SCOPe 2.04: Family c.26.1.1: Class I aminoacyl-tRNA synthetases (RS), catalytic domain

Lineage for Family c.26.1.1: Class I aminoacyl-tRNA synthetases (RS), catalytic domain

1. Root: SCOPe 2.04

2. Class c: Alpha and beta proteins (a/b) [51349] (148 folds)

3. Fold c.26: Adenine nucleotide alpha hydrolase-like [52373] (3 superfamilies)
   core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145

4. Superfamily c.26.1: Nucleotidylyl transferase [52374] (6 families)

5. Family c.26.1.1: Class I aminoacyl-tRNA synthetases (RS), catalytic domain [52375] (13 proteins)
   contains a conserved all-alpha subdomain at the C-terminal extension

Proteins:

1. Arginyl-tRNA synthetase (ArgRS) [52392] (2 species)

   1. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [52393] (3 PDB entries)

   2. Species Thermus thermophilus [TaxId:274] [69454] (1 PDB entry)

2. Class I lysyl-tRNA synthetase [75159] (1 species)
   similar domain organization to GluRS

   • Species Pyrococcus horikoshii [TaxId:53953] [75160] (1 PDB entry)

3. Cysteinyl-tRNA synthetase (CysRS) [75161] (1 species)

   • Species Escherichia coli [TaxId:562] [75162] (3 PDB entries)
     Uniprot P21888

4. Glutaminyl-tRNA synthetase (GlnRS) [52380] (2 species)

   1. Species Escherichia coli K-12 [TaxId:83333] [159495] (1 PDB entry)

   2. Species Escherichia coli [TaxId:562] [52381] (17 PDB entries)

5. Glutamyl-Q tRNA-Asp synthetase YadB [102257] (1 species)
   truncated GluRS and GlnRS homologue lacking the anticodon-binding domain; glutamylates the modified base queuosine (Q) of tRNA-Asp

   • Species Escherichia coli [TaxId:562] [102258] (2 PDB entries)

6. Glutamyl-tRNA synthetase (GluRS) [52382] (1 species)
   Catalytic domain is very similar to that of GlnRS

   • Species Thermus thermophilus [TaxId:274] [52383] (11 PDB entries)

7. Isoleucyl-tRNA synthetase (IleRS) [52387] (2 species)

   1. Species Staphylococcus aureus [TaxId:1280] [52389] (3 PDB entries)

   2. Species Thermus thermophilus [TaxId:274] [52388] (3 PDB entries)

8. Leucyl-tRNA synthetase (LeuRS) [82356] (1 species)

   • Species Thermus thermophilus [TaxId:274] [82357] (3 PDB entries)
     contains a non-conserved insertion (residues 581-633) that forms a separate subdomain; possible rudiment Zn finger

9. Methionyl-tRNA synthetase (MetRS) [52384] (3 species)

   1. Species Escherichia coli [TaxId:562] [52386] (9 PDB entries)

   2. Species Pyrococcus abyssi [TaxId:29292] [110490] (1 PDB entry)
      Uniprot Q9V011 1-606 # C-domain 616-722 is solved separately: 1MKH

   3. Species Thermus thermophilus [TaxId:274] [52385] (1 PDB entry)

10. Tryptophanyl-tRNA synthetase (TrpRS) [52378] (5 species)
    overall structure is similar to TyrRS

    1. Species Bacillus stearothermophilus [TaxId:1422] [52379] (11 PDB entries)

    2. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [255912] (4 PDB entries)

    3. Species Human (Homo sapiens) [TaxId:9606] [102256] (11 PDB entries)
       Uniprot P23381 94-471

    4. Species Thermotoga maritima [TaxId:2336] [187734] (1 PDB entry)

    5. Species Thermus thermophilus HB8 [TaxId:300852] [188378] (1 PDB entry)

11. Tyrosyl-tRNA synthetase (TyrRS) [52376] (6 species)

    1. Species Bacillus stearothermophilus, nca 1503 [TaxId:1422] [52377] (7 PDB entries)

    2. Species Escherichia coli [TaxId:316407] [188087] (3 PDB entries)

    3. Species Human (Homo sapiens) [TaxId:9606] [82355] (4 PDB entries)

    4. Species Methanococcus jannaschii [TaxId:2190] [89611] (7 PDB entries)

    5. Species Staphylococcus aureus [TaxId:1280] [69453] (4 PDB entries)

    6. Species Thermus thermophilus [TaxId:274] [82354] (2 PDB entries)

12. Valyl-tRNA synthetase (ValRS) [52390] (1 species)

    • Species Thermus thermophilus [TaxId:274] [52391] (3 PDB entries)

13. automated matches [190581] (8 species)
    not a true protein

    1. Species Archaeoglobus fulgidus [TaxId:2234] [187585] (1 PDB entry)

    2. Species Escherichia coli [TaxId:562] [188048] (3 PDB entries)

    3. Species Methanocaldococcus jannaschii [TaxId:2190] [188187] (8 PDB entries)

    4. Species Methanocaldococcus jannaschii [TaxId:243232] [193079] (8 PDB entries)

    5. Species Thermus thermophilus HB8 [TaxId:300852] [233866] (1 PDB entry)

    6. Species Thermus thermophilus [TaxId:274] [254946] (3 PDB entries)

    7. Species Vibrio cholerae [TaxId:243277] [196171] (1 PDB entry)

    8. Species Yersinia pestis [TaxId:214092] [189402] (1 PDB entry)

More info for Family c.26.1.1: Class I aminoacyl-tRNA synthetases (RS), catalytic domain

Timeline for Family c.26.1.1: Class I aminoacyl-tRNA synthetases (RS), catalytic domain:

• Family c.26.1.1: Class I aminoacyl-tRNA synthetases (RS), catalytic domain first appeared (with stable ids) in SCOP 1.55
  
• Family c.26.1.1: Class I aminoacyl-tRNA synthetases (RS), catalytic domain appears in SCOPe 2.03
  
• Family c.26.1.1: Class I aminoacyl-tRNA synthetases (RS), catalytic domain appears in SCOPe 2.05
  
• Family c.26.1.1: Class I aminoacyl-tRNA synthetases (RS), catalytic domain appears in the current release, SCOPe 2.08