Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (S. cerevisiae) |
SUB280 | D. Finley Lab; Finley et al., 1994
PMID:8035826 PMCID:PMC359070 |
MATa, lys2-801, leu2-3, 112, ura3-52, his3-D200, trp 1–1, ubi1-D1::TRP1, ubi2-D2::ura3, ubi3-Dub-2, ubi4-D2::LEU2 [pUB39 Ub, LYS2] [pUB100, HIS3] | |
| Strain, strain background (S. cerevisiae) |
SUB280 Ub (WT, S57A, S57D) |
Lee et al., 2017
PMID:29130884 PMCID:PMC5706963 |
MATa, SUB280 [RPS31 (WT, S57A, S57D; URA3)] | |
| Strain, strain background (S. cerevisiae) |
NHY318 | This paper | MATa, SUB280 arg4::KANMX | |
| Strain, strain background (S. cerevisiae) |
SEY6210 | S. Emr Lab; Robinson et al., 1988
PMID:3062374 PMCID:PMC365587 |
RRID:ATCC: 96099 | WT: MATα leu2-3,112 ura4-52 his3-D200 trp1-D901 lys2-801 suc2-D9 |
| Strain, strain background (S. cerevisiae) |
SEY6210.1 | S. Emr Lab; Robinson et al., 1988
PMID:3062374 PMCID:PMC365587 |
WT: MATa leu2-3,112 ura4-52 his3-D200 trp1-D901 lys2-801 suc2-D9 | |
| Strain, strain background (S. cerevisiae) |
NHY175 | This paper | MATα, SEY6210 gin4::NATMX | |
| Strain, strain background (S. cerevisiae) |
NHY117 | This paper | MATα, SEY6210 sks1::TRP1 | |
| Strain, strain background (S. cerevisiae) |
NHY118 | This paper | MATα, SEY6210 vhs1::TRP1 | |
| Strain, strain background (S. cerevisiae) |
NHY196 | This paper | MATa, SEY6210.1 sks1::TRP1 vhs1::TRP1 | |
| Strain, strain background (S. cerevisiae) |
NHY177 | This paper | MATα, SEY6210 gin4::NATMX sks1::TRP1 | |
| Strain, strain background (S. cerevisiae) |
NHY179 | This paper | MATα, SEY6210 gin4::NATMX vhs1::TRP1 | |
| Strain, strain background (S. cerevisiae) |
NHY181 | This paper | MATα, SEY6210 gin4::NATMX sks1::TRP1 vhs1::TRP1 | |
| Strain, strain background (S. cerevisiae) |
JMY1312 | This paper | MATα, SEY6210 arg4::KANMX FLAG-RPS3::TRP1, FLAG-RPL40B::TRP1 | |
| Strain, strain background (S. cerevisiae) |
NHY326 | This paper | MATa, JMY1312 sks1::TRP1 vhs1::TRP1 | |
| Strain, strain background (E. coli) |
Rosetta 2 (DE3) | Millipore (Burlington, MA) | Cat# 71400 | F-
ompT hsdSB(rB- mB-) gal dcm (DE3) pRARE2 (CamR) Competent Cells - Novagen |
| Strain, strain background (E. coli) |
C41 (DE3) | Lucigen Corporation (Middleton, WI) | F– ompT hsdSB (rB - mB -) gal dcm (DE3) Competent Cells |
|
| Recombinant DNA | pRS415 | Stratagene | (Empty Backbone) Yeast Centromere Plasmid (LEU2) GenBank: U03449 |
|
| Recombinant DNA | pRS416 | Sikorski and Hieter, 1989 | (Empty Backbone) Yeast Centromere Plasmid (URA3) GenBank: U03450 |
|
| Recombinant DNA | pJAM1303 | This paper | pNative-Sks1 in pRS416 (URA3); yeast expression | |
| Recombinant DNA | pJAM1304 | This paper | pNative-Sks1 in pRS415 (LEU2); yeast expression | |
| Recombinant DNA | pJAM1280 | This paper | pTDH3-Sks1 in pRS415 (LEU2); yeast expression | |
| Recombinant DNA | pJAM1253 | This paper | pNative_Vhs1 in pRS415 (LEU2); yeast expression | |
| Recombinant DNA | pRS327 | PMID:14989082 | RRID:Addgene_51787 | (Empty Backbone) multicopy (YEp) vector with a 2 μm origin of replication (LYS2); yeast expression |
| Recombinant DNA | pJAM1746 | This paper | pTDH3-Gin4 in pRS327; yeast expression | |
| Recombinant DNA | pJAM1749 | This paper | pTDH3-Kcc4 in pRS327; yeast expression | |
| Recombinant DNA | pJAM1743 | This paper | pTDH3-Sks1 in pRS327; yeast expression | |
| Recombinant DNA | pJAM1740 | This paper | pTDH3-Vhs1 in pRS327; yeast expression | |
| Recombinant DNA | pJAM1771 | This paper | pTDH3-Vhs1 K41R (kinase dead) in pRS327; yeast expression | |
| Recombinant DNA | pJAM1240 | This paper | 6XHis-Sks1 in pET15b, AmpR; E. coli expression | |
| Recombinant DNA | pJAM1169 | This paper | Vhs1-6XHis in pET23d, AmpR; E. coli expression | |
| Recombinant DNA | pJAM983 | This paper | Gin4-6XHis in pET23d, AmpR; E. coli expression | |
| Recombinant DNA | pJAM1116 | This paper | Hal4-6XHis in pET23d, AmpR; E. coli expression | |
| Recombinant DNA | pJAM1118 | This paper | Hal5-6XHis in pET23d, AmpR; E. coli expression | |
| Recombinant DNA | pJAM1120 | This paper | Kkq8-6XHis in pET23d, AmpR; E. coli expression | |
| Recombinant DNA | pJAM1336 | This paper | Snf1-6XHis in pET23d, AmpR; E. coli expression | |
| Recombinant DNA | pJAM585 | This paper | 6XHis-Npr1 in pCOLADuet, KmR; E. coli expression | |
| Recombinant DNA | pJAM1270 | This paper | Ksp1-6XHis in pET23d, AmpR; E. coli expression |
|
| Recombinant DNA | pJAM1186 | This paper | GST-Slt2 in pGEX6p1; E. coli expression | |
| Recombinant DNA | pJAM1335 | This paper | Frk1-6XHis in pET23d, AmpR; E. coli expression | |
| Recombinant DNA | pJAM987 | This paper | Kcc4-6XHis in pET23d, AmpR; E. coli expression | |
| Recombinant DNA | pJAM1306 | This paper | Kin1-6XHis in pET23d, AmpR; E. coli expression | |
| Recombinant DNA | pJAM1307 | This paper | Kin2-6XHis in pET23d, AmpR; E. coli expression | |
| Recombinant DNA | pJAM1272 | This paper | Ypl150w-6XHis in pET23d, AmpR; E. coli expression | |
| Recombinant DNA | pJAM1167 | This paper | 6XHis-GST-UBD, AmpR;E. coli expression | |
| Recombinant DNA | pJAM1235 | This paper | Ubiquitin in pBG100; E. coli expression | |
| Recombinant DNA | pJAM1236 | This paper | Ubiquitin S57A in pBG100; E. coli expression | |
| Recombinant DNA | pJAM1237 | This paper | Ubiquitin S65A in pBG100; E. coli expression | |
| Recombinant DNA | pJAM995 | This paper | di-Ub in pET23d, AmpR; E. coli expression | |
| Recombinant DNA | pJAM996 | This paper | tri-Ub in pET23d, AmpR; E. coli expression | |
| Antibody | α-Flag (FLAG(R) M2) mouse monoclonal | Sigma (St. Louis, MO) | RRID:AB_262044 | WB (1:1000) |
| Antibody | α-Ubiquitin (VU101) mouse monoclonal; clone VU-1 | LifeSensors (Malvern, PA) | Cat# VU101 RRID:AB_2716558 |
WB (1:1000) |
| Antibody | α-Glucose-6-Phosphate Dehydrogenase (G6PDH), yeast rabbit polyclonal | Sigma (St. Louis, MO) | Cat# A9521 RRID:AB_258454 |
WB (1:10000) |
| Antibody | α-pSer57 Ubiquitin rabbit polyclonal | This paper | WB (1:1000) | |
| Antibody | K48-linkage Specific Polyubiquitin rabbit monoclonal; clone D9D5 | Cell Signaling Technology (Danvers, MA) | Cat# 8081 RRID:AB_10859893 |
WB (1:1000) |
| Antibody | K63-linkage Specific Polyubiquitin rabbit monoclonal; clone Apu3 | Millipore (Burlington, MA) | Cat# 05–1308 RRID:AB_1587580 |
WB (1:1000) |
| Antibody | IRDye 680RD-Goat anti-mouse polyclonal | LI-COR Biosciences (Lincoln, NE) | Cat# 926–68070 RRID:AB_10956588 |
WB (1:10000) |
| Antibody | IRDye 800CW-Goat anti-rabbit polyclonal | LI-COR Biosciences (Lincoln, NE) | Cat# 926–32211 RRID:AB_621843 |
WB (1:10000) |
| Commercial assay, kit | PTMScan Ubiquitin Remnant Motif (α-K-ε-GG) | Cell Signaling Technology (Danvers, MA) | RRID:Cat# 5562 | bead-conjugated for immunoprecipitation of –GG-εK-conjugated peptides |
| Chemical compound, drug | EZ view Red Anti-FLAG M2 Affinity Gel | Sigma (St. Louis, MO) | Cat# F2426-1ML RRID:AB_2616449 |
mouse-monoclonal; clone M2 bead-conjugated for immunoprecipitation of FLAG-conjugated proteins |
| Chemical compound, drug | L-Lysine-13C6,13N2hydrochloride | Sigma (St. Louis, MO) | Cat# 608041–1G | |
| Chemical compound, drug | L-Arginine-13C6,13N4hydrochloride | Sigma (St. Louis, MO) | Cat# 608033–1G | |
| Chemical compound, drug | Sodium arsenate dibasic heptahydrate | Sigma (St. Louis, MO) | Cat# A6756 | Synonym: arsenate |
| Chemical compound, drug | Hydrogen peroxide | Fisher (Hampton, NH) | Cat# H325-500 | Synonym: H2O2 |
| Chemical compound, drug | Hydroxyurea | INDOFINE Chemical Company, Inc (Hillsborough, NJ) | Cat# BIO-216 | |
| Chemical compound, drug | S-(2-Aminoethyl)-L-cysteine hydrochloride | Sigma (St. Louis, MO) | Cat# A2636-1G | Synonym: L-4-Thialysine hydrochloride, thialysine |
| Chemical compound, drug | L-Canavanine | Sigma (St. Louis, MO) | Cat. # C1625 | Synonym: canavanine |
| Chemical compound, drug | DL-2-Aminoadipic acid | Sigma (St. Louis, MO) | Cat. # A0637 | |
| Chemical compound, drug | MG132 | Apexbio (Houston, TX) | Cat. # A2585 | |
| Chemical compound, drug | Protease inhibitor cocktail (cOmplete Tablets, Mini) | Roche (Basel, Switzerland) | Cat# 04693159001 | |
| Chemical compound, drug | PhosSTOP | Roche (Basel, Switzerland) | Cat# 04906837001 | |
| Chemical compound, drug | Phos-tag Acrylamide | NARD | Cat# AAL-107 | |
| Software, algorithm | MaxQuant Version 1.6.5.0 |
Max Planck Institute of Biochemistry | RRID:SCR_014485 | |
| Software, algorithm | Skyline Version 20.1.0.155 |
MacCoss Lab Software | RRID:SCR_014080 | |
| Software, algorithm | Adobe Illustrator CS5.1 Version 15.1.0 |
Adobe (San Jose, CA) | RRID:SCR_010279 | |
| Software, algorithm | Image Studio Lite Version 5.2 |
LI-COR Biosciences (Lincoln, NE) | RRID:SCR_013715 |