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Literature summary extracted from

  • Mukai, T.; Crnkovic, A.; Umehara, T.; Ivanova, N.; Kyrpides, N.; Soll, D.
    RNA-dependent cysteine biosynthesis in bacteria and archaea (2017), mBio, 8, e00561-17 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.9.1.2 phylogenetic analysis and tree Bacteria
2.9.1.2 phylogenetic analysis and tree Archaea

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.9.1.2 O-phospho-L-seryl-tRNASec + selenophosphate + H2O Bacteria
-
 L-selenocysteinyl-tRNASec + 2 phosphate
-
 ?
2.9.1.2 O-phospho-L-seryl-tRNASec + selenophosphate + H2O Archaea
-
 L-selenocysteinyl-tRNASec + 2 phosphate
-
 ?
6.1.1.27 ATP + O-phospho-L-serine + tRNACys Archaeoglobus fulgidus
-
 AMP + diphosphate + O-phospho-L-seryl-tRNACys
-
 ?
6.1.1.27 ATP + O-phospho-L-serine + tRNACys Methanococcus maripaludis
-
 AMP + diphosphate + O-phospho-L-seryl-tRNACys
-
 ?
6.1.1.27 ATP + O-phospho-L-serine + tRNACys Candidatus Bathyarchaeota
-
 AMP + diphosphate + O-phospho-L-seryl-tRNACys
-
 ?
6.1.1.27 ATP + O-phospho-L-serine + tRNACys Candidatus Parcubacteria
-
 AMP + diphosphate + O-phospho-L-seryl-tRNACys
-
 ?
6.1.1.27 ATP + O-phospho-L-serine + tRNACys Chloroflexi
-
 AMP + diphosphate + O-phospho-L-seryl-tRNACys
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.9.1.2 Archaea
-
-
-
2.9.1.2 Bacteria
-
-
-
6.1.1.27 Archaeoglobus fulgidus
-
-
-
6.1.1.27 Candidatus Bathyarchaeota
-
-
-
6.1.1.27 Candidatus Parcubacteria
-
-
-
6.1.1.27 Chloroflexi
-
-
-
6.1.1.27 Methanococcus maripaludis
-
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.9.1.2 additional information bacterial SepCysS charges bacterial tRNACys species with cysteine in vitro. Sep-tRNACys is converted by Sep-tRNA:Cys-tRNA synthase (SepCysS) to Cys-tRNACys Bacteria ?
-
-
2.9.1.2 additional information Sep-tRNACys is converted by Sep-tRNA:Cys-tRNA synthase (SepCysS) to Cys-tRNACys Archaea ?
-
-
2.9.1.2 O-phospho-L-seryl-tRNASec + selenophosphate + H2O
-
 Bacteria L-selenocysteinyl-tRNASec + 2 phosphate
-
 ?
2.9.1.2 O-phospho-L-seryl-tRNASec + selenophosphate + H2O
-
 Archaea L-selenocysteinyl-tRNASec + 2 phosphate
-
 ?
6.1.1.27 ATP + O-phospho-L-serine + tRNACys
-
 Archaeoglobus fulgidus AMP + diphosphate + O-phospho-L-seryl-tRNACys
-
 ?
6.1.1.27 ATP + O-phospho-L-serine + tRNACys
-
 Methanococcus maripaludis AMP + diphosphate + O-phospho-L-seryl-tRNACys
-
 ?
6.1.1.27 ATP + O-phospho-L-serine + tRNACys
-
 Candidatus Bathyarchaeota AMP + diphosphate + O-phospho-L-seryl-tRNACys
-
 ?
6.1.1.27 ATP + O-phospho-L-serine + tRNACys
-
 Candidatus Parcubacteria AMP + diphosphate + O-phospho-L-seryl-tRNACys
-
 ?
6.1.1.27 ATP + O-phospho-L-serine + tRNACys
-
 Chloroflexi AMP + diphosphate + O-phospho-L-seryl-tRNACys
-
 ?

Synonyms

EC Number Synonyms Comment Organism
2.9.1.2 Sep-tRNA:Cys-tRNA synthase
-
 Bacteria
2.9.1.2 Sep-tRNA:Cys-tRNA synthase
-
 Archaea
2.9.1.2 SepCysS
-
 Bacteria
2.9.1.2 SepCysS
-
 Archaea
6.1.1.27 O-phosphoseryl-tRNA synthetase
-
 Archaeoglobus fulgidus
6.1.1.27 O-phosphoseryl-tRNA synthetase
-
 Methanococcus maripaludis
6.1.1.27 O-phosphoseryl-tRNA synthetase
-
 Candidatus Bathyarchaeota
6.1.1.27 O-phosphoseryl-tRNA synthetase
-
 Candidatus Parcubacteria
6.1.1.27 O-phosphoseryl-tRNA synthetase
-
 Chloroflexi
6.1.1.27 SepRS
-
 Archaeoglobus fulgidus
6.1.1.27 SepRS
-
 Methanococcus maripaludis
6.1.1.27 SepRS
-
 Candidatus Bathyarchaeota
6.1.1.27 SepRS
-
 Candidatus Parcubacteria
6.1.1.27 SepRS
-
 Chloroflexi

Cofactor

EC Number Cofactor Comment Organism Structure
6.1.1.27 ATP
-
 Archaeoglobus fulgidus
6.1.1.27 ATP
-
 Methanococcus maripaludis
6.1.1.27 ATP
-
 Candidatus Bathyarchaeota
6.1.1.27 ATP
-
 Candidatus Parcubacteria
6.1.1.27 ATP
-
 Chloroflexi

General Information

EC Number General Information Comment Organism
2.9.1.2 evolution search in all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota, TACK, and Asgard) and two groups of bacteria (Candidatus Parcubacteria and Chloroflexi), phylogenetic analysis and tree, overview. The archaea carrying full-length SepCysE employ Sec and SepRS is often found in Pyl-utilizing archaea and Chloroflexi bacteria. SepRS-SepCysS-SepCysE- and the selenocysteine-encoding systems are shared by the Euryarchaeota class I methanogens, the Crenarchaeota AK8/W8A-19 group, and an Asgard archaeon. Ancient archaea may have used both systems. In contrast, bacteria may have obtained the SepRS-SepCysS system from archaea. The SepRS-SepCysS system sometimes coexists with a pyrrolysine-encoding system in both archaea and bacteria Bacteria
2.9.1.2 evolution search in all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota, TACK, and Asgard) and two groups of bacteria (Candidatus Parcubacteria and Chloroflexi), phylogenetic analysis and tree, overview. The archaea carrying full-length SepCysE employ Sec and SepRS is often found in Pyl-utilizing archaea and Chloroflexi bacteria. SepRS-SepCysS-SepCysE- and the selenocysteine-encoding systems are shared by the Euryarchaeota class I methanogens, the Crenarchaeota AK8/W8A-19 group, and an Asgard archaeon. Ancient archaea may have used both systems. In contrast, bacteria may have obtained the SepRS-SepCysS system from archaea. The SepRS-SepCysS system sometimes coexists with a pyrrolysine-encoding system in both archaea and bacteria Archaea
2.9.1.2 metabolism possible contributions of the SepRS-SepCysS system for sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes Bacteria
2.9.1.2 metabolism possible contributions of the SepRS-SepCysS system for sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes Archaea