Skip to main content

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.