SCOPe 2.04: Family d.104.1.1: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

Lineage for Family d.104.1.1: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

1. Root: SCOPe 2.04

2. Class d: Alpha and beta proteins (a+b) [53931] (380 folds)

3. Fold d.104: Class II aaRS and biotin synthetases [55680] (1 superfamily)
   contains large mixed beta-sheet

4. Superfamily d.104.1: Class II aaRS and biotin synthetases [55681] (5 families)

5. Family d.104.1.1: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain [55682] (16 proteins)

Proteins:

1. Alanyl-tRNA synthetase (AlaRS) [103155] (1 species)

   • Species Aquifex aeolicus [TaxId:63363] [103156] (6 PDB entries)

2. Asparagine synthetase [55705] (1 species)

   • Species Escherichia coli [TaxId:562] [55706] (2 PDB entries)

3. Aspartyl-tRNA synthetase (AspRS) [55696] (5 species)

   1. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [55697] (3 PDB entries)

   2. Species Escherichia coli [TaxId:562] [55699] (3 PDB entries)

   3. Species Pyrococcus kodakaraensis [TaxId:311400] [55698] (1 PDB entry)

   4. Species Thermus thermophilus, AspRS-1 [TaxId:274] [55700] (3 PDB entries)

   5. Species Thermus thermophilus, AspRS-2 [TaxId:274] [90008] (1 PDB entry)
      non-discriminating and archaeal-type enzyme

4. ATP phosphoribosyltransferase regulatory subunit HisZ [118058] (2 species)
   shares histidine-binding site with the HisRS catalytic domain

   1. Species Lactococcus lactis [TaxId:1358] [143639] (2 PDB entries)
      Uniprot Q02147 6-323

   2. Species Thermotoga maritima [TaxId:2336] [118059] (1 PDB entry)
      Uniprot Q9X0D3

5. Glycyl-tRNA synthetase (GlyRS) [55692] (1 species)

   • Species Thermus thermophilus [TaxId:274] [55693] (3 PDB entries)

6. Glycyl-tRNA synthetase (GlyRS) alpha chain [75504] (1 species)

   • Species Thermotoga maritima [TaxId:2336] [75505] (1 PDB entry)
     TM0216

7. Histidyl-tRNA synthetase (HisRS) [55688] (4 species)

   1. Species Escherichia coli [TaxId:562] [55689] (4 PDB entries)

   2. Species Staphylococcus aureus [TaxId:1280] [55690] (1 PDB entry)

   3. Species Thermoplasma acidophilum [TaxId:2303] [143637] (1 PDB entry)
      Uniprot Q9HLX5 3-329

   4. Species Thermus thermophilus [TaxId:274] [55691] (3 PDB entries)

8. Hypothetical protein PF1951 [103157] (1 species)

   • Species Pyrococcus furiosus [TaxId:2261] [103158] (1 PDB entry)
     AspRS-related protein

9. Lysyl-tRNA synthetase (LysRS) [55685] (3 species)
   contains an insertion of LEM/SAP-like HeH motif, residues 337-379

   1. Species Escherichia coli, gene lysS [TaxId:562] [55687] (2 PDB entries)

   2. Species Escherichia coli, gene lysU [TaxId:562] [55686] (5 PDB entries)

   3. Species Geobacillus stearothermophilus [TaxId:1422] [225969] (1 PDB entry)

10. Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS [55701] (1 species)

    • Species Thermus thermophilus [TaxId:274] [55702] (11 PDB entries)
      identical sequence to Thermus aquaticus, TaxId: 271

11. Phenyl-tRNA synthetase (PheRS) beta subunit, PheT, central domain [55703] (1 species)
    this domain is non-catalytic

    • Species Thermus thermophilus [TaxId:274] [55704] (11 PDB entries)
      identical sequence to Thermus aquaticus, TaxId: 271

12. Prolyl-tRNA synthetase (ProRS) [64347] (3 species)

    1. Species Methanocaldococcus jannaschii [TaxId:2190] [90010] (1 PDB entry)

    2. Species Methanothermobacter thermautotrophicus [TaxId:145262] [90009] (4 PDB entries)

    3. Species Thermus thermophilus [TaxId:274] [64348] (4 PDB entries)

13. Seryl-tRNA synthetase (SerRS) [55683] (1 species)

    • Species Thermus thermophilus, strain hb27 [TaxId:274] [55684] (4 PDB entries)

14. The aaRS-like accessory subunit of mitochondrial polymerase gamma, N-terminal domain [64349] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [143638] (1 PDB entry)
       Uniprot Q9UHN1 66-355

    2. Species Mouse (Mus musculus) [TaxId:10090] [64350] (2 PDB entries)

15. Threonyl-tRNA synthetase (ThrRS) [55694] (2 species)

    1. Species Escherichia coli [TaxId:562] [55695] (5 PDB entries)

    2. Species Staphylococcus aureus [TaxId:1280] [103154] (2 PDB entries)

16. automated matches [193659] (5 species)
    not a true protein

    1. Species Campylobacter jejuni [TaxId:197] [256056] (2 PDB entries)

    2. Species Campylobacter jejuni [TaxId:354242] [256055] (1 PDB entry)

    3. Species Escherichia coli K-12 [TaxId:83333] [227935] (4 PDB entries)

    4. Species Pyrococcus abyssi [TaxId:29292] [193660] (6 PDB entries)

    5. Species Trypanosoma brucei [TaxId:999953] [237835] (1 PDB entry)

More info for Family d.104.1.1: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

Timeline for Family d.104.1.1: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain:

• Family d.104.1.1: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain first appeared (with stable ids) in SCOP 1.55, called Family d.104.1.1: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalyic domain
  
• Family d.104.1.1: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain appears in SCOPe 2.03
  
• Family d.104.1.1: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain appears in SCOPe 2.05
  
• Family d.104.1.1: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain appears in the current release, SCOPe 2.08