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PPM1K protein phosphatase, Mg2+/Mn2+ dependent 1K [ Homo sapiens (human) ]

Gene ID: 152926, updated on 2-Nov-2024

Summary

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Official Symbol
PPM1Kprovided by HGNC
Official Full Name
protein phosphatase, Mg2+/Mn2+ dependent 1Kprovided by HGNC
Primary source
HGNC:HGNC:25415
See related
Ensembl:ENSG00000163644 MIM:611065; AllianceGenome:HGNC:25415
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
BDP; PTMP; BCKDH; PP2Cm; MSUDMV; PP2Ckappa; UG0882E07
Summary
This gene encodes a member of the PPM family of Mn2+/Mg2+-dependent protein phosphatases. The encoded protein, essential for cell survival and development, is targeted to the mitochondria where it plays a key role in regulation of the mitochondrial permeability transition pore. [provided by RefSeq, Sep 2012]
Expression
Broad expression in heart (RPKM 22.0), endometrium (RPKM 10.0) and 22 other tissues See more
Orthologs
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Genomic context

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See PPM1K in Genome Data Viewer
Location:
4q22.1
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (88257620..88284561, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (91588591..91615539, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (89178772..89205713, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATP binding cassette subfamily G member 2 (JR blood group) Neighboring gene RNA, U6atac small nuclear 31, pseudogene Neighboring gene RNA, U6 small nuclear 1298, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:89165283-89165815 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:89188029-89188528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21710 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:89205598-89206121 Neighboring gene RNA, U6 small nuclear 112, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:89217507-89218473 Neighboring gene PPM1K divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21712 Neighboring gene uncharacterized LOC124900731

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 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. Genetic determinant for amino acid metabolites and changes in body weight and insulin resistance in response to weight-loss diets: the Preventing Overweight Using Novel Dietary Strategies (POUNDS LOST) trial. Xu M, et al. Circulation, 2013 Mar 26. PMID 23446828, Free PMC Article
  2. Effect of the interaction between diet composition and the PPM1K genetic variant on insulin resistance and β cell function markers during weight loss: results from the Nutrient Gene Interactions in Human Obesity: implications for dietary guidelines (NUGENOB) randomized trial. Goni L, et al. Am J Clin Nutr, 2017 Sep. PMID 28768654
  3. The role of PP5 and PP2C in cardiac health and disease. Neumann J, et al. Cell Signal, 2021 Sep. PMID 33964402
  4. Characterization of a novel human protein phosphatase 2C family member, PP2Ckappa. Dai J, et al. Int J Mol Med, 2006 Jun. PMID 16685424
  5. Identification of a novel PP2C-type mitochondrial phosphatase. Joshi M, et al. Biochem Biophys Res Commun, 2007 Apr 27. PMID 17336929, Free PMC Article

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PPM1K-regulated impaired catabolism of branched-chain amino acids orchestrates polycystic ovary syndrome.
    Title: PPM1K-regulated impaired catabolism of branched-chain amino acids orchestrates polycystic ovary syndrome.
  2. The role of PP5 and PP2C in cardiac health and disease.
    Title: The role of PP5 and PP2C in cardiac health and disease.
  3. Effects of PPM1K rs1440581 and rs7678928 on serum branched-chain amino acid levels and risk of cardiovascular disease.
    Title: Effects of PPM1K rs1440581 and rs7678928 on serum branched-chain amino acid levels and risk of cardiovascular disease.
  4. three Mg(2+) were located in the active site of the PPM1K N94K instead of two Mg(2+) in the PPM1K wild type
    Title: Crystal structure and catalytic activity of the PPM1K N94K mutant.
  5. Branched chain amino acids related genetic variant rs1440581 was associated with an increased risk of incident T2 Diabetes in a Chinese population. This variant might modify effect of weight gain on development in Insulin resistance.
    Title: Association of branched chain amino acids related variant rs1440581 with risk of incident diabetes and longitudinal changes in insulin resistance in Chinese.
  6. PPM1K rs1440581 may affect changes in glucose metabolism during weight loss, and this effect is dependent on dietary fat and carbohydrate intakes.
    Title: Effect of the interaction between diet composition and the PPM1K genetic variant on insulin resistance and β cell function markers during weight loss: results from the Nutrient Gene Interactions in Human Obesity: implications for dietary guidelines (NUGENOB) randomized trial.
  7. miR-204 and miR-211 directly repress PPM1K expression via 3'UTR.
    Title: Regulation of PP2Cm expression by miRNA-204/211 and miRNA-22 in mouse and human cells.
  8. Overweight people with the C allele of the branched-chain amino acid/aromatic amino acid ratio-associated variant rs1440581 may benefit less in weight loss and improved insulin sensitivity than those without it on a energy-restricted high-fat diet.
    Title: Genetic determinant for amino acid metabolites and changes in body weight and insulin resistance in response to weight-loss diets: the Preventing Overweight Using Novel Dietary Strategies (POUNDS LOST) trial.
  9. The 2.4 A PP2Cm structure reveals a central beta-sandwich with two bound metal ions in the active-site cleft.
    Title: Structural and biochemical characterization of human mitochondrial branched-chain α-ketoacid dehydrogenase phosphatase.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Submit: New GeneRIF Correction See all GeneRIFs (13)

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

Associated conditions

Description Tests
Maple syrup urine disease, mild variant
MedGen: C3554575 OMIM: 615135 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites.
EBI GWAS Catalog
Does parental expressed emotion moderate genetic effects in ADHD? An exploration using a genome wide association scan.
EBI GWAS Catalog
Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
EBI GWAS Catalog
Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption.
EBI GWAS Catalog
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of protein phosphatase, Mg2+/Mn2+ dependent, 1K (PPM1K) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

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

  • FLJ35131, DKFZp667B084, DKFZp761G058

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables [3-methyl-2-oxobutanoate dehydrogenase (lipoamide)]-phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables manganese ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
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 branched-chain amino acid catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein dephosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of intracellular signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of mitochondrial membrane permeability involved in apoptotic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in mitochondrial matrix ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
  
located_in mitochondrion HTP PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
protein phosphatase Mn(2+)-dependent 1K
Names
PP2C domain-containing protein phosphatase 1K
PP2C-kappa
PP2C-type mitochondrial phosphoprotein phosphatase
[3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)]-phosphatase, mitochondrial
branched-chain I+/--ketoacid dehydrogenase phosphatase
branched-chain alpha-ketoacid dehydrogenase phosphatase
protein phosphatase 1K, mitochondrial
protein phosphatase 2C family member
protein phosphatase 2C kappa
NP_689755.3
XP_005262832.1
XP_006714174.1
XP_016863292.1
XP_016863295.1
XP_047305628.1
XP_047305629.1
XP_047305630.1
XP_047305631.1
XP_054205018.1
XP_054205019.1
XP_054205020.1
XP_054205021.1
XP_054205022.1
XP_054205023.1
XP_054205024.1
XP_054205025.1

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_032931.1 RefSeqGene

    Range
    5271..32212
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_152542.5 → NP_689755.3  protein phosphatase Mn(2+)-dependent 1K

    See identical proteins and their annotated locations for NP_689755.3

    Status: REVIEWED

    Source sequence(s)
    AC097484, AC108213, AY435431
    Consensus CDS
    CCDS3629.1
    UniProtKB/Swiss-Prot
    B2RAZ1, Q05CT5, Q49AB5, Q4W5E6, Q56AN8, Q8IUZ7, Q8IXG7, Q8N3J5, Q8ND70, Q96NT4
    UniProtKB/TrEMBL
    A0A0A0MQZ4
    Related
    ENSP00000477341.1, ENST00000608933.6
    Conserved Domains (1) summary
    cd00143
    Location:95 → 346
    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 ...

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

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    88257620..88284561 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007803.3 → XP_016863292.1  protein phosphatase Mn(2+)-dependent 1K isoform X1

    UniProtKB/Swiss-Prot
    B2RAZ1, Q05CT5, Q49AB5, Q4W5E6, Q56AN8, Q8IUZ7, Q8IXG7, Q8N3J5, Q8ND70, Q96NT4
    UniProtKB/TrEMBL
    A0A0A0MQZ4
    Conserved Domains (1) summary
    cd00143
    Location:95 → 346
    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 ...

  2. XM_006714111.5 → XP_006714174.1  protein phosphatase Mn(2+)-dependent 1K isoform X1

    See identical proteins and their annotated locations for XP_006714174.1

    UniProtKB/Swiss-Prot
    B2RAZ1, Q05CT5, Q49AB5, Q4W5E6, Q56AN8, Q8IUZ7, Q8IXG7, Q8N3J5, Q8ND70, Q96NT4
    UniProtKB/TrEMBL
    A0A0A0MQZ4
    Conserved Domains (1) summary
    cd00143
    Location:95 → 346
    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 ...

  3. XM_017007806.3 → XP_016863295.1  protein phosphatase Mn(2+)-dependent 1K isoform X2

  4. XM_047449672.1 → XP_047305628.1  protein phosphatase Mn(2+)-dependent 1K isoform X3

  5. XM_047449675.1 → XP_047305631.1  protein phosphatase Mn(2+)-dependent 1K isoform X6

  6. XM_047449674.1 → XP_047305630.1  protein phosphatase Mn(2+)-dependent 1K isoform X5

  7. XM_005262775.5 → XP_005262832.1  protein phosphatase Mn(2+)-dependent 1K isoform X4

    UniProtKB/TrEMBL
    V9GYZ5
    Conserved Domains (1) summary
    cl00120
    Location:95 → 184
    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 ...

  8. XM_047449673.1 → XP_047305629.1  protein phosphatase Mn(2+)-dependent 1K isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    91588591..91615539 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054349044.1 → XP_054205019.1  protein phosphatase Mn(2+)-dependent 1K isoform X1

    UniProtKB/Swiss-Prot
    B2RAZ1, Q05CT5, Q49AB5, Q4W5E6, Q56AN8, Q8IUZ7, Q8IXG7, Q8N3J5, Q8ND70, Q96NT4

  2. XM_054349043.1 → XP_054205018.1  protein phosphatase Mn(2+)-dependent 1K isoform X1

    UniProtKB/Swiss-Prot
    B2RAZ1, Q05CT5, Q49AB5, Q4W5E6, Q56AN8, Q8IUZ7, Q8IXG7, Q8N3J5, Q8ND70, Q96NT4

  3. XM_054349045.1 → XP_054205020.1  protein phosphatase Mn(2+)-dependent 1K isoform X2

  4. XM_054349046.1 → XP_054205021.1  protein phosphatase Mn(2+)-dependent 1K isoform X3

  5. XM_054349050.1 → XP_054205025.1  protein phosphatase Mn(2+)-dependent 1K isoform X6

  6. XM_054349049.1 → XP_054205024.1  protein phosphatase Mn(2+)-dependent 1K isoform X5

  7. XM_054349047.1 → XP_054205022.1  protein phosphatase Mn(2+)-dependent 1K isoform X4

  8. XM_054349048.1 → XP_054205023.1  protein phosphatase Mn(2+)-dependent 1K isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N3J5.1 GenPept UniProtKB/Swiss-Prot:Q8N3J5

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