniProtKB:P60487}.
-!- CATALYTIC ACTIVITY: O-phospho-L(or D)-serine + H(2)O = L(or D)-
serine + phosphate. {ECO:0000269|PubMed:15580268}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:14522954,
ECO:0000269|PubMed:15580268};
Note=Divalent metal ions. Mg(2+) is the most effective.
{ECO:0000269|PubMed:14522954, ECO:0000269|PubMed:15580268};
-!- ACTIVITY REGULATION: Inhibited by NaF, Zn(2+), Ca(2+), Mn(2+) and
EDTA. {ECO:0000269|PubMed:15580268}.
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:14522954}.
-!- INTERACTION:
P29066:Arrb1 (xeno); NbExp=2; IntAct=EBI-4303060, EBI-4303019;
-!- SUBCELLULAR LOCATION: Cytoplasm, cytosol
{ECO:0000269|PubMed:15580268}. Cytoplasm, cytoskeleton
{ECO:0000269|PubMed:15580268}. Cell projection, ruffle membrane
{ECO:0000269|PubMed:15580268}; Peripheral membrane protein
{ECO:0000269|PubMed:15580268}; Cytoplasmic side
{ECO:0000269|PubMed:15580268}. Cell projection, lamellipodium
membrane {ECO:0000269|PubMed:15580268}; Peripheral membrane
protein {ECO:0000269|PubMed:15580268}; Cytoplasmic side
{ECO:0000269|PubMed:15580268}. Cell membrane
{ECO:0000269|PubMed:15580268}; Peripheral membrane protein
{ECO:0000269|PubMed:15580268}; Cytoplasmic side
{ECO:0000269|PubMed:15580268}. 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.
{ECO:0000269|PubMed:15580268}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing, Alternative initiation; Named isoforms=3;
Name=CIN {ECO:0000303|PubMed:23223568};
IsoId=Q96GD0-1; Sequence=Displayed;
Name=Long BGIN {ECO:0000303|PubMed:23223568};
IsoId=Q6ZT62-1; Sequence=External;
Note=Based on a naturally occurring readthrough transcript which
produces a SH3BP1-PDXP fusion protein. Translation initiation
occurs at a non-canonical CUG codon.
{ECO:0000269|PubMed:23223568};
Name=Short BGIN {ECO:0000303|PubMed:23223568};
IsoId=Q6ZT62-2; Sequence=External;
Note=Produced by alternative initiation at Met-73 of isoform
long BGIN. {ECO:0000269|PubMed:23223568};
-!- TISSUE SPECIFICITY: 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).
{ECO:0000269|PubMed:14522954, ECO:0000269|PubMed:15580268,
ECO:0000269|PubMed:23223568}.
-!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily.
{ECO:0000305}.
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EMBL; AY125047; AAM94358.1; -; mRNA.
EMBL; Z83844; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; BC000320; AAH00320.1; -; mRNA.
EMBL; BC009756; AAH09756.2; -; mRNA.
EMBL; BC064922; AAH64922.1; -; mRNA.
CCDS; CCDS13953.1; -. [Q96GD0-1]
RefSeq; NP_064711.1; NM_020315.4. [Q96GD0-1]
UniGene; Hs.632762; -.
PDB; 2CFR; X-ray; 2.40 A; A=1-296.
PDB; 2CFS; X-ray; 2.40 A; A=1-296.
PDB; 2CFT; X-ray; 1.80 A; A=1-296.
PDB; 2OYC; X-ray; 1.72 A; A=2-296.
PDB; 2P27; X-ray; 1.90 A; A=2-296.
PDB; 2P69; X-ray; 2.25 A; A=2-296.
PDB; 5GYN; X-ray; 2.00 A; A=1-296.
PDBsum; 2CFR; -.
PDBsum; 2CFS; -.
PDBsum; 2CFT; -.
PDBsum; 2OYC; -.
PDBsum; 2P27; -.
PDBsum; 2P69; -.
PDBsum; 5GYN; -.
ProteinModelPortal; Q96GD0; -.
SMR; Q96GD0; -.
BioGrid; 121330; 12.
IntAct; Q96GD0; 2.
MINT; Q96GD0; -.
STRING; 9606.ENSP00000215904; -.
DrugBank; DB00114; Pyridoxal Phosphate.
DEPOD; Q96GD0; -.
iPTMnet; Q96GD0; -.
PhosphoSitePlus; Q96GD0; -.
BioMuta; PDXP; -.
DMDM; 44888310; -.
REPRODUCTION-2DPAGE; IPI00025340; -.
UCD-2DPAGE; Q96GD0; -.
EPD; Q96GD0; -.
MaxQB; Q96GD0; -.
PaxDb; Q96GD0; -.
PeptideAtlas; Q96GD0; -.
PRIDE; Q96GD0; -.
ProteomicsDB; 76616; -.
Ensembl; ENST00000215904; ENSP00000215904; ENSG00000241360. [Q96GD0-1]
GeneID; 57026; -.
KEGG; hsa:57026; -.
UCSC; uc003atm.2; human. [Q96GD0-1]
CTD; 57026; -.
DisGeNET; 57026; -.
EuPathDB; HostDB:ENSG00000241360.1; -.
GeneCards; PDXP; -.
HGNC; HGNC:30259; PDXP.
HPA; HPA000531; -.
MIM; 609246; gene.
neXtProt; NX_Q96GD0; -.
OpenTargets; ENSG00000241360; -.
PharmGKB; PA134882132; -.
eggNOG; KOG2882; Eukaryota.
eggNOG; COG0647; LUCA.
GeneTree; ENSGT00510000047020; -.
HOGENOM; HOG000068104; -.
HOVERGEN; HBG049429; -.
InParanoid; Q96GD0; -.
KO; K07758; -.
OMA; RFMFECI; -.
OrthoDB; EOG091G0I92; -.
PhylomeDB; Q96GD0; -.
TreeFam; TF314344; -.
BRENDA; 3.1.3.74; 2681.
SABIO-RK; Q96GD0; -.
SIGNOR; Q96GD0; -.
ChiTaRS; PDXP; human.
EvolutionaryTrace; Q96GD0; -.
GenomeRNAi; 57026; -.
PRO; PR:Q96GD0; -.
Proteomes; UP000005640; Chromosome 22.
Bgee; ENSG00000241360; Expressed in 93 organ(s), highest expression level in prefrontal cortex.
CleanEx; HS_PDXP; -.
ExpressionAtlas; Q96GD0; baseline and differential.
Genevisible; Q96GD0; HS.
GO; GO:0005911; C:cell-cell junction; IEA:Ensembl.
GO; GO:0005856; C:cytoskeleton; IEA:UniProtKB-SubCell.
GO; GO:0005829; C:cytosol; IDA:UniProtKB.
GO; GO:0031258; C:lamellipodium membrane; IEA:UniProtKB-SubCell.
GO; GO:0032587; C:ruffle membrane; IEA:UniProtKB-SubCell.
GO; GO:0031072; F:heat shock protein binding; IDA:MGI.
GO; GO:0000287; F:magnesium ion binding; ISS:UniProtKB.
GO; GO:0098519; F:nucleotide phosphatase activity, acting on free nucleotides; IBA:GO_Central.
GO; GO:0004721; F:phosphoprotein phosphatase activity; IDA:UniProtKB.
GO; GO:0004647; F:phosphoserine phosphatase activity; IEA:UniProtKB-EC.
GO; GO:0042803; F:protein homodimerization activity; IEA:Ensembl.
GO; GO:0033883; F:pyridoxal phosphatase activity; ISS:UniProtKB.
GO; GO:0031247; P:actin rod assembly; IDA:MGI.
GO; GO:0071318; P:cellular response to ATP; IDA:MGI.
GO; GO:0030836; P:positive regulation of actin filament depolymerization; IMP:UniProtKB.
GO; GO:0006470; P:protein dephosphorylation; IDA:UniProtKB.
GO; GO:0032361; P:pyridoxal phosphate catabolic process; ISS:UniProtKB.
GO; GO:0032465; P:regulation of cytokinesis; IMP:UniProtKB.
GO; GO:0007088; P:regulation of mitotic nuclear division; IMP:UniProtKB.
Gene3D; 3.40.50.1000; -; 3.
InterPro; IPR036412; HAD-like_sf.
InterPro; IPR006357; HAD-SF_hydro_IIA.
InterPro; IPR023214; HAD_sf.
InterPro; IPR006349; PGP_euk.
Pfam; PF13344; Hydrolase_6; 1.
PIRSF; PIRSF000915; PGP-type_phosphatase; 1.
SUPFAM; SSF56784; SSF56784; 1.
TIGRFAMs; TIGR01460; HAD-SF-IIA; 1.
TIGRFAMs; TIGR01452; PGP_euk; 1.
1: Evidence at protein level;
3D-structure; Alternative initiation; Alternative splicing;
Cell membrane; Cell projection; Complete proteome; Cytoplasm;
Cytoskeleton; Direct protein sequencing; Hydrolase; Magnesium;
Membrane; Metal-binding; Pyridoxal phosphate; Reference proteome.
CHAIN 1 296 Pyridoxal phosphate phosphatase.
/FTId=PRO_0000068837.
REGION 58 62 Substrate binding.
ACT_SITE 25 25 Nucleophile.
{ECO:0000269|PubMed:15580268}.
ACT_SITE 27 27 Proton donor.
{ECO:0000305|PubMed:15580268}.
METAL 25 25 Magnesium.
METAL 27 27 Magnesium; via carbonyl oxygen.
METAL 238 238 Magnesium.
BINDING 182 182 Substrate.
BINDING 213 213 Substrate.
MUTAGEN 25 25 D->N: Abolishes phosphatase activity.
{ECO:0000269|PubMed:15580268}.
HELIX 9 18 {ECO:0000244|PDB:2OYC}.
STRAND 20 24 {ECO:0000244|PDB:2OYC}.
TURN 27 29 {ECO:0000244|PDB:2OYC}.
STRAND 30 32 {ECO:0000244|PDB:2OYC}.
HELIX 40 49 {ECO:0000244|PDB:2OYC}.
STRAND 53 58 {ECO:0000244|PDB:2OYC}.
HELIX 65 74 {ECO:0000244|PDB:2OYC}.
HELIX 82 84 {ECO:0000244|PDB:2OYC}.
STRAND 85 87 {ECO:0000244|PDB:2OYC}.
HELIX 88 99 {ECO:0000244|PDB:2OYC}.
STRAND 104 106 {ECO:0000244|PDB:2OYC}.
STRAND 109 114 {ECO:0000244|PDB:2OYC}.
HELIX 116 124 {ECO:0000244|PDB:2OYC}.
STRAND 143 148 {ECO:0000244|PDB:2OYC}.
HELIX 156 166 {ECO:0000244|PDB:2OYC}.
STRAND 171 176 {ECO:0000244|PDB:2OYC}.
STRAND 181 183 {ECO:0000244|PDB:2OYC}.
STRAND 189 191 {ECO:0000244|PDB:2OYC}.
HELIX 193 204 {ECO:0000244|PDB:2OYC}.
HELIX 217 225 {ECO:0000244|PDB:2OYC}.
HELIX 230 232 {ECO:0000244|PDB:2OYC}.
STRAND 233 238 {ECO:0000244|PDB:2OYC}.
TURN 240 242 {ECO:0000244|PDB:2OYC}.
HELIX 243 250 {ECO:0000244|PDB:2OYC}.
STRAND 253 261 {ECO:0000244|PDB:2OYC}.
HELIX 264 272 {ECO:0000244|PDB:2OYC}.
HELIX 276 278 {ECO:0000244|PDB:2OYC}.
STRAND 281 286 {ECO:0000244|PDB:2OYC}.
HELIX 287 293 {ECO:0000244|PDB:2OYC}.
SEQUENCE 296 AA; 31698 MW; 33466C35A76B458C CRC64;
MARCERLRGA ALRDVLGRAQ GVLFDCDGVL WNGERAVPGA PELLERLARA GKAALFVSNN
SRRARPELAL RFARLGFGGL RAEQLFSSAL CAARLLRQRL PGPPDAPGAV FVLGGEGLRA
ELRAAGLRLA GDPSAGDGAA PRVRAVLVGY DEHFSFAKLR EACAHLRDPE CLLVATDRDP
WHPLSDGSRT PGTGSLAAAV ETASGRQALV VGKPSPYMFE CITENFSIDP ARTLMVGDRL
ETDILFGHRC GMTTVLTLTG VSRLEEAQAY LAAGQHDLVP HYYVESIADL TEGLED


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San Jose, CA 95123
CA 95123
Tel (408) 780-0908,
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Genprice Inc, Invoices and accounting
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GENTAUR Poland Sp. z o.o.


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