Structural Classification of Proteins

Fold: Ribosomal protein S5 domain 2-like

: core: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossover

Lineage:

Root: scop
Class: Alpha and beta proteins (a+b) [53931]
Mainly antiparallel beta sheets (segregated alpha and beta regions)
Fold: Ribosomal protein S5 domain 2-like [54210]
core: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossover

Superfamilies:

Ribosomal protein S5 domain 2-like [54211] (12)
uperfamily
1. Translational machinery components [54212] (8)
  1. Elongation factor G (EF-G), domain IV [54213]
    1. Thermus thermophilus [TaxId: 274] [54214] (9)
    2. Thermus thermophilus, EF-G-2 [TaxId: 274] [142925] (2)
      SQ Q5SI76 448-562
      TTHA1498
  2. Elongation factor 2 (eEF-2), domain IV [82575]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82576] (22)
      SQ P32324
  3. Ribosomal protein S5, C-terminal domain [54215]
    1. Bacillus stearothermophilus [TaxId: 1422] [54216] (1)
    2. Thermus thermophilus [TaxId: 274] [54217] (36)
      SQ P27152 ! SQ P80373
    3. Escherichia coli [TaxId: 562] [159906] (24)
      SQ P0A7W1 78-158
  4. Ribosomal protein S9 [54218]
    1. Thermus thermophilus [TaxId: 274] [54219] (39)
      SQ P80374
    2. Escherichia coli [TaxId: 562] [159907] (26)
      SQ P0A7X3 3-129
2. RNase P protein [54220] (3)
  1. RNase P protein [54221]
    1. Bacillus subtilis [TaxId: 1423] [54222] (1)
    2. Staphylococcus aureus [TaxId: 1280] [54223] (1)
    3. Thermotoga maritima [TaxId: 2336] [89821] (1)
3. DNA gyrase/MutL, second domain [54224] (7)
  1. DNA mismatch repair protein MutL [54225]
    1. Escherichia coli [TaxId: 562] [54226] (6)
  2. DNA mismatch repair protein PMS2 [69656]
    1. Human (Homo sapiens) [TaxId: 9606] [69657] (3)
  3. DNA gyrase B [54227]
    1. Escherichia coli [TaxId: 562] [54228] (1)
    2. Thermus thermophilus [TaxId: 274] [75352] (1)
  4. DNA topoisomerase II [102751]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102752] (2)
  5. Topoisomerase IV subunit B [102753]
    1. Escherichia coli [TaxId: 562] [102754] (1)
  6. Topoisomerase VI-B subunit [82577]
    contains an H2TH domain inserted in front of this domain and after the N-terminal ATPase domain
    1. Archaeon Sulfolobus shibatae [TaxId: 2286] [82578] (10)
4. Hsp90 middle domain [102755] (1)
  related to the DNA gyrase/MutL family; contains extra C-terminal alpha/beta subdomain
  1. Heat shock protein hsp82 [102756]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102757] (3)
5. Ribonuclease PH domain 1-like [54229] (14)
  1. Ribonuclease PH, domain 1 [102758]
    1. Aquifex aeolicus [TaxId: 63363] [102759] (4)
    2. Pseudomonas aeruginosa [TaxId: 287] [102760] (2)
    3. Bacillus subtilis [TaxId: 1423] [102761] (3)
  2. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 [54230]
    duplication of two-domain units formed by domains 1-2 and 4-5
    1. Streptomyces antibioticus [TaxId: 1890] [54231] (2)
  3. Exosome complex exonuclease RRP42 [159908]
    1. Human (Homo sapiens) [TaxId: 9606] [159909] (1)
      SQ Q15024 5-191
  4. Exosome complex exonuclease RRP46 [159910]
    1. Human (Homo sapiens) [TaxId: 9606] [159911] (1)
      SQ Q9NQT4 25-146
  5. Exosome complex exonuclease RRP45 [159912]
    1. Human (Homo sapiens) [TaxId: 9606] [159913] (1)
      SQ Q86Y41 1-184
  6. Exosome complex exonuclease RRP43 [159914]
    1. Human (Homo sapiens) [TaxId: 9606] [159915] (1)
      SQ Q96B26 7-187
  7. Exosome complex exonuclease MTR3 [159916]
    1. Human (Homo sapiens) [TaxId: 9606] [159917] (1)
      SQ Q5RKV6 29-175
  8. Exosome complex exonuclease RRP41 [159918]
    1. Human (Homo sapiens) [TaxId: 9606] [159919] (1)
      SQ Q9NPD3 7-151
  9. Exosome complex exonuclease 2,ECX2 [159920]
    1. Archaeoglobus fulgidus [TaxId: 2234] [159921] (6)
      SQ O29756 3-178
    2. Sulfolobus solfataricus [TaxId: 2287] [159922] (51)
      SQ Q9UXC0 1-191
  10. Exosome complex exonuclease 1, ECX1 [159923]
    1. Sulfolobus solfataricus [TaxId: 2287] [159924] (50)
      SQ Q9UXC2 8-155
    2. Archaeoglobus fulgidus [TaxId: 2234] [159925] (6)
      SQ O29757 10-153
6. GHMP Kinase, N-terminal domain [54232] (10)
  1. Galactokinase [102762]
    1. Lactococcus lactis [TaxId: 1358] [102763] (1)
    2. Archaeon Pyrococcus furiosus [TaxId: 2261] [102764] (1)
    3. Human (Homo sapiens) [TaxId: 9606] [117793] (1)
      SQ P51570
  2. Homoserine kinase [54233]
    1. Archaeon Methanococcus jannaschii [TaxId: 2190] [54234] (5)
  3. Mevalonate kinase [75353]
    1. Archaeon Methanococcus jannaschii [TaxId: 2190] [75354] (2)
    2. Rat (Rattus norvegicus) [TaxId: 10116] [75355] (2)
  4. Phosphomevalonate kinase (PMK) [75356]
    1. Streptococcus pneumoniae r6 [TaxId: 171101] [75357] (1)
  5. Mevalonate 5-diphosphate decarboxylase [64219]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64220] (1)
  6. 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE [89822]
    1. Thermus thermophilus [TaxId: 274] [89823] (1)
    2. Escherichia coli [TaxId: 562] [102765] (1)
7. Early switch protein XOL-1, N-terminal domain [89824] (1)
  diverged from the GHMP Kinase family; lost the ATP-binding site
  1. Early switch protein XOL-1, N-terminal domain [89825]
    1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89826] (1)
8. UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC [89827] (1)
  duplication; there are two structural repeats of this fold; each repeat is elaborated with additional structures forming the active site
  1. UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC [89828]
    1. Aquifex aeolicus [TaxId: 63363] [89829] (34)
      SQ O67648 3-270
9. Imidazole glycerol phosphate dehydratase [102766] (3)
  duplication; there are two structural repeats of this fold
  1. Imidazole glycerol phosphate dehydratase [102767]
    1. Fungus (Filobasidiella neoformans) [TaxId: 5207] [102768] (1)
    2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142926] (32)
      SQ P34047 159-255! SQ P34047 73-158
    3. Staphylococcus aureus [TaxId: 1280] [142927] (12)
      SQ P64373 1-84! SQ P64373 85-179
10. ATP-dependent protease Lon (La), catalytic domain [102769] (2)
  contains extra C-terminal alpha/beta subdomain
  1. ATP-dependent protease Lon (La), catalytic domain [102770]
    1. Escherichia coli [TaxId: 562] [102771] (2)
    2. Methanococcus jannaschii [TaxId: 2190] [117794] (1)
      SQ Q58812 456-640 # MJ1417
11. YigZ N-terminal domain-like [102772] (2)
  modification of the common fold; contains extra alpha-beta unit after strand 2, the extra strand is inserted between strands 3 and 4
  1. Hypothetical protein YigZ, N-terminal domain [102773]
    1. Escherichia coli [TaxId: 562] [102774] (1)
      two-domain structure is similar to the C-terminal region of EF-G (domains IV and V)
  2. Hypothetical protein TTHA1053, N-terminal domain [142928]
    1. Thermus thermophilus [TaxId: 274] [142929] (1)
      SQ Q5SJF5 2-124
12. Formaldehyde-activating enzyme, FAE [117795] (1)
  modification of the common fold; contains extra alpha-beta unit after strand 2, the extra strand extends beta-sheet antiparallel to strand 3
  1. Formaldehyde-activating enzyme, FAE [117796]
    1. Methylobacterium extorquens [TaxId: 408] [117797] (2)
      SQ Q9FA38