Table 4.
Association of essential divalent metals and the products of ubiquitous genes.
| Protein function | EC number (if available) | Functional dependence on metals | Metals in at least some structures |
| Products of ubiquitous genes, according to [196] | |||
| Translation and ribosomal biogenesis | |||
| Ribosomal proteins (33 in total) | Mg | Mg, Zn (see main text) | |
| Seryl-tRNA synthetase | 6.1.1.11 | Mg, Zn | Mn [218], Zn [219] |
| Methionyl tRNA synthetase | 6.1.1.10 | Mg, Zn | Zn [220] |
| Histidyl tRNA synthetase | 6.1.1.21 | Mg | No metals seen |
| Tryptophanyl- tRNA synthetase | 6.1.1.2 | Mg, Zn | Mg |
| Tyrosyl- tRNA synthetase | 6.1.1.1 | Mg | No metals seen |
| Phenylalanyl- tRNA synthetase | 6.1.1.20 | Mg, Zn | Mg |
| Aspartyl- tRNA synthetase | 6.1.1.12 | Mg | Mg, Mn [221] |
| Valyl-tRNA synthetase | 6.1.1.9 | Mg | Zn [222] |
| Isoleucyl-tRNA synthetase | 6.1.1.5 | Mg, Zn | Zn [223,224] |
| Leucyl-tRNA synthetase | 6.1.1.4 | Mg | Zn [225] |
| Threonyl-tRNA synthetase | 6.1.1.2 | Mg, Zn | Zn [226] |
| Arginyl-tRNA synthetase | 6.1.1.19 | Mg | No metals seen |
| Prolyl-tRNA synthetase | 6.1.1.15 | Mg, Zn | Mg, Zn [227], Mn [228] |
| Alanyl-tRNA synthetase | 6.1.1.7 | Mg, Zn | Mg, Zn [229] |
| Translation elongation factor G | 3.6.5.3 | Mg | Mg |
| Translation elongation factor P/translation initiatiation factor eIF5-a | Zn (PDB entry 2E9H) | ||
| Translation initiation factor 2 | Zn [230] | ||
| Translation initiation factor IF-1 | No divalent metals | ||
| Pseudouridylate synthase | 5.4.99.12 | Mg, Zn [217] | No metals seen |
| Methionine aminopeptidase | 3.4.11.18 | Mn, Zn, or Co | Mn or Zn or Co |
| Transcription | |||
| Transcription antiterminator NusG | - | - | No metals seen |
| DNA-directed RNA polymerase, subunits α, β, β' | 2.7.7.6 | Mg | Mg, Mn, Zn [231] |
| Replication | |||
| DNA polymerase III, subunit β | 2.7.7.7 | Mg | Mg [232] |
| Clamp loader ATPase (DNA polymerase III, subunit γ and τ) | 2.7.7.7. | Mg | Mg, Zn [233] |
| Topoisomerase IA | 5.99.1.2 | Mg | No metals seen |
| Repair and Recombination | |||
| 5'-3' exonuclease (including N-terminal domain of PoII) | 3.1.11.a | Mg | Mg |
| RecA/RadA recombinase | - | - | Mg |
| Chaperone function | |||
| Chaperonin GroEL | 3.6.4.9 | Mg | Mg |
| O-sialoglycoprotease/apurinic endonuclease | 3.4.24.57 | Zn [239] | Mg, Fe [234] |
| Nucleotide and amino acid metabolism metabolism | |||
| Thymidylate kinase | 2.7.4.9 | Mg | Mg |
| Thioredoxin reductase | 1.8.1.9 | - | No metals seen |
| Thioredoxin | - | Zn [235] | |
| CDP-diglyceride-synthase | 2.7.7.41 | Mg | No entries |
| Energy conversion | |||
| Phosphomannomutase | 5.4.2.8 | Mg | Mg, Zn [236] |
| Catalytic subunit of the membrane ATP synthase | 3.6.1.34 | Mg | Mg |
| Proteolipid subunits of the membrane ATP synthase | 3.6.1.34 | - | No metals seen |
| Triosephosphate isomerase | 5.3.1.1 | - | No metals seen |
| Coenzymes | |||
| Glycine hydroxymethyltransferase | 2.1.2.1 | Mg | No metals seen |
| Secretion | |||
| Preprotein translocase subunit SecY | - | - | Zn [237] |
| Signal recognition particle GTPase FtsY | - | - | Mg |
| Miscellanous | |||
| Predicted GTPase | - | - | No metal ligands in the structures |
| Additional ubiquitous gene products from ref. [215] | |||
| DNA primase (dnaG) | 2.7.7.- | - | Zn [238] |
| S-adenosylmethionine-6-N', N'-adenosyl (rRNA) dimethyltransferase (KsgA) | 2.1.1.48 | Mg | No metals seen |
| Transcription pausing, L factor (NusA) | - | - | No metals seen |
The lists of ubiquitous genes were extracted from refs. [196,215]. The data on metal dependence were taken from the BRENDA database [185], the presence of metals was as listed in the Protein Data Bank [140] entries. According to the BRENDA database [185], the enzymatic activity of most Mg-dependent enzymes could be routinely restored by Mn. As concentration of Mg2+ ions in the cell is ca. 10-2 M, whereas that of Mn2+ ions is ca. 10-6 M, the data on the functional importance of Mn were not included in the table.