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

Summary

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: mouse all
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Genomic context

Location:: 2p21

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (44168875..44246928)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (44174224..44253771)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (44396014..44461785)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Circ_0090231 knockdown protects vascular smooth muscle cells from ox-LDL-induced proliferation, migration and invasion via miR-942-5p/PPM1B axis during atherosclerosis.
Title: Circ_0090231 knockdown protects vascular smooth muscle cells from ox-LDL-induced proliferation, migration and invasion via miR-942-5p/PPM1B axis during atherosclerosis.
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.
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.
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.
[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].
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.
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.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (23)

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH12314 (e-PCR)
- UniSTS:39221

A004I37 (e-PCR)
- UniSTS:58735

RH36905 (e-PCR)
- UniSTS:87932

RH93945 (e-PCR)
- UniSTS:86915

PPM1B (e-PCR)
- UniSTS:278940

RH68945 (e-PCR)
- UniSTS:61359

D2S4020 (e-PCR)
- UniSTS:226028

MARC_16411-16412:1018631330:1 (e-PCR)
- UniSTS:268025

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	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	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
involved_in regulation of canonical NF-kappaB signal transduction	IBA Inferred from Biological aspect of Ancestor more info

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

EC 3.1.3.16

NP_002697.1

EC 3.1.3.16

NP_808907.1

EC 3.1.3.16

NP_808908.1

EC 3.1.3.16

XP_011531238.1

EC 3.1.3.16

XP_047300791.1

EC 3.1.3.16

XP_047300792.1

EC 3.1.3.16

XP_047300793.1

EC 3.1.3.16

XP_054198656.1

EC 3.1.3.16

XP_054198657.1

EC 3.1.3.16

XP_054198658.1

EC 3.1.3.16

XP_054198659.1

EC 3.1.3.16

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

NG_011678.2 RefSeqGene

Range

5002..67599

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

44168875..44246928

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_047444837.1 → XP_047300793.1 protein phosphatase 1B isoform X4
XM_047444835.1 → XP_047300791.1 protein phosphatase 1B isoform X1

UniProtKB/Swiss-Prot

O75688, Q461Q2, Q4J6C1, Q4J6C2, Q658R4, Q96ER6, Q9HAY8
XM_047444836.1 → XP_047300792.1 protein phosphatase 1B isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

44174224..44253771

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054342682.1 → XP_054198657.1 protein phosphatase 1B isoform X2
XM_054342684.1 → XP_054198659.1 protein phosphatase 1B isoform X4
XM_054342681.1 → XP_054198656.1 protein phosphatase 1B isoform X1

UniProtKB/Swiss-Prot

O75688, Q461Q2, Q4J6C1, Q4J6C2, Q658R4, Q96ER6, Q9HAY8
XM_054342683.1 → XP_054198658.1 protein phosphatase 1B isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.