Structural Classification of Proteins
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Superfamily: Ribosomal protein S5 domain 2-like

link to SUPERFAMILY database - Superfamily

Lineage:

  1. Root: scop
  2. Class: Alpha and beta proteins (a+b) [53931]
    Mainly antiparallel beta sheets (segregated alpha and beta regions)
  3. Fold: Ribosomal protein S5 domain 2-like [54210]
    core: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossover
  4. Superfamily: Ribosomal protein S5 domain 2-like [54211]
    link to SUPERFAMILY database - Superfamily

Families:

  1. Translational machinery components [54212] (8)
    1. Elongation factor G (EF-G), domain IV [54213]
      1. Thermus thermophilus [TaxId: 274] [54214] (9) picpic
      2. Thermus thermophilus, EF-G-2 [TaxId: 274] [142925] (2) picpic
        SQ Q5SI76 448-562
        TTHA1498
    2. Elongation factor 2 (eEF-2), domain IV [82575]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82576] (22) picpic
        SQ P32324
    3. Ribosomal protein S5, C-terminal domain [54215]
      1. Bacillus stearothermophilus [TaxId: 1422] [54216] (1) picpic
      2. Thermus thermophilus [TaxId: 274] [54217] (36) picpic
        SQ P27152 ! SQ P80373
      3. Escherichia coli [TaxId: 562] [159906] (24) picpic
        SQ P0A7W1 78-158
    4. Ribosomal protein S9 [54218]
      1. Thermus thermophilus [TaxId: 274] [54219] (39) picpic
        SQ P80374
      2. Escherichia coli [TaxId: 562] [159907] (26) picpic
        SQ P0A7X3 3-129
  2. RNase P protein [54220] (3)
    1. RNase P protein [54221]
      1. Bacillus subtilis [TaxId: 1423] [54222] (1) picpic
      2. Staphylococcus aureus [TaxId: 1280] [54223] (1) picpic
      3. Thermotoga maritima [TaxId: 2336] [89821] (1) picpic
  3. DNA gyrase/MutL, second domain [54224] (7)
    1. DNA mismatch repair protein MutL [54225]
      1. Escherichia coli [TaxId: 562] [54226] (6) picpic
    2. DNA mismatch repair protein PMS2 [69656]
      1. Human (Homo sapiens) [TaxId: 9606] [69657] (3) picpic
    3. DNA gyrase B [54227]
      1. Escherichia coli [TaxId: 562] [54228] (1) picpic
      2. Thermus thermophilus [TaxId: 274] [75352] (1) picpic
    4. DNA topoisomerase II [102751]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102752] (2) picpic
    5. Topoisomerase IV subunit B [102753]
      1. Escherichia coli [TaxId: 562] [102754] (1) picpic
    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) picpic
  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) picpic
  5. Ribonuclease PH domain 1-like [54229] (14)
    1. Ribonuclease PH, domain 1 [102758]
      1. Aquifex aeolicus [TaxId: 63363] [102759] (4) picpic
      2. Pseudomonas aeruginosa [TaxId: 287] [102760] (2) picpic
      3. Bacillus subtilis [TaxId: 1423] [102761] (3) picpic
    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) picpic
    3. Exosome complex exonuclease RRP42 [159908]
      1. Human (Homo sapiens) [TaxId: 9606] [159909] (1) picpic
        SQ Q15024 5-191
    4. Exosome complex exonuclease RRP46 [159910]
      1. Human (Homo sapiens) [TaxId: 9606] [159911] (1) picpic
        SQ Q9NQT4 25-146
    5. Exosome complex exonuclease RRP45 [159912]
      1. Human (Homo sapiens) [TaxId: 9606] [159913] (1) picpic
        SQ Q86Y41 1-184
    6. Exosome complex exonuclease RRP43 [159914]
      1. Human (Homo sapiens) [TaxId: 9606] [159915] (1) picpic
        SQ Q96B26 7-187
    7. Exosome complex exonuclease MTR3 [159916]
      1. Human (Homo sapiens) [TaxId: 9606] [159917] (1) picpic
        SQ Q5RKV6 29-175
    8. Exosome complex exonuclease RRP41 [159918]
      1. Human (Homo sapiens) [TaxId: 9606] [159919] (1) picpic
        SQ Q9NPD3 7-151
    9. Exosome complex exonuclease 2,ECX2 [159920]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159921] (6) picpic
        SQ O29756 3-178
      2. Sulfolobus solfataricus [TaxId: 2287] [159922] (51) picpic
        SQ Q9UXC0 1-191
    10. Exosome complex exonuclease 1, ECX1 [159923]
      1. Sulfolobus solfataricus [TaxId: 2287] [159924] (50) picpic
        SQ Q9UXC2 8-155
      2. Archaeoglobus fulgidus [TaxId: 2234] [159925] (6) picpic
        SQ O29757 10-153
  6. GHMP Kinase, N-terminal domain [54232] (10)
    1. Galactokinase [102762]
      1. Lactococcus lactis [TaxId: 1358] [102763] (1) picpic
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [102764] (1) picpic
      3. Human (Homo sapiens) [TaxId: 9606] [117793] (1) picpic
        SQ P51570
    2. Homoserine kinase [54233]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [54234] (5) picpic
    3. Mevalonate kinase [75353]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [75354] (2) picpic
      2. Rat (Rattus norvegicus) [TaxId: 10116] [75355] (2) picpic
    4. Phosphomevalonate kinase (PMK) [75356]
      1. Streptococcus pneumoniae r6 [TaxId: 171101] [75357] (1) picpic
    5. Mevalonate 5-diphosphate decarboxylase [64219]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64220] (1) picpic
    6. 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE [89822]
      1. Thermus thermophilus [TaxId: 274] [89823] (1) picpic
      2. Escherichia coli [TaxId: 562] [102765] (1) picpic
  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) picpic
  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) picpic
        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) picpic
      2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142926] (32) picpic
        SQ P34047 159-255! SQ P34047 73-158
      3. Staphylococcus aureus [TaxId: 1280] [142927] (12) picpic
        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) picpic
      2. Methanococcus jannaschii [TaxId: 2190] [117794] (1) picpic
        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) picpic
        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) picpic
        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) picpic
        SQ Q9FA38
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MRC site Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009
Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk