Table 3

Counts of each family in selected genomes

Protein family name and number of genes (proteins) per genome

Additional information about counts of each family in selected genomes.

HUMAN

ARATH

YEAST

PSEAE

MYCTU

SULSO

HELPY


1. Rossmann fold MTase

49 (64)

70 (81)

30

55

37

31

26

Rossmann fold methyltransferase (MTase) makes the list of 10 most commonly used sequence and structure families [15]. In analyzed genomes, 4.6% of Rossmann fold MTase does not have motif-I (Gly-rich) and may lack MTase activity. Fold: Rossmann-fold.

2. Met synthase activating domain

1

0

0

1

1

0

0

Present in many bacteria and metazoan. Fold: Met synthase activation domain-like.

3. MTase class III

1

3 (4)

2

8

6

7

1

Human genome encodes protein similar to diphthine synthase but not other Class-III MTases (i.e. from tetrapyrrole biosynthesis pathway) identified in analyzed genomes. Fold: Tetrapyrrole-methyltransferase.

4. SPOUT MTase

3

5

2

4

6

1

2

Every analyzed here genome has at least one putative SPOUT rRNA MTase, in archaea the same base of tRNA is methylated by Rossmann-fold instead of SPOUT MTase. Fold: α/β knot.

5. SET domain MTase

25 (34)

34 (41)

5

0

0

0

0

Present in all Eukaryota with sporadic lateral transfer to bacteria and archaea (but not identified in prokaryotic genomes analyzed here). In S. cerevisiae all selected sequences similar to SET-domain MTases are conserved within smart00317 domain (in contrast to SET-domain proteins other then MTases). Fold: β-clip.

6. methylene transferase

0

4

0

1

10

0

1

This enzyme performs cyclopropane fatty acid synthesis and is important for Mycobacterium survival. Fold: Rossmann-fold.

7. Nicotianamine synthase

0

4

0

0

0

0

0

This is plant enzyme has similarity to proteins with unknown function infrequently distributed in bacteria, archaea and fungi (discussed earlier). Fold: Rossmann-fold (predicted).

8. spermidine synthase &9. spermine synthase

1

3

2

3

1

1

1

The mammalian enzyme is highly specific but the bacterial enzyme can use other acceptors then SAM and can synthesize spermine. Spermidine synthase but not spermine synthase is essential for survival of Arabidopsis and S. cerevisiae [142-144]. Fold: Rossmann-fold.

10. aclacynomycin-10-hydroxylase

0

0

0

0

0

0

0

Was found in Streptomyces purpurascens only. Fold: Rossmann-fold.

11. isoprenylcysteine O-MTase

2

2

1

0

3

0

0

ICMT enzymes are present in all eukaryotic organisms [145]. Fold: unknown (predicted: all-α).

12. fluorinating enzyme

0

0

0

0

0

0

0

Gene encoding fluorinating enzyme was identified in Streptomyces cattleya but not yet in plants synthesizing fluorinated metabolites. Fold: Rossmann-like and β-barrel.

13. QueA

0

0

0

1

0

0

1

QueA (tRNA ribosyltransferase – isomerase) homologs are found only in bacteria. Fold: QueA-like (TIM-barrel and β-barrel).

14. SAM decarboxylase

1

4

1

2

?

2

?

SAM decarboxylase activity has been purified from all three domains of Life. However M. tuberculosis and H. pylori lack clearly identifiable homologue of this enzyme. Fold: SAM-decarboxylase.

15. SAM synthetase

2

4 (5)

2

1

1

1

1

SAM synthases from bacteria and eukaryotes are closely related at the sequence level and have very similar structures [73]. SAM synthase is involved in development and abiotic stress tolerance in plants and have complex expression pattern [146, 147]. Fold: SAM-synthetase.

16. ACC synthase

2

12

0

0

0

0

0

ACC is the precursor of important plant hormone – ethylene. Human homologs have different function. Fold: PLP-dependent transferases.

17. N-acyl-homoserine lactone synthase

0

0

0

2

0

0

0

Found in some bacteria only. Fold: GNAT.

18. Met repressor

0

0

0

0

0

0

0

Found in some enterobacteria and gamma proteobacteria only. Fold: ribbon-helix-helix.

19. CBS domain

5

10

5

7

4

9

3

Numbers of SAM-binding CBS domains presented here are approximate because of strong similarity to CBS domains binding other adenosine derivatives. Fold: CBS-domain.

20. DAPA synthase

0

1

1

6

2

0

1

Biotin biosynthesis is unique to plants, some fungi and most bacteria. Fold: PLP-dependent transferases.

21. SAM-dependent radical

9 (13)

13 (14)

5

18

11

24

11

Human lacks SAM-dependent radical enzyme from biotin and thiamine biosynthetic pathways. Those enzymes generate highly oxidizing 5'-deoxyadenosyl radical in an anaerobic reducing environment, and utilize this radical as catalytic and stoichiometric oxidant in many different enzymatic reactions [148]. Those enzymes are essential for anaerobic growth. Fold:TIM-barrel.


Number of genes and proteins encoded by selected genomes were counted for each SAM-binding protein family. SULSO Sulfolobus solfataricus (Archaea), PSEAE Pseudomonas aeruginosa (Gamma proteobacteria), HELPY Helicobacter pylori J99 (Proteobacteria), MYCTU Mycobacterium tuberculosis (Actinobacteria), YEAST Saccharomyces cerevisiae (Eukaryota), ARATH Arabidopsis thaliana (Eukaryota), HUMAN Homo sapiens (Eukaryota).

Kozbial and Mushegian BMC Structural Biology 2005 5:19   doi:10.1186/1472-6807-5-19

Open Data