Human Gene PPME1 (ENST00000328257.13_4) from GENCODE V47lift37

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Description: protein phosphatase methylesterase 1, transcript variant 1 (from RefSeq NM_016147.3)
Gencode Transcript: ENST00000328257.13_4
Gencode Gene: ENSG00000214517.10_8
Transcript (Including UTRs)
Position: hg19 chr11:73,882,334-73,965,748 Size: 83,415 Total Exon Count: 14 Strand: +
Coding Region
Position: hg19 chr11:73,882,467-73,964,555 Size: 82,089 Coding Exon Count: 14

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr11:73,882,334-73,965,748)			mRNA (may differ from genome)		Protein (386 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards	HGNC
Malacards	MGI	OMIM	PubMed	Reactome	UniProtKB
BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: PPME1_HUMAN DESCRIPTION: RecName: Full=Protein phosphatase methylesterase 1; Short=PME-1; EC=3.1.1.89; FUNCTION: Demethylates proteins that have been reversibly carboxymethylated. Demethylates PPP2CB (in vitro) and PPP2CA. Binding to PPP2CA displaces the manganese ion and inactivates the enzyme. CATALYTIC ACTIVITY: [Phosphatase 2A protein]-leucine methyl ester + H(2)O = [phosphatase 2A protein]-leucine + methanol. SUBUNIT: Binds PPP2CA and PPP2CB. PTM: Phosphorylated by SIK1 following increases in intracellular sodium, leading to dissociation from the protein phosphatase 2A (PP2A) complex and subsequent dephosphorylation of sodium/potassium-transporting ATPase ATP1A1 (By similarity). SIMILARITY: Belongs to the AB hydrolase superfamily. SEQUENCE CAUTION: Sequence=AAG22477.1; Type=Erroneous translation; Note=Wrong choice of CDS;

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: PPME1 Diseases sorted by gene-association score: malignant glioma (5)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D013749 Tetrachlorodibenzodioxin D000082 Acetaminophen D001554 Benzene D008767 Methylmercury Compounds D018817 N-Methyl-3,4-methylenedioxyamphetamine D011078 Polychlorinated Biphenyls D012643 Selenium D014635 Valproic Acid D014810 Vitamin E C006632 arsenic trioxide more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 44.92 RPKM in Testis Total median expression: 1020.87 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-46.70	133	-0.351	Picture	PostScript	Text
3' UTR	-366.40	1193	-0.307	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR016812 - PPase_methylesterase_euk

Pfam Domains:
PF00561 - alpha/beta hydrolase fold
PF12146 - Serine aminopeptidase, S33
PF12697 - Alpha/beta hydrolase family

SCOP Domains:
53474 - alpha/beta-Hydrolases

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3C5V - X-ray MuPIT

3C5W - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q9Y570


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	Genome Browser	Genome Browser
Gene Details	Gene Details		Gene Details	Gene Details	Gene Details
Gene Sorter	Gene Sorter		Gene Sorter	Gene Sorter	Gene Sorter
	RGD	Ensembl		WormBase	SGD
				Protein Sequence	Protein Sequence
				Alignment	Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0004864 protein phosphatase inhibitor activity GO:0016787 hydrolase activity GO:0019888 protein phosphatase regulator activity GO:0019901 protein kinase binding GO:0019903 protein phosphatase binding GO:0045296 cadherin binding GO:0051721 protein phosphatase 2A binding GO:0051722 protein C-terminal methylesterase activity GO:0051723 protein methylesterase activity GO:0052689 carboxylic ester hydrolase activity Biological Process: GO:0000086 G2/M transition of mitotic cell cycle GO:0006482 protein demethylation GO:0032515 negative regulation of phosphoprotein phosphatase activity GO:0043666 regulation of phosphoprotein phosphatase activity Cellular Component: GO:0005654 nucleoplasm

Descriptions from all associated GenBank mRNAs


	LF207789 - JP 2014500723-A/15292: Polycomb-Associated Non-Coding RNAs. AK022725 - Homo sapiens cDNA FLJ12663 fis, clone NT2RM4002213, highly similar to Protein phosphatase methylesterase 1 (EC 3.1.1.-). BC003046 - Homo sapiens protein phosphatase methylesterase 1, mRNA (cDNA clone MGC:664 IMAGE:3536415), complete cds. BC050705 - Homo sapiens protein phosphatase methylesterase 1, mRNA (cDNA clone MGC:60306 IMAGE:6161935), complete cds. AK225647 - Homo sapiens mRNA for protein phosphatase methylesterase-1 variant, clone: STM01943. AF157028 - Homo sapiens protein phosphatase methylesterase-1 (PME-1) mRNA, complete cds. AK001381 - Homo sapiens cDNA FLJ10519 fis, clone NT2RP2000816, weakly similar to MAGNESIUM-CHELATASE 30 KD SUBUNIT. HM005579 - Homo sapiens clone HTL-S-39 testicular secretory protein Li 39 mRNA, complete cds. CU678344 - Synthetic construct Homo sapiens gateway clone IMAGE:100018192 5' read PPME1 mRNA. AB385584 - Synthetic construct DNA, clone: pF1KB9511, Homo sapiens PPME1 gene for protein phosphatase methylesterase 1, complete cds, without stop codon, in Flexi system. DQ895778 - Synthetic construct Homo sapiens clone IMAGE:100010238; FLH187539.01L; RZPDo839A07149D protein phosphatase methylesterase 1 (PPME1) gene, encodes complete protein. DQ892348 - Synthetic construct clone IMAGE:100004978; FLH187543.01X; RZPDo839A07150D protein phosphatase methylesterase 1 (PPME1) gene, encodes complete protein. KJ893906 - Synthetic construct Homo sapiens clone ccsbBroadEn_03300 PPME1 gene, encodes complete protein. MA443366 - JP 2018138019-A/15292: Polycomb-Associated Non-Coding RNAs. JD443883 - Sequence 424907 from Patent EP1572962. JD229555 - Sequence 210579 from Patent EP1572962. LF369202 - JP 2014500723-A/176705: Polycomb-Associated Non-Coding RNAs. LF369201 - JP 2014500723-A/176704: Polycomb-Associated Non-Coding RNAs. MA604779 - JP 2018138019-A/176705: Polycomb-Associated Non-Coding RNAs. MA604778 - JP 2018138019-A/176704: Polycomb-Associated Non-Coding RNAs. AK025414 - Homo sapiens cDNA: FLJ21761 fis, clone COLF6809, highly similar to AF157028 Homo sapiens protein phosphatase methylesterase-1 (PME-1) mRNA. AF111853 - Homo sapiens PRO0750 mRNA, complete cds. BX537528 - Homo sapiens mRNA; cDNA DKFZp686K08101 (from clone DKFZp686K08101). AK123288 - Homo sapiens cDNA FLJ41294 fis, clone BRAMY2039872, moderately similar to Homo sapiens protein phosphatase methylesterase-1 (PME-1) mRNA. LF369198 - JP 2014500723-A/176701: Polycomb-Associated Non-Coding RNAs. AF193049 - Homo sapiens PP2593 mRNA, complete cds. LF369197 - JP 2014500723-A/176700: Polycomb-Associated Non-Coding RNAs. AK025879 - Homo sapiens cDNA: FLJ22226 fis, clone HRC01736, highly similar to AF157028 Homo sapiens protein phosphatase methylesterase-1 (PME-1) mRNA. AK095005 - Homo sapiens cDNA FLJ37686 fis, clone BRHIP2014063. JD313490 - Sequence 294514 from Patent EP1572962. JD086062 - Sequence 67086 from Patent EP1572962. JD288548 - Sequence 269572 from Patent EP1572962. JD093260 - Sequence 74284 from Patent EP1572962. JD501371 - Sequence 482395 from Patent EP1572962. JD193086 - Sequence 174110 from Patent EP1572962. JD384246 - Sequence 365270 from Patent EP1572962. JD218051 - Sequence 199075 from Patent EP1572962. JD426394 - Sequence 407418 from Patent EP1572962. JD508682 - Sequence 489706 from Patent EP1572962. JD151038 - Sequence 132062 from Patent EP1572962. JD255227 - Sequence 236251 from Patent EP1572962. JD422819 - Sequence 403843 from Patent EP1572962. DQ575630 - Homo sapiens piRNA piR-43742, complete sequence. JD556083 - Sequence 537107 from Patent EP1572962. JD104753 - Sequence 85777 from Patent EP1572962. LF369195 - JP 2014500723-A/176698: Polycomb-Associated Non-Coding RNAs. JD269067 - Sequence 250091 from Patent EP1572962. JD565356 - Sequence 546380 from Patent EP1572962. JD223412 - Sequence 204436 from Patent EP1572962. LF369194 - JP 2014500723-A/176697: Polycomb-Associated Non-Coding RNAs. JD459184 - Sequence 440208 from Patent EP1572962. JD204982 - Sequence 186006 from Patent EP1572962. JD252170 - Sequence 233194 from Patent EP1572962. JD452076 - Sequence 433100 from Patent EP1572962. JD271126 - Sequence 252150 from Patent EP1572962. JD192882 - Sequence 173906 from Patent EP1572962. JD149695 - Sequence 130719 from Patent EP1572962. JD217037 - Sequence 198061 from Patent EP1572962. LF369193 - JP 2014500723-A/176696: Polycomb-Associated Non-Coding RNAs. JD082642 - Sequence 63666 from Patent EP1572962. JD411253 - Sequence 392277 from Patent EP1572962. JD561591 - Sequence 542615 from Patent EP1572962. LF369192 - JP 2014500723-A/176695: Polycomb-Associated Non-Coding RNAs. JD303681 - Sequence 284705 from Patent EP1572962. JD162690 - Sequence 143714 from Patent EP1572962. JD229161 - Sequence 210185 from Patent EP1572962. JD508310 - Sequence 489334 from Patent EP1572962. JD516506 - Sequence 497530 from Patent EP1572962. JD297408 - Sequence 278432 from Patent EP1572962. JD039289 - Sequence 20313 from Patent EP1572962. MA604775 - JP 2018138019-A/176701: Polycomb-Associated Non-Coding RNAs. MA604774 - JP 2018138019-A/176700: Polycomb-Associated Non-Coding RNAs. MA604772 - JP 2018138019-A/176698: Polycomb-Associated Non-Coding RNAs. MA604771 - JP 2018138019-A/176697: Polycomb-Associated Non-Coding RNAs. MA604770 - JP 2018138019-A/176696: Polycomb-Associated Non-Coding RNAs. MA604769 - JP 2018138019-A/176695: Polycomb-Associated Non-Coding RNAs.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q9Y570 (Reactome details) participates in the following event(s): R-HSA-8856951 PP2A demethylation by PPME1 R-HSA-69273 Cyclin A/B1/B2 associated events during G2/M transition R-HSA-69275 G2/M Transition R-HSA-453274 Mitotic G2-G2/M phases R-HSA-69278 Cell Cycle (Mitotic) R-HSA-1640170 Cell Cycle

Other Names for This Gene


	Alternate Gene Symbols: B3KMU6, B5MEE7, ENST00000328257.1, ENST00000328257.10, ENST00000328257.11, ENST00000328257.12, ENST00000328257.2, ENST00000328257.3, ENST00000328257.4, ENST00000328257.5, ENST00000328257.6, ENST00000328257.7, ENST00000328257.8, ENST00000328257.9, J3QT22, NM_016147, PME1, PP2593, PPME1_HUMAN, PRO0750, Q8WYG8, Q9NVT5, Q9UI18, Q9Y570, uc317slt.1, uc317slt.2 UCSC ID: ENST00000328257.13_4 RefSeq Accession: NM_016147.3 Protein: Q9Y570 (aka PPME1_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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