PKMYT1

protein kinase, membrane associated tyrosine/threonine 1
Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase (PKMYT1) is a member of the serine/threonine protein kinase family. This kinase preferentially phosphorylates and inactivates cyclin-dependent kinase 1 (CDK1), and thus negatively regulates cell cycle G2/M transition. This kinase is associated with the membrane throughout the cell cycle. Its activity is highly regulated during the cell cycle. Protein kinases AKT1/PKB and PLK (Polo-like kinase) have been shown to phosphorylate and regulate the activity of this kinase. Alternatively spliced transcript variants encoding distinct isoforms have been reported.

TCGA Data Summary

These figures show a summary of data collected by the cancer genome atlas for PKMYT1. The mutations heatmaps shows the fraction samples with each type of genetic mutation, while the copy number variation shows the percentage of samples where a deletion or amplication was dectected. Finally, the mRNA expression tab shows the amount of mRNA detected on a log-2 scale for each cancer type. The X-axis cancer type abbreviations are described here. This summary of the cancer genome atlas (TCGA) was collated from firebrowse developed by the Broad Institute. The code used to produce these figures is available through github.


PDB Kinase Domains

Kinase Domain Structure:

  • Title: Structure of human Membrane-associated Tyrosine- and Threonine-specific cdc2-inhibitory kinase MYT1 (PKMYT1)
  • Resolution: 1.7

Associated Compounds:

  • DIMETHYL SULFOXIDE
  • 1,2-ETHANEDIOL
View This Structure on RCSB PDB

Kinase Domain Structure:

  • Title: CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH PHA-848125
  • Resolution: 1.7

Associated Compounds:

  • N,1,4,4-TETRAMETHYL-8-{[4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE
  • DI(HYDROXYETHYL)ETHER
View This Structure on RCSB PDB

Kinase Domain Structure:

  • Title: CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH MK1775
  • Resolution: 2.13

Associated Compounds:

  • 1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one
  • DI(HYDROXYETHYL)ETHER
View This Structure on RCSB PDB

Kinase Domain Structure:

  • Title: CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN (de-phosphorylated) IN COMPLEX WITH SARACATINIB
  • Resolution: 1.8

Associated Compounds:

  • 1,2-ETHANEDIOL
  • N-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-7-[2-(4-METHYLPIPERAZIN-1-YL)ETHOXY]-5-(TETRAHYDRO-2H-PYRAN-4-YLOXY)QUINAZOLIN-4-AMINE
  • DI(HYDROXYETHYL)ETHER
View This Structure on RCSB PDB

Kinase Domain Structure:

  • Title: CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN (UNTREATED) IN COMPLEX WITH SARACATINIB
  • Resolution: 2.7

Associated Compounds:

  • 1,2-ETHANEDIOL
  • N-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-7-[2-(4-METHYLPIPERAZIN-1-YL)ETHOXY]-5-(TETRAHYDRO-2H-PYRAN-4-YLOXY)QUINAZOLIN-4-AMINE
View This Structure on RCSB PDB

Kinase Domain Structure:

  • Title: CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH BOSUTINIB
  • Resolution: 1.56

Associated Compounds:

  • 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile
  • DIMETHYL SULFOXIDE
  • 1,2-ETHANEDIOL
  • DI(HYDROXYETHYL)ETHER
View This Structure on RCSB PDB

Kinase Domain Structure:

  • Title: CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH Bosutinib isomer
  • Resolution: 1.5

Associated Compounds:

  • 1,2-ETHANEDIOL
  • DI(HYDROXYETHYL)ETHER
  • 4-[(3,5-DICHLORO-4-METHOXYPHENYL)AMINO]-6-METHOXY-7-[3-(4-METHYLPIPERAZIN-1-YL)PROPOXY]QUINOLINE-3-CARBONITRILE
View This Structure on RCSB PDB

Kinase Domain Structure:

  • Title: CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH Dasatinib
  • Resolution: 1.92

Associated Compounds:

  • N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE
  • CHLORIDE ION
  • 1,2-ETHANEDIOL
  • PHOSPHOTHREONINE
View This Structure on RCSB PDB

Kinase Domain Structure:

  • Title: CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH Pelitinib
  • Resolution: 2.25

Associated Compounds:

  • (2E)-N-{4-[(3-chloro-4-fluorophenyl)amino]-3-cyano-7-ethoxyquinolin-6-yl}-4-(dimethylamino)but-2-enamide
  • 1,2-ETHANEDIOL
  • SULFATE ION
View This Structure on RCSB PDB

Interaction Networks

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system drawing from natural language processing systems and structured databases. It collects mechanistic and causal assertions, represents them in a standardized form (INDRA Statements), and assembles them into various modeling formalisms including causal graphs and dynamical models. More information on this work can be found on Github. In this particular figure, several interaction-types are depicted; physical complexes (blue), phosphorylation (black), and general up- or downregulation (green and red, respectively). Biomacromolecules are represented as squares, small molecule as circles, and biological processes and diamonds. The thickness of each line reflects a confidence score, with thicker lines higher in confidence.

Affinity Purification - Mass Spectrometry


PRM Peptides

The calibration reverse curve plot with linear robust regression analysis is shown [1]. The observed concentrations of the stable isotopically labeled peptide surrogate was obtained for each peptide using LC-MS in parallel reaction mode with a constant quantity of natural isotope abundance peptide as the internal standard (25 fmol/µL) [2]. The analyte matrix was a tryptic digest of pooled patient derived xenografts (1 µg/µL) that was prepared according to CPTAC-SOP. Each of the three most intense peptide fragment ions is depicted as a different symbol. The measurements from replicate LC-MS analyses are depicted as the same symbol [3] The LOD was determined using a non-parametric method with eight LC-MS analyses without added analyte [4]. The LOQ was generated from the LOD [5]. The plots are dimensioned such that the theoretical line is at a 45° angle to facilitate assessment of peptide recovery and performance. The LOD, LOQ, and regression parameters are summarize in the Table.

  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855883/
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494192/
  3. https://proteomics.cancer.gov/sites/default/files/assay-characterization-guidance-document.pdf
  4. http://clinchem.aaccjnls.org/content/50/4/732
  5. “Algorithms, Routines and S Functions for Robust Statistics” (CRC Press, Boca Raton, Florida, USA, 1993)

View Peptide Parameters

The calibration reverse curve plot with linear robust regression analysis is shown [1]. The observed concentrations of the stable isotopically labeled peptide surrogate was obtained for each peptide using LC-MS in parallel reaction mode with a constant quantity of natural isotope abundance peptide as the internal standard (25 fmol/µL) [2]. The analyte matrix was a tryptic digest of pooled patient derived xenografts (1 µg/µL) that was prepared according to CPTAC-SOP. Each of the three most intense peptide fragment ions is depicted as a different symbol. The measurements from replicate LC-MS analyses are depicted as the same symbol [3] The LOD was determined using a non-parametric method with eight LC-MS analyses without added analyte [4]. The LOQ was generated from the LOD [5]. The plots are dimensioned such that the theoretical line is at a 45° angle to facilitate assessment of peptide recovery and performance. The LOD, LOQ, and regression parameters are summarize in the Table.

  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855883/
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494192/
  3. https://proteomics.cancer.gov/sites/default/files/assay-characterization-guidance-document.pdf
  4. http://clinchem.aaccjnls.org/content/50/4/732
  5. “Algorithms, Routines and S Functions for Robust Statistics” (CRC Press, Boca Raton, Florida, USA, 1993)

View Peptide Parameters

The calibration reverse curve plot with linear robust regression analysis is shown [1]. The observed concentrations of the stable isotopically labeled peptide surrogate was obtained for each peptide using LC-MS in parallel reaction mode with a constant quantity of natural isotope abundance peptide as the internal standard (25 fmol/µL) [2]. The analyte matrix was a tryptic digest of pooled patient derived xenografts (1 µg/µL) that was prepared according to CPTAC-SOP. Each of the three most intense peptide fragment ions is depicted as a different symbol. The measurements from replicate LC-MS analyses are depicted as the same symbol [3] The LOD was determined using a non-parametric method with eight LC-MS analyses without added analyte [4]. The LOQ was generated from the LOD [5]. The plots are dimensioned such that the theoretical line is at a 45° angle to facilitate assessment of peptide recovery and performance. The LOD, LOQ, and regression parameters are summarize in the Table.

  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855883/
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494192/
  3. https://proteomics.cancer.gov/sites/default/files/assay-characterization-guidance-document.pdf
  4. http://clinchem.aaccjnls.org/content/50/4/732
  5. “Algorithms, Routines and S Functions for Robust Statistics” (CRC Press, Boca Raton, Florida, USA, 1993)

View Peptide Parameters


Available Assays, Plasmids, Cell Lines and Animal Models
BioID Plasmids
These plasmids are generated by Ben Major's lab and are available through Addgene. These lentiviral expression plasmids have been used to generate protein-proximity or protein-protein interaction networks using the miniTurbo biotin ligase-based proximity-dependent biotinylation or traditional immuno-purification approaches coupled with mass spectrometry. More information about these plasmids can be found at the following links:
NanoBRET Assay
A PKMYT1 NanoBRET Assay has been developed and validated. NanoLuc®-fused PKMYT1 is available from Promega by special request. Additional information about this assay is available here.
Horizon KO HAP1 Cell Lines
PKMYT1
IMPC Mouse KO
MGI:2137630

Kinase Tissue Expression Summary

The expression of kinases varies widely across the human tissues assayed by the GTEx project and the Human Proteome Map. To gain a better understanding of the kinase tissue distribution, we've created an application that describes and summarizes the expression of each dark kinase in the context of the rest of the kinome. This interactive window onto the full applications shows the data associated with PKMYT1. The graph summarizes the expression of the kinase across all the organ systems.

The full application can further explored at the Kinase Expression Data Application.


Reactome Pathways

The Reactome Knowledgebase of Human Biological Pathways and Processes is a curated and peer-reviewed knowledgebase available online as an open access resource that can be freely used and distributed by all members of the biological research community. This view of the reactome database is focused on PKMYT1 and displays the pathways associated with PKMYT1.