KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Actin | Abcam | Cat#ab6276; RRID: AB_2223210 |
| Histone H3 | Cell Signaling Technologies | Cat#4499; RRID: AB_10544537 |
| Phospho-MAPK/CDK Substrate | Cell Signaling Technologies | Cat#2325; RRID: AB_331820 |
| PKL | ProteinTech | Cat#22456-1-AP; RRID: AB_10918271 |
| PKL | Santa Cruz | Cat#SC-D10; RRID: AB_2163668 |
| PKL pS113 (A/G purified) | Covance-Custom Antibody | N/A |
| PKL pS12 (A/G purified) | Covance-Custom Antibody | N/A |
| PKM2 | ProteinTech | Cat#15822-1-AP; RRID: AB_1851537 |
| Bacterial and Virus Strains | ||
| ReColi (Strain: C321.ΔA) | Lajoie et al., 2013 | Addgene Cat#68306 |
| ElectroMAX™ DH10B™ E. coli | Invitrogen | Cat#18290015 |
| Biological Samples | ||
| Primary Rat Hepatocytes | Yale Liver Center Cellular and Molecular Physiology Core Facility | https://medicine.yale.edu/intmed/livercenter/core-facilities/cellular-molecular-physiologycore-facility/ |
| Chemicals, Peptides, and Recombinant Proteins | ||
| CDK1/CyclinA2 | SignalChem | Cat#C22-18G-05 |
| CDK2/CyclinA2 | SignalChem | Cat#C29-10G-05 |
| CDK4/CyclinD1 | SignalChem | Cat#C31-10G-05 |
| CDK5/p35 | SignalChem | Cat#C33-10BG-05 |
| CDK6/CyclinD3 | SignalChem | Cat#C35-10H-05 |
| Aphidicolin from Nigrospora sphaerica | Sigma | Cat#A0781 |
| Nocodazole | Sigma | Cat#M1404 |
| Dinaciclib | Selleckchem | Cat#S2768 |
| Dimedone (light) | Sigma | Cat#D153303 |
| Iodoacetamide | Sigma | Cat#I1149 |
| IBMX | Sigma | Cat#I7018 |
| Critical Commercial Assays | ||
| Insulin radioimmunoassay | Millipore | Cat#RI-13K |
| NEFA-HR(2) | Wako | Cat#434-91795 |
| Triglyceride-SL | Sekisui | Cat#236-99 |
| Glucose-SL | Sekisui | Cat#235-60 |
| Deposited Data | ||
| PKL pS113 | wwPDB | 6ECK |
| PKL pS12 | wwPDB | 6ECH |
| Mass Spectrometry-based Phosphoproteomics | ProteomeXchange | PXD010209 |
| Experimental Models: Cell Lines | ||
| McA-RH7777 | ATCC | Cat# CRL-1601; RRID: CVCL_0444 |
| Experimental Models: Organisms/Strains | ||
| Male Sprague-Dawley Rats | Charles River Laboratories | RRID: RGD_734476 |
| Oligonucleotides | ||
| Control ASO (5′- CCTTCCCTGAAGGTTCCTCC-3′) | Samuel et al., 2007 | Ionis Pharmaceuticals |
| PKCε ASO (5′-GCCAGCTCGATCTTGCGCCC-3′) | Samuel et al., 2007 | Ionis Pharmaceuticals |
| Recombinant DNA | ||
| PCRT7 tetR pLtetO MBP-rPKL S12TAG Amp | This Paper | Addgene Cat#107155 |
| PCRT7 tetR pLtetO MBP-rPKL WT Amp | This Paper | Addgene Cat#107156 |
| PCRT7 tetR pLtetO MBP-rPKL S113TAG Amp | This Paper | Addgene Cat#107157 |
| PCRT7 tetR pLtetO MBP-rPKM2 Amp | This Paper | Addgene Cat#107158 |
| Targeted CDK peptide library in pCRT7 NT Topo arabinose | This Paper | Addgene Cat#73446 |
| SepOTSλ | Pirman et al., 2015 | Addgene Cat#68292 |
| Software and Algorithms | ||
| Maxquant v 1.5.1.2 | Cox and Mann, 2008 | http://www.coxdocs.org/doku.php?id=maxquant:common:download_and_installation |
| Perseus v 1.5.0.31 | Tyanova et al., 2016 | http://www.coxdocs.org/doku.php?id=perseus:start |
| MASCOT | Perkins et al., 1999 | http://www.matrixscience.com |
| pLogo v 1.2.0 | O’Shea et al., 2013 | https://plogo.uconn.edu/ |
| MotifX v 1.2 | Schwartz and Gygi, 2005 | https://motif-x.med.harvard.edu/motif-x.html |
| Omicsintegrator | Tuncbag et al., 2016 | http://fraenkel-nsf.csbi.mit.edu/omicsintegrator/ |
| MagTran v 1.03 b2 | Zhang and Marshall, 1998 | Available from the developer, Dr. Zhongqi Zang |
| Skyline v 4.2.0.19072 | MacLean et al., 2010 | https://skyline.ms/project/home/software/Skyline/begin.view |
| Graphpad Prism v 7.01 | Graphpad Software | https://www.graphpad.com/ |
| Codon Optimization Tool | IDT | http://www.idtdna.com/site/account/login?returnurl=%2FCodonOpt |
| HKL2000 | HKL research, Inc. | http://www.hkl-xray.com/hkl-2000 |
| Phaser v 2.7.0 | McCoy et al., 2007 | https://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software |
| COOT v 0.8.7 | Emsley et al., 2010 | https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ |
| Refmac5.8.0230 | Murshudov et al., 2011 | http://www.ccp4.ac.uk/html/refmac5.html |
| CCP4 software suite | Winn et al., 2011 | http://www.ccp4.ac.uk/ |
| Phenix v 1.13-2998 | Adams et al., 2010 | https://www.phenix-online.org |
| Other | ||
| Regular Chow | Harlan | Cat#TD2018 |
| High-fat safflower oil-based diet | Research Diets | Cat#D12492 |
| Kinase Assay Buffer I | SignalChem | Cat#K01-09-01 |
| Kinase Dilution Buffer III | SignalChem | Cat#K23-09-01 |
| Lysyl Endopeptidase | Wako | Cat#125-02543 |
| Sequencing Grade Modified Trypsin | Promega | Cat#V511x |
| Titansphere TiO2 | GL Science | Cat#5020-75000 |
| Acid Labile Surfactant | Protea | Cat#ALS-110 |
| CytoBuster | Millipore | Cat#71009 |
| Superdex S200 Column | GE Healthcare Lifesciences | Cat# 17517501 |
| Hypersep Retain PEP 30mg Cartridge | Thermo Scientific | Cat# 60107-201 |
| Ultra-4 Centrifugal Filter Unit | Amicon | Cat#UFC8030 |