Reagents and tools table
| Reagent/resource | Reference or source | Identifier or catalog number |
|---|---|---|
| Experimental models | ||
| E. coli XL1 blue | Agilent | 200249 |
| E. coli BL21 Rosetta DE3 | Novagen | 70954-3 |
| E. coli ΔclpB::kan | Katikaridis et al, 2021 | |
| E. coli ΔclpB | This study | |
| E. coli ΔclpP | Dougan et al, 2002 | |
| Recombinant DNA | ||
| Plasmids used in this study | See Appendix Table S2 | Appendix Table S2 |
| Antibodies | ||
| ClpC-specific antibody | Davids Biotechnologie | Self-made |
| anti-rabbit alkaline phosphatase conjugate | Vector Laboratories | AP-1000 |
| Oligonucleotides and other sequence-based reagents | ||
| pDS56 fw seq | Sigma-Aldrich | 5’-CTTTGTCTTCACCTCGAG-3' |
| SaClpC 400 bp seq | Sigma-Aldrich | 5’-CGTGCACAAGTTGTGAAAG-3' |
| SaClpC 1000 bp seq | Sigma-Aldrich | 5’-GTTTCCAACCTGTACAAG-3' |
| SaClpC 1600 bp seq | Sigma-Aldrich | 5’-CTAAACGACCAATTGGTAGC-3' |
| SaClpC 2000 bp seq | Sigma-Aldrich | 5’-CAACGATTTGCTGGATTC-3' |
| SaClpC E32A fw | Sigma-Aldrich | 5’-GGAACAGcACACCTATTATTGG-3' |
| SaClpC E32A rv | Sigma-Aldrich | 5’-CCAATAATAGGTGTgCTGTTCC-3' |
| SaClpC E106A fw | Sigma-Aldrich | 5’-GTTGGAACGGcACATATTTTATTAGGC-3' |
| SaClpC E106A rv | Sigma-Aldrich | 5’-GCCTAATAAAATATGTgCCGTTCCAAC-3' |
| SaClpC K85A fw | Sigma-Aldrich | 5’-[Phos]CACCTAGAGCTgcAAAAGTCATTGAATTATCG-3‘ |
| SaClpC K85A rv | Sigma-Aldrich | 5’-[Phos] TATAATGCAATGTACCAACATGATCTTG-3‘ |
| SaClpC D356A fw | Sigma-Aldrich | 5’-GGATTAAGAGcTCGTTACG-3' |
| SaClpC D356A rv | Sigma-Aldrich | 5’-CGTAACGAgCTCTTAATCC-3' |
| SaClpC R9A fw | Sigma-Aldrich | 5’-[Phos]GATTAACTGAGgcTGCACAGCGCGTATTAGC-3' |
| SaClpC R9A rv | Sigma-Aldrich | 5’-[Phos]TACCAAATAAGGATCCTCTCATAGTTAATTTCTCCTC-3' |
| SaClpC R122A fw | Sigma-Aldrich | 5’-[Phos]GTGTTGCAGCAgcAGTTTTTGCAAATCTAGA-3' |
| SaClpC R122A rv | Sigma-Aldrich | 5’-[Phos]CTTCATTTTCACGAATCAAGCCTAATAAAATATGTTC-3' |
| SaClpC N462A fw | Sigma-Aldrich | 5’-[Phos]AATGAATGGAAGgcTGCACAAAATGGCATGT-3' |
| SaClpC N462A rv | Sigma-Aldrich | 5’-[Phos]TTTAGCTTCTTCATATTGCTTTTCAAGTTTTGTTTG-3' |
| SaClpC T7D fw | Sigma-Aldrich | 5’-GGTAGATTAgaTGAGCGTGCAC-3' |
| SaClpC T7D rv | Sigma-Aldrich | 5’-GTGCACGCTCAtcTAATCTACC-3' |
| MtClpC K85A fw | Sigma-Aldrich | 5’-[Phos]TACCCCCCGCGCCgcAAAGGTCCTCGAG-3' |
| MtClpC K85A rv | Sigma-Aldrich | 5’-[Phos]AACGGAATGTGCCCAGACGGCGCCTGCTG-3' |
| MtClpC D364A fw | Sigma-Aldrich | 5’-[Phos]TCAAGGGCCTGCGGGcCCGGTACGAGGC-3' |
| MtClpC D364A rv | Sigma-Aldrich | 5’-[Phos]GGATCTCGATGGTGTGCTCCACCGTCGGCTCACC-3' |
| Chemicals, enzymes and other reagents | ||
| Kanamycin | Sigma | K4000 |
| Ampicillin | Roth | K029.2 |
| Protino™ Ni-IDA | Macherey-Nagel | MN745210.30 |
| Protease inhibitor Pepstatin A | Roth | 2936.3 |
| Protease inhibitor Aprotinin | Roth | A162.3 |
| Protease inhibitor Leupeptin | Roth | CN33.4 |
| DNaseI | Roche | 10104159001 |
| Phusion HF DNA-Polymerase | ThermoScientific | F-530 |
| T4 DNA Ligase | NEB | M0202L |
| Imidazole | Roth | 3899.4 |
| Pyruvate kinase | Sigma | P7768 |
| FITC-casein (Casein fluorescein isothiocyanate) | Sigma | C0528 |
| Bradford reagent | BioRad | 5000006 |
| Phospho-L-Arginine (lithium salt hydrate) | Cayman Chemical | 23123 |
| Arg | Sigma | A8094 |
| ATP | Sigma | A26209 |
| NADH | Sigma | 43420 |
| PK/LDH | Sigma-Aldrich | P0294 |
| PEP (Phospho(enol)pyruvic acid trisodium salt hydrate) | Sigma | P7002 |
| ATPγS | Roche | 11162306001 |
| Glutaraldehyde | Sigma | G6403 |
| SYPRO Ruby Protein Gel Stain | Thermo Fisher | S12000 |
| Uranyl acetate | Ted Pella | 19481 |
| IPTG (Isopropyl-β-D-1-thiogalactopyranoside) | Roth | CN08.3 |
| BSA | Serva | 11930.04 |
| ECF substrate | GE Healthcare | RPN3685 |
| Software | ||
| FIJI | https://imagej.net/software/fiji/downloads | |
| Prism 10 | Graphpad | |
| ChimeraX 1.8 | Pettersen et al, 2021 | |
| Prometheus Panta Analysis software (version 1.4.3) | NanoTemper | |
| EPU software | ThermoFisher | |
| EMAN2 v.2.12 | Tang et al, 2007 | |
| IMAGIC-4D | van Heel et al, 1996 | |
| cryoSPARC v4.7.1 | Huber et al, 2018 | |
| Clustal Omega | https://www.ebi.ac.uk/Tools/msa/clustalo/ | |
| Jalview | Waterhouse et al, 2009 | |
| Refeyn DiscoverMP software | Refeyn TwoMP | |
| AlphaFold 3 | Jumper et al, 2021; Varadi et al, 2024 | |
| AlphaFill | Hekkelman et al, 2023 | |
| Phenix v.1.21.2 | Adams et al, 2010 | |
| Coot v.0.9 | Emsley et al, 2010 | |
| Other | ||
| French Pressure cell press | Sim-Aminco | |
| Superdex S200 | Cytiva | 28-9893-35 |
| CLARIOstarplus plate reader | BMG Labtech | |
| PrometheusTM Panta | NanoTemper | |
| PrometheusTM standard capillaries | NanoTemper | PR-C002 |
| ÄKTA pure | Cytiva | |
| Superose 6 Increase 10/300 GL column | Cytiva | 29-0915-96 |
| Talos L120C electron microscope | Thermo Fisher Scientific | |
| Image-Reader LAS-4000 | Fujifilm | |
| Refeyn Mass Photometer | Refeyn | |
| GloQube | Quorum | |
| Vitrobot Mark IV | Thermo Fisher Scientific | |
| Talos Arctica | Thermo Fisher Scientific | |
| 300-kV Titan Krios G2 microscope | Thermo Fisher Scientific | |
| 96-well plates (black) | Greiner | 655079 |
| 96-well plates (transparent) | Greiner | 655180 |