Table 1.
Gene name, function, PDB accession number, crystal structure and resolution according to RCSB PDB, SCL according to Swissprot, available inhibitors, sequence conservation and essentiality in K. pneumoniae for the 36 protein targets identified by this study. N/A = not available, N/D = not determined.
| Gene | Protein Function | PDB Accession No. | Crystal Structure and Resolution | SCL | Known Inhibitor | Conservation and Essentiality in K. pneumoniae | |||
|---|---|---|---|---|---|---|---|---|---|
| Alignment | aa Identity | Bitscore | Essentiality Status | ||||||
| bamD | Outer membrane protein assembly factor BamD | P0AC02 | 5D0O 2.90 Å |
Cell outer membrane; Lipid anchor | Inhibitory peptide [19], IMB-H4 [20] | 100% | 94% | 479 | Essential |
| cydX | Cytochrome bd-I ubiquinol oxidase subunit X | P56100 | 6RKO 2.68 Å |
Cell inner membrane; Single-pass membrane protein | N/A | 100% | 100% | 77 | N/A |
| dnaT | Primosomal protein 1 | P0A8J2 | 4OU6 1.96 Å |
N/D | N/A | 100% | 76% | 285 | N/A |
| fabA | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase | P0A6Q3 | 4KEH 2Å |
Cytoplasm | 3-Decynoyl-NAC [21] | 100% | 99% | 349 | Essential |
| ftsB | Cell division protein FtsB |
P0A6S5 |
4IFF 2.30 Å |
Cell inner membrane | N/A | 84% | 100% | 181 | Essential |
| ftsL | Cell division protein FtsL | P0AEN4 | N/D | Cell inner membrane | N/A | 100% | 96% | 238 | Essential |
| ftsQ | Cell division protein FtsQ | P06136 | 2VH1 2.70 Å |
Cell inner membrane; Single-pass type II membrane protein | N/A | 96% | 89% | 486 | Essential |
| hemD | Uroporphyrinogen-III synthase | P09126 | N/D | N/D | N/A | 100% | 99% | 497 | Essential |
| higA | Antitoxin HigA | P67701 | 6JQ4 2 Å |
N/D | N/A | 100% | 99% | 279 | N/A |
| hipB | Antitoxin HipB | P23873 | 2WIU 2.35 Å |
N/D | N/A | 100% | 98% | 176 | Essential |
| holD | DNA polymerase III subunit psi | P28632 | 3SXU 1.85 Å |
N/D | N/A | 84% | 98% | 224 | N/A |
| iraM | Anti-adapter protein IraM | P75987 | N/D | Cytoplasm | N/A | 99% | 62% | 149 | N/A |
| lolA | Outer membrane lipoprotein carrier protein | P61316 | 1IWL 1.56 Å |
Periplasm | MAC13243 [22] | 100% | 94% | 399 | Essential |
| lolB | Outer membrane lipoprotein LolB | P61320 | 1IWM 1.90 Å |
Cell outer membrane; Lipid anchor | N/A | 100% | 100% | 426 | Essential |
| lptA | Lipopolysaccharide export system protein LptA | P0ADV1 | 2R19 2.16 Å |
Periplasm | Thanatin [23], Compound IMB-881 [24] |
100% | 85% | 328 | Essential |
| lptD | LPS assembly protein LptD | P31554 | 4RHB 3.35 Å |
Cell outer membrane | Inhibitory peptide JB-95 [25] | 100% | 84% | 1407 | Essential |
| lptE | LPS assembly lipoprotein LptE | P0ADC1 | 4RHB 3.35 Å |
Cell outer membrane | N/A | 102% | 72% | 295 | Essential |
| mreD | Rod shape-determining protein MreD | P0ABH4 | N/D | Cell inner membrane; Multi-pass membrane protein | N/A | 100% | 100% | 310 | N/A |
| mukB | Chromosome partition protein MukB | P22523 | 1QHL 2.20 Å |
Nucleoid | NSC260594, Michellamine B [26] | 100% | 92% | 2774 | Essential |
| mukE | Chromosome partition protein MukE | P22524 | 3EUH 2.90 Å |
Nucleoid | N/A | 100% | 95% | 458 | Essential |
| mukF | Chromosome partition protein MukF | P60293 | 3EUH 2.90 Å |
Nucleoid | N/A | 100% | 97% | 878 | Essential |
| pheM | Phenylalanine tRNA ligase operon leader peptide | P0AD74 | N/D | N/D | N/A | 100% | 100% | 30 | N/A |
| priB | Primosomal replication protein N | P07013 | 5WQV 1.97 Å |
N/D | N/A | 100% | 93% | 205 | N/A |
| safA | Two-component-system connector protein SafA | P76136 | N/D | Cell inner membrane; Single-pass type II membrane protein | N/A | 98% | 100% | 127 | N/A |
| secE | Protein translocase subunit SecE | P0AG96 | 5GAE 3.33 Å |
Cell inner membrane; Multi-pass membrane protein | N/A | 100% | 98% | 240 | Essential |
| trpL | trp operon leader peptide | P0AD92 | N/D | N/D | N/A | 100% | 100% | 32 | N/A |
| tusE | Sulfurtransferase TusE | P0AB18 | N/D | Cytoplasm | N/A | 100% | 90% | 204 | Essential |
| wzyE | Probable ECA polymerase | P27835 | N/D | Cell inner membrane | N/A | 100% | 87% | 744 | N/A |
| ycaR | UPF0434 protein YcaR | P0AAZ7 | N/D | Cytoplasm | N/A | 100% | 100% | 125 | N/A |
| yciS | Lipopolysaccharide assembly protein A | P0ACV4 | N/D | Cell inner membrane | N/A | 100% | 87% | 177 | N/A |
| ydfO | Uncharacterized protein YdfO | P76156 | 2HH8 N/D |
N/D | N/A | 100% | 79% | 228 | N/A |
| ydhL | Uncharacterized protein YdhL | P64474 | N/D | N/D | N/A | 96% | 98% | 152 | N/A |
| ygfZ | tRNA-modifying protein YgfZ | P0ADE8 | 1VLY 1.30 Å |
Cytoplasm | N/A | 100% | 84% | 573 | N/A |
| yqeL | Uncharacterized protein YqeL | C1P613 | N/D | N/D | N/A | N/A | N/A | N/A | N/A |
| yrfF | Putative membrane protein IgaA homolog | P45800 | 4UZM N/D |
Cell inner membrane; Multi-pass membrane protein | N/A | 100% | 73% | 1089 | N/A |
| zipA | Cell division protein ZipA | P77173 | 1F46 1.50 Å |
Cell inner membrane; Single-pass type I membrane protein | Antimicrobial compounds [27,28] | 101% | 98% | 646 | Essential |