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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 Mg, Zn Mn [218], Zn [219]
Methionyl tRNA synthetase Mg, Zn Zn [220]
Histidyl tRNA synthetase Mg No metals seen
Tryptophanyl- tRNA synthetase Mg, Zn Mg
Tyrosyl- tRNA synthetase Mg No metals seen
Phenylalanyl- tRNA synthetase Mg, Zn Mg
Aspartyl- tRNA synthetase Mg Mg, Mn [221]
Valyl-tRNA synthetase Mg Zn [222]
Isoleucyl-tRNA synthetase Mg, Zn Zn [223, 224]
Leucyl-tRNA synthetase Mg Zn [225]
Threonyl-tRNA synthetase Mg, Zn Zn [226]
Arginyl-tRNA synthetase Mg No metals seen
Prolyl-tRNA synthetase Mg, Zn Mg, Zn [227], Mn [228]
Alanyl-tRNA synthetase Mg, Zn Mg, Zn [229]
Translation elongation factor G 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 Mg, Zn [217] No metals seen
Methionine aminopeptidase Mn, Zn, or Co Mn or Zn or Co
Transcription antiterminator NusG - - No metals seen
DNA-directed RNA polymerase, subunits α, β, β' Mg Mg, Mn, Zn [231]
DNA polymerase III, subunit β Mg Mg [232]
Clamp loader ATPase (DNA polymerase III, subunit γ and τ) Mg Mg, Zn [233]
Topoisomerase IA 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 Mg Mg
O-sialoglycoprotease/apurinic endonuclease Zn [239] Mg, Fe [234]
Nucleotide and amino acid metabolism metabolism
Thymidylate kinase Mg Mg
Thioredoxin reductase - No metals seen
Thioredoxin   - Zn [235]
CDP-diglyceride-synthase Mg No entries
Energy conversion
Phosphomannomutase Mg Mg, Zn [236]
Catalytic subunit of the membrane ATP synthase Mg Mg
Proteolipid subunits of the membrane ATP synthase - No metals seen
Triosephosphate isomerase - No metals seen
Glycine hydroxymethyltransferase Mg No metals seen
Preprotein translocase subunit SecY - - Zn [237]
Signal recognition particle GTPase FtsY - - Mg
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) 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.