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Table 4 Association of essential divalent metals and the products of ubiquitous genes.

From: On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth

Products of ubiquitous genes, according to [196]
Protein function EC number (if available) Functional dependence on metals Metals in at least some structures
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
  1. 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.