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

Gene ID: 5495, updated on 12-Oct-2019

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
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

Genomic context

See PPM1B in Genome Data Viewer
Location:
2p21
Exon count:
9
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (44168803..44247330)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (44395984..44471570)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 455, pseudogene Neighboring gene leucine rich pentatricopeptide repeat containing Neighboring gene uncharacterized LOC102723904 Neighboring gene RNA, U6 small nuclear 566, pseudogene Neighboring gene ribosomal protein L12 pseudogene 19 Neighboring gene solute carrier family 3 member 1 Neighboring gene prolyl endopeptidase like

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Antiviral mechanism by IFN-stimulated genes, organism-specific biosystem (from REACTOME)
    Antiviral mechanism by IFN-stimulated genes, organism-specific biosystemThe ISG proteins generated by IFN pathways plays key roles in the induction of innate and adaptive immune responses.
  • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
    Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
  • ISG15 antiviral mechanism, organism-specific biosystem (from REACTOME)
    ISG15 antiviral mechanism, organism-specific biosystemInterferon-stimulated gene 15 (ISG15) is a member of the ubiquitin-like (Ubl) family. It is strongly induced upon exposure to type I Interferons (IFNs), viruses, bacterial LPS, and other stresses. On...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Interferon Signaling, organism-specific biosystem (from REACTOME)
    Interferon Signaling, organism-specific biosystemInterferons (IFNs) are cytokines that play a central role in initiating immune responses, especially antiviral and antitumor effects. There are three types of IFNs:Type I (IFN-alpha, -beta and others...
  • MAPK Signaling Pathway, organism-specific biosystem (from WikiPathways)
    MAPK Signaling Pathway, organism-specific biosystemThe mitogen-activated protein kinase (MAPK) cascade is a highly conserved module that is involved in various cellular functions, including cell proliferation, differentiation and migration. Mammals e...
  • MAPK signaling pathway, organism-specific biosystem (from KEGG)
    MAPK signaling pathway, organism-specific biosystemThe mitogen-activated protein kinase (MAPK) cascade is a highly conserved module that is involved in various cellular functions, including cell proliferation, differentiation and migration. Mammals e...
  • MAPK signaling pathway, conserved biosystem (from KEGG)
    MAPK signaling pathway, conserved biosystemThe mitogen-activated protein kinase (MAPK) cascade is a highly conserved module that is involved in various cellular functions, including cell proliferation, differentiation and migration. Mammals e...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC21657

Gene Ontology Provided by GOA

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

General protein information

Preferred Names
protein phosphatase 1B
Names
Ser/Thr protein phosphatase type 2C beta 2 isoform
protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform
protein phosphatase 2C-like protein
NP_001028729.1
NP_002697.1
NP_808907.1
NP_808908.1
XP_011531238.1
XP_016859884.1
XP_016859885.1
XP_016859886.1

NCBI Reference Sequences (RefSeq)

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_011678.1 RefSeqGene

    Range
    5015..70786
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001033557.3NP_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/Swiss-Prot
    O75688
    Related
    ENSP00000387287.3, ENST00000409432.7
    Conserved Domains (2) summary
    cd00143
    Location:23295
    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:289365
    PP2C_C; Protein serine/threonine phosphatase 2C, C-terminal domain
  2. NM_002706.6NP_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
    Related
    ENSP00000282412.4, ENST00000282412.9
    Conserved Domains (2) summary
    cd00143
    Location:23295
    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:289365
    PP2C_C; Protein serine/threonine phosphatase 2C, C-terminal domain
  3. NM_177968.4NP_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/Swiss-Prot
    O75688
    Related
    ENSP00000367813.2, ENST00000378551.6
    Conserved Domains (2) summary
    cd00143
    Location:23295
    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:289365
    PP2C_C; Protein serine/threonine phosphatase 2C, C-terminal domain
  4. NM_177969.3NP_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)
    AA742374, AL833035, BC012002, DA128532
    Consensus CDS
    CCDS1818.1
    UniProtKB/Swiss-Prot
    O75688
    Related
    ENSP00000326089.4, ENST00000345249.8
    Conserved Domains (1) summary
    pfam07830
    Location:278
    PP2C_C; Protein serine/threonine phosphatase 2C, C-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    44168803..44247330
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004396.2XP_016859885.1  protein phosphatase 1B isoform X2

  2. XM_017004397.2XP_016859886.1  protein phosphatase 1B isoform X4

  3. XM_017004395.2XP_016859884.1  protein phosphatase 1B isoform X1

  4. XM_011532936.3XP_011531238.1  protein phosphatase 1B isoform X3

    Conserved Domains (2) summary
    cd00143
    Location:23295
    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:289365
    PP2C_C; Protein serine/threonine phosphatase 2C, C-terminal domain

RNA

  1. XR_001738794.2 RNA Sequence

    Related
    ENST00000378540.8

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.
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