Human Gene PPM1B (uc002rtt.3) Description and Page Index
  Description: Homo sapiens protein phosphatase, Mg2+/Mn2+ dependent, 1B (PPM1B), transcript variant 1, mRNA.
RefSeq Summary (NM_002706): 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].
Transcript (Including UTRs)
   Position: hg19 chr2:44,396,000-44,458,611 Size: 62,612 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr2:44,428,339-44,457,857 Size: 29,519 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:44,396,000-44,458,611)mRNA (may differ from genome)Protein (479 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: PPM1B_HUMAN
DESCRIPTION: RecName: Full=Protein phosphatase 1B; EC=3.1.3.16; AltName: Full=Protein phosphatase 2C isoform beta; Short=PP2C-beta;
FUNCTION: Enzyme with a broad specificity. Dephosphorylates CDK2 and CDK6 in vitro.
CATALYTIC ACTIVITY: A phosphoprotein + H(2)O = a protein + phosphate.
COFACTOR: Binds 2 magnesium or manganese ions per subunit (By similarity).
SUBUNIT: Monomer (By similarity). Interacts with PAK6.
INTERACTION: P49407:ARRB1; NbExp=4; IntAct=EBI-1047039, EBI-743313; P32121:ARRB2; NbExp=3; IntAct=EBI-1047039, EBI-714559;
TISSUE SPECIFICITY: Highly expressed in heart and skeletal muscle.
SIMILARITY: Belongs to the PP2C family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PPM1B
CDC HuGE Published Literature: PPM1B

-  MalaCards Disease Associations
  MalaCards Gene Search: PPM1B
Diseases sorted by gene-association score: hypotonia-cystinuria syndrome* (15)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.25 RPKM in Muscle - Skeletal
Total median expression: 534.61 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -209.10428-0.489 Picture PostScript Text
3' UTR -149.30754-0.198 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
IPR001932 - PP2C-like
IPR012911 - PP2C_C
IPR000222 - PP2C_Mn2_Asp60_BS
IPR015655 - Protein_Pase_2C

Pfam Domains:
PF00481 - Protein phosphatase 2C
PF07830 - Protein serine/threonine phosphatase 2C, C-terminal domain

SCOP Domains:
81601 - Protein serine/threonine phosphatase 2C, C-terminal domain
81606 - Protein serine/threonine phosphatase 2C, catalytic domain

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

2P8E
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O75688
FrontTopSide
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004721 phosphoprotein phosphatase activity
GO:0004722 protein serine/threonine phosphatase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0030145 manganese ion binding
GO:0043169 cation binding
GO:0046872 metal ion binding

Biological Process:
GO:0006470 protein dephosphorylation
GO:0006499 N-terminal protein myristoylation
GO:0032688 negative regulation of interferon-beta production
GO:0035970 peptidyl-threonine dephosphorylation
GO:0043124 negative regulation of I-kappaB kinase/NF-kappaB signaling
GO:0050687 negative regulation of defense response to virus
GO:1901223 negative regulation of NIK/NF-kappaB signaling

Cellular Component:
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  DQ023509 - Homo sapiens PPM1B beta isoform variant 4 (PPM1B) mRNA, complete cds, alternatively spliced.
AK056009 - Homo sapiens cDNA FLJ31447 fis, clone NT2NE2000913, highly similar to Protein phosphatase 2C isoform beta (EC 3.1.3.16).
DQ023510 - Homo sapiens PPM1B beta isoform variant 5 (PPM1B) mRNA, complete cds, alternatively spliced.
AK291214 - Homo sapiens cDNA FLJ77281 complete cds, highly similar to Homo sapiens protein phosphatase 1B (formerly 2C),magnesium-dependent, beta isoform (PPM1B), transcript variant 2,mRNA.
DQ023508 - Homo sapiens PPM1B beta isoform variant 2 (PPM1B) mRNA, complete cds, alternatively spliced.
DQ023511 - Homo sapiens PPM1B beta isoform variant 6 (PPM1B) mRNA, partial cds, alternatively spliced.
BC064381 - Homo sapiens protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform, mRNA (cDNA clone MGC:74583 IMAGE:5734287), complete cds.
AJ271832 - Homo sapiens mRNA for protein phosphatase 1B2 (PPM1B2 gene).
AJ271835 - Homo sapiens mRNA for protein phosphatase 1B1 (PPM1B1 gene).
BC012002 - Homo sapiens protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform, mRNA (cDNA clone IMAGE:4517367), complete cds.
AL833035 - Homo sapiens mRNA; cDNA DKFZp666O168 (from clone DKFZp666O168).
AB464099 - Synthetic construct DNA, clone: pF1KB8150, Homo sapiens PPM1B gene for protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform, without stop codon, in Flexi system.
AJ005801 - Homo sapiens mRNA for protein phosphatase 2C (beta).
AF294792 - Homo sapiens Ser/Thr protein phosphatase type 2C beta 2 isoform mRNA, complete cds, alternatively spliced.
AF136972 - Homo sapiens protein phosphatase 2C-like protein mRNA, complete cds.
JD271926 - Sequence 252950 from Patent EP1572962.
JD056799 - Sequence 37823 from Patent EP1572962.
JD484754 - Sequence 465778 from Patent EP1572962.
JD520869 - Sequence 501893 from Patent EP1572962.
JD192223 - Sequence 173247 from Patent EP1572962.
JD126461 - Sequence 107485 from Patent EP1572962.
JD126462 - Sequence 107486 from Patent EP1572962.
JD130548 - Sequence 111572 from Patent EP1572962.
JD328839 - Sequence 309863 from Patent EP1572962.
JD438591 - Sequence 419615 from Patent EP1572962.
HQ448711 - Synthetic construct Homo sapiens clone IMAGE:100072155; CCSB008740_01 protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform (PPM1B) gene, encodes complete protein.
KJ891861 - Synthetic construct Homo sapiens clone ccsbBroadEn_01255 PPM1B gene, encodes complete protein.
JD093541 - Sequence 74565 from Patent EP1572962.
JD283946 - Sequence 264970 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04010 - MAPK signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein O75688 (Reactome details) participates in the following event(s):

R-HSA-1169405 ISGylation of protein phosphatase 1 beta (PP2CB)
R-HSA-1169408 ISG15 antiviral mechanism
R-HSA-1169410 Antiviral mechanism by IFN-stimulated genes
R-HSA-913531 Interferon Signaling
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: NM_002706, NP_002697, O75688, PP2CB, PPM1B_HUMAN, Q461Q2, Q4J6C1, Q4J6C2, Q658R4, Q96ER6, Q9HAY8
UCSC ID: uc002rtt.3
RefSeq Accession: NM_002706
Protein: O75688 (aka PPM1B_HUMAN)
CCDS: CCDS1817.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002706.4
exon count: 6CDS single in 3' UTR: no RNA size: 2636
ORF size: 1440CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2933.00frame shift in genome: no % Coverage: 99.47
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.