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PPM1B protein phosphatase, Mg2+/Mn2+ dependent 1B [ Homo sapiens (human) ]

Gene ID: 5495, updated on 3-Apr-2024

Summary

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Official Symbol
PPM1Bprovided by HGNC
Official Full Name
protein phosphatase, Mg2+/Mn2+ dependent 1Bprovided by HGNC
Primary source
HGNC:HGNC:9276
See related
Ensembl:ENSG00000138032 MIM:603770; AllianceGenome:HGNC:9276
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PP2CB; PP2CBETA; PP2C-beta; PPC2BETAX; PP2C-beta-X
Summary
The protein encoded by this gene is a member of the PP2C family of Ser/Thr protein phosphatases. PP2C family members are known to be negative regulators of cell stress response pathways. This phosphatase has been shown to dephosphorylate cyclin-dependent kinases (CDKs), and thus may be involved in cell cycle control. Overexpression of this phosphatase is reported to cause cell-growth arrest or cell death. Alternative splicing results in multiple transcript variants encoding different isoforms. Additional transcript variants have been described, but currently do not represent full-length sequences. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in fat (RPKM 9.6), brain (RPKM 8.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
2p21
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (44168875..44246928)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (44174224..44253771)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (44396014..44461785)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 566, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11430 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11431 Neighboring gene PPM1B divergent transcript Neighboring gene Sharpr-MPRA regulatory region 13633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15684 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:44415461-44416353 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:44461053-44461554 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:44461555-44462054 Neighboring gene uncharacterized LOC124906174 Neighboring gene ribosomal protein L12 pseudogene 19 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:44513823-44514378 Neighboring gene solute carrier family 3 member 1 Neighboring gene prolyl endopeptidase like

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Protein Phosphatase PPM1B Inhibits Gastric Cancer Progression and Serves as a Favorable Prognostic Biomarker. Li R, et al. Appl Immunohistochem Mol Morphol, 2022 May-Jun 01. PMID 35319516
  2. PPM1B depletion induces premature senescence in human IMR-90 fibroblasts. Park JH, et al. Mech Ageing Dev, 2014 Jun. PMID 24674756
  3. Cadmium is a potent inhibitor of PPM phosphatases and targets the M1 binding site. Pan C, et al. Sci Rep, 2013. PMID 23903585, Free PMC Article
  4. Uniquely conserved non-translated regions are involved in generation of the two major transcripts of protein phosphatase 2Cbeta. Seroussi E, et al. J Mol Biol, 2001 Sep 21. PMID 11563908
  5. The cloning expression and tissue distribution of human PP2Cbeta. Marley AE, et al. FEBS Lett, 1998 Jul 10. PMID 9684878

See all (115) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RBM10 regulates the tumorigenic potential of human cancer cells by modulating PPM1B and YBX1 activities.
    Title: RBM10 regulates the tumorigenic potential of human cancer cells by modulating PPM1B and YBX1 activities.
  2. Pleckstrin-2-promoted PPM1B degradation plays an important role in transforming growth factor-beta-induced breast cancer cell invasion and metastasis.
    Title: Pleckstrin-2-promoted PPM1B degradation plays an important role in transforming growth factor-β-induced breast cancer cell invasion and metastasis.
  3. Protein Phosphatase PPM1B Inhibits Gastric Cancer Progression and Serves as a Favorable Prognostic Biomarker.
    Title: Protein Phosphatase PPM1B Inhibits Gastric Cancer Progression and Serves as a Favorable Prognostic Biomarker.
  4. [TRIM59 regulates invasion and migration of nasopharyngeal carcinoma cells by targeted modulation of PPM1B].
    Title: [TRIM59 regulates invasion and migration of nasopharyngeal carcinoma cells by targeted modulation of PPM1B].
  5. Protein phosphatase PPM1B inhibits DYRK1A kinase through dephosphorylation of pS258 and reduces toxic tau aggregation.
    Title: Protein phosphatase PPM1B inhibits DYRK1A kinase through dephosphorylation of pS258 and reduces toxic tau aggregation.
  6. Relationship between the Levels of mRNA Expression for Protein Phosphatase 1B and Proteins Involved in Cytoskeleton Remodeling in Squamous Cell Carcinoma of the Larynx and Hypopharynx.
    Title: Relationship between the Levels of mRNA Expression for Protein Phosphatase 1B and Proteins Involved in Cytoskeleton Remodeling in Squamous Cell Carcinoma of the Larynx and Hypopharynx.
  7. TRIM59 promotes tumor growth in hepatocellular carcinoma and regulates the cell cycle by degradation of protein phosphatase 1B.
    Title: TRIM59 promotes tumor growth in hepatocellular carcinoma and regulates the cell cycle by degradation of protein phosphatase 1B.
  8. Results indicate that protein phosphatase 1B (PPM1B) negatively regulates cancer cell motility and invasiveness through dephosphorylating Rho guanine nucleotide dissociation inhibitor 1 (RhoGDI1).
    Title: Protein phosphatase 1B dephosphorylates Rho guanine nucleotide dissociation inhibitor 1 and suppresses cancer cell migration and invasion.
  9. PPM1B plays a negative role in the activation of the p38-RB1-E2F1 pathway and that targeting PPM1B could be useful in certain types of cancer by stimulating chemotherapy-induced cell death.
    Title: PPM1B depletion in U2OS cells supresses cell growth through RB1-E2F1 pathway and stimulates bleomycin-induced cell death.
  10. This study has identified PPM1B and miR-186 as potential diagnostic markers in bladder cancer. Promotion of PPM1B and suppression of miR-186 may offer effective therapeutic strategies in the treatment of bladder cancer.
    Title: miR-186 downregulates protein phosphatase PPM1B in bladder cancer and mediates G1-S phase transition.
Submit: New GeneRIF Correction See all GeneRIFs (22)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC21657

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables magnesium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables manganese ion binding IEA
Inferred from Electronic Annotation
more info
  
enables myosin phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein serine/threonine phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein serine/threonine phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in N-terminal protein myristoylation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of canonical NF-kappaB signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of canonical NF-kappaB signal transduction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of defense response to virus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of interferon-beta production IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of non-canonical NF-kappaB signal transduction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in peptidyl-threonine dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in peptidyl-threonine dephosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of canonical Wnt signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein dephosphorylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein phosphatase 1B
Names
protein phosphatase 2C-like protein
NP_001028729.1
NP_002697.1
NP_808907.1
NP_808908.1
XP_011531238.1
XP_047300791.1
XP_047300792.1
XP_047300793.1
XP_054198656.1
XP_054198657.1
XP_054198658.1
XP_054198659.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011678.2 RefSeqGene

    Range
    5002..67599
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001033557.3 → NP_001028729.1  protein phosphatase 1B isoform 5

    See identical proteins and their annotated locations for NP_001028729.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate 3' terminal exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (5) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AA742374, DA128532, DQ023510
    Consensus CDS
    CCDS46271.1
    UniProtKB/TrEMBL
    C9JIR6
    Related
    ENSP00000387287.3, ENST00000409432.7
    Conserved Domains (2) summary
    cd00143
    Location:23 → 295
    PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...
    pfam07830
    Location:289 → 365
    PP2C_C; Protein serine/threonine phosphatase 2C, C-terminal domain

  2. NM_002706.6 → NP_002697.1  protein phosphatase 1B isoform 1

    See identical proteins and their annotated locations for NP_002697.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AL833035, BC064381, DA128532
    Consensus CDS
    CCDS1817.1
    UniProtKB/Swiss-Prot
    O75688, Q461Q2, Q4J6C1, Q4J6C2, Q658R4, Q96ER6, Q9HAY8
    UniProtKB/TrEMBL
    B3KP90
    Related
    ENSP00000282412.4, ENST00000282412.9
    Conserved Domains (2) summary
    cd00143
    Location:23 → 295
    PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...
    pfam07830
    Location:289 → 368
    PP2C_C; Protein serine/threonine phosphatase 2C, C-terminal domain

  3. NM_177968.4 → NP_808907.1  protein phosphatase 1B isoform 2

    See identical proteins and their annotated locations for NP_808907.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 3' terminal exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC013717, DA128532, DQ023508
    Consensus CDS
    CCDS1816.1
    UniProtKB/TrEMBL
    A8K599
    Related
    ENSP00000367813.2, ENST00000378551.6
    Conserved Domains (2) summary
    cd00143
    Location:23 → 295
    PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...
    pfam07830
    Location:289 → 368
    PP2C_C; Protein serine/threonine phosphatase 2C, C-terminal domain

  4. NM_177969.4 → NP_808908.1  protein phosphatase 1B isoform 3

    See identical proteins and their annotated locations for NP_808908.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon, and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AL833035, BC012002, DA128532
    Consensus CDS
    CCDS1818.1
    UniProtKB/Swiss-Prot
    O75688
    Related
    ENSP00000326089.4, ENST00000345249.8
    Conserved Domains (1) summary
    pfam07830
    Location:2 → 81
    PP2C_C; Protein serine/threonine phosphatase 2C, C-terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    44168875..44246928
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532936.4 → XP_011531238.1  protein phosphatase 1B isoform X2

    UniProtKB/TrEMBL
    Q4J6C0
    Conserved Domains (2) summary
    cd00143
    Location:23 → 295
    PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...
    pfam07830
    Location:289 → 365
    PP2C_C; Protein serine/threonine phosphatase 2C, C-terminal domain

  2. XM_047444837.1 → XP_047300793.1  protein phosphatase 1B isoform X4

  3. XM_047444835.1 → XP_047300791.1  protein phosphatase 1B isoform X1

    UniProtKB/Swiss-Prot
    O75688, Q461Q2, Q4J6C1, Q4J6C2, Q658R4, Q96ER6, Q9HAY8

  4. XM_047444836.1 → XP_047300792.1  protein phosphatase 1B isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    44174224..44253771
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054342682.1 → XP_054198657.1  protein phosphatase 1B isoform X2

  2. XM_054342684.1 → XP_054198659.1  protein phosphatase 1B isoform X4

  3. XM_054342681.1 → XP_054198656.1  protein phosphatase 1B isoform X1

    UniProtKB/Swiss-Prot
    O75688, Q461Q2, Q4J6C1, Q4J6C2, Q658R4, Q96ER6, Q9HAY8

  4. XM_054342683.1 → XP_054198658.1  protein phosphatase 1B isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001033556.1: Suppressed sequence

    Description
    NM_001033556.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which appears to be falsely primed from an intronic A-tract and may not be complete at the 3' end.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75688.1 GenPept UniProtKB/Swiss-Prot:O75688

Gene LinkOut

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