Structural Classification of Proteins
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Superfamily: Nucleic acid-binding proteins

link to SUPERFAMILY database - Superfamily

Lineage:

  1. Root: scop
  2. Class: All beta proteins [48724]
  3. Fold: OB-fold [50198]
    barrel, closed or partly opened n=5, S=10 or S=8; greek-key
  4. Superfamily: Nucleic acid-binding proteins [50249]
    link to SUPERFAMILY database - Superfamily

Families:

  1. Anticodon-binding domain [50250] (7)
    barrel, closed; n=5, S=10
    1. Aspartyl-tRNA synthetase (AspRS) [50251]
      this is N-terminal domain in prokaryotic enzymes and the first "visible" domain in eukaryotic enzymes
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50252] (3) picpic
      2. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [50253] (1) picpic
      3. Thermus thermophilus, AspRS-2 [TaxId: 274] [89323] (1) picpic
        non-discriminating and archaeal-type enzyme
      4. Escherichia coli [TaxId: 562] [50254] (3) picpic
      5. Thermus thermophilus, AspRS-1 [TaxId: 274] [50255] (3) picpic
    2. Lysyl-tRNA synthetase (LysRS) [50256]
      1. Escherichia coli, gene lysS [TaxId: 562] [50257] (4) picpic
      2. Escherichia coli, gene lysU [TaxId: 562] [50258] (5) picpic
  2. RecG "wedge" domain [69259] (1)
    1. RecG "wedge" domain [69260]
      1. Thermotoga maritima [TaxId: 2336] [69261] (1) picpic
  3. DNA helicase RuvA subunit, N-terminal domain [50259] (3)
    barrel, closed; n=5, S=10
    1. DNA helicase RuvA subunit, N-terminal domain [50260]
      tetramer; binds Holliday junction
      1. Escherichia coli [TaxId: 562] [50261] (5) picpic
      2. Mycobacterium leprae [TaxId: 1769] [50262] (1) picpic
      3. Thermus thermophilus [TaxId: 274] [82098] (1) picpic
  4. Single strand DNA-binding domain, SSB [50263] (17)
    barrel, closed; n=5, S=10
    1. ssDNA-binding protein [50264]
      1. Human (Homo sapiens), mitochondria [TaxId: 9606] [50265] (4) picpic
        SQ Q04837
      2. Escherichia coli [TaxId: 562] [50266] (5) picpic
        SQ P02339
      3. Mycobacterium tuberculosis [TaxId: 1773] [101760] (4) picpic
      4. Deinococcus radiodurans [TaxId: 1299] [110194] (1) picpic
        SQ Q9RY51
    2. Archaeal ssDNA-binding protein [89324]
      similar to the domains of the Replication protein A
      1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [89325] (1) picpic
    3. Replication protein A 70 KDa subunit (RPA70) [50267]
      duplication: consists of three domains of this fold; contains zinc-finger insert in the C-terminal domain, residues 479-511
      1. Human (Homo sapiens) [TaxId: 9606] [50268] (6) picpic
    4. Replication protein A 32 KDa subunit (RPA32) fragment [50269]
      1. Human (Homo sapiens) [TaxId: 9606] [50270] (10) picpic
    5. Replication protein A 14 KDa (RPA14) subunit [50271]
      1. Human (Homo sapiens) [TaxId: 9606] [50272] (10) picpic
    6. CDC13 ssDNA-binding domain [74948]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74949] (2) picpic
    7. Telomere end binding protein alpha subunit [50273]
      duplication: consists of three domains of this fold
      1. Oxytricha nova [TaxId: 200597] [50274] (18) picpic
    8. Core domain of telomere end binding protein beta subunit [50275]
      1. Oxytricha nova [TaxId: 200597] [50276] (14) picpic
    9. Protection of telomeres protein 1, Pot1 [101761]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [101762] (2) picpic
      2. Human (Homo sapiens) [TaxId: 9606] [117190] (1) picpic
        SQ Q9NUX5 6-299
    10. OB-fold domains of BRCA2 [82099]
      duplication: tandem repeat of three OB-fold domains
      1. Mouse (Mus musculus) [TaxId: 10090] [82100] (2) picpic
      2. Rat (Rattus norvegicus) [TaxId: 10116] [82101] (1) picpic
    11. Primosomal replication protein N, PriB [117191]
      1. Escherichia coli [TaxId: 562] [117192] (4) picpic
        SQ P07013
    12. Hypothetical protein At4g28440 (F20O9.120) [117193]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117194] (1) picpic
        SQ O49453 14-145
  5. Myf domain [50277] (7)
    1. Domain B2 of PheRS-beta, PheT [50278]
      1. Thermus thermophilus [TaxId: 274] [50279] (9) picpic
        identical sequence to Thermus aquaticus, TaxId: 271
    2. C-terminal domain of methionyl-tRNA synthetase, MetRS-CD [82102]
      1. Archaeon Pyrococcus abyssi [TaxId: 29292] [82103] (1) picpic
    3. EMAP II [50280]
      domain of the p43 protein
      1. Human (Homo sapiens) [TaxId: 9606] [50281] (3) picpic
    4. C-terminal domain of metazoan tyrosyl-tRNA synthetase, TyrRS [89326]
      EMAP II-like domain found in vertebrata and insect enzymes; free domain possesses a cytokine activity
      1. Human (Homo sapiens) [TaxId: 9606] [89327] (1) picpic
    5. Structure-specific tRNA-binding protein TRBP111 [89328]
      1. Escherichia coli [TaxId: 562] [89329] (1) picpic
        YgjH
      2. Aquifex aeolicus [TaxId: 63363] [101763] (1) picpic
        aq_422; putative methionyl-tRNA synthetase beta subunit
    6. TRBP111 homolog CsaA [63770]
      possesses export-related chaperone and tRNA-binding activities
      1. Thermus thermophilus [TaxId: 274] [63771] (1) picpic
  6. Cold shock DNA-binding domain-like [50282] (56)
    barrel, closed; n=5, S=8
    1. Major cold shock protein [50283]
      1. Escherichia coli [TaxId: 562] [50284] (2) picpic
      2. Bacillus subtilis [TaxId: 1423] [50285] (6) picpic
      3. Bacillus caldolyticus [TaxId: 1394] [50286] (8) picpic
      4. Thermotoga maritima [TaxId: 2336] [69262] (1) picpic
    2. Y-box protein 1 cold shock domain (YB1-CSD) [69263]
      1. Human (Homo sapiens) [TaxId: 9606] [69264] (1) picpic
    3. S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase [50287]
      1. Escherichia coli [TaxId: 562] [50288] (1) picpic
      2. Streptomyces antibioticus [TaxId: 1890] [50289] (1) picpic
    4. S1 domain of NusA [69265]
      1. Thermotoga maritima [TaxId: 2336] [69266] (2) picpic
      2. Mycobacterium tuberculosis [TaxId: 1773] [69267] (4) picpic
    5. C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) [88670]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [88671] (1) picpic
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117195] (7) picpic
        SQ P34087
      3. Human (Homo sapiens) [TaxId: 9606] [141309] (4) picpic
        SQ P62487 78-171
    6. Translational initiation factor 1, IF1 [50290]
      1. Escherichia coli [TaxId: 562] [50291] (3) picpic
    7. Archaeal initiation factor-1a, aIF1a [63772]
      evolutionary link between IF1 and eIF1a
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [63773] (1) picpic
    8. Translation initiation factor-1a, eIF1a [50292]
      1. Human (Homo sapiens) [TaxId: 9606] [50293] (1) picpic
    9. Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain [74950]
      1. Human (Homo sapiens) [TaxId: 9606] [74951] (2) picpic
        SQ P05198
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101764] (1) picpic
      3. Sulfolobus solfataricus [TaxId: 2287] [141310] (1) picpic
        SQ Q97Z79 1-84
    10. Viral structural mimic of eIF2alpha [74952]
      1. Vaccinia virus [TaxId: 10245] [74953] (1) picpic
      2. Myxoma virus, m156r [TaxId: 10273] [74954] (1) picpic
    11. Rho termination factor, RNA-binding domain [68910]
      1. Escherichia coli [TaxId: 562] [68911] (14) picpic
        SQ P03002
    12. C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a) [50296]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [50297] (2) picpic
      2. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [50298] (1) picpic
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [82104] (1) picpic
      4. Leishmania infantum [TaxId: 5671] [110195] (1) picpic
        SQ Q9N9V6
      5. Leishmania mexicana [TaxId: 5665] [117196] (1) picpic
        SQ Q9N9V6 97% sequence identity
    13. C-terminal domain of eIF5a homologue (Hex1) [82105]
      1. Filamentous fungi (Neurospora crassa) [TaxId: 5141] [82106] (1) picpic
    14. N-terminal domain of ribosomal protein L2 [50299]
      incomplete OB-fold lacking the last strand
      1. Bacillus stearothermophilus [TaxId: 1422] [50300] (2) picpic
      2. Archaeon Haloarcula marismortui [TaxId: 2238] [50301] (40) picpic
        SQ P20276
        includes the N-terminal tail
      3. Thermus thermophilus [TaxId: 274] [159084] (5) picpic
        SQ Q72I07 1-125
      4. Deinococcus radiodurans [TaxId: 1299] [159085] (5) picpic
        SQ Q9RXJ9 33-127
      5. Escherichia coli [TaxId: 562] [159086] (27) picpic
        SQ P60422 3-124
    15. Ribosomal protein S12 [50302]
      1. Thermus thermophilus [TaxId: 274] [50303] (36) picpic
        SQ P17293
      2. Escherichia coli [TaxId: 562] [159087] (25) picpic
        SQ P0A7S3 1-123
    16. Ribosomal protein S17 [50304]
      1. Thermus thermophilus [TaxId: 274] [50305] (45) picpic
        SQ P24321
      2. Bacillus stearothermophilus [TaxId: 1422] [50306] (1) picpic
      3. Escherichia coli [TaxId: 562] [159088] (26) picpic
        SQ P02373 3-82
    17. Ribosomal protein S28e [101765]
      incomplete OB-fold lacking the last strand
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101766] (1) picpic
      2. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [101767] (1) picpic
    18. Elongation factor P middle and C-terminal domains [110196]
      duplication: contains two domains of this fold
      1. Thermus thermophilus HB8 [TaxId: 300852] [110197] (1) picpic
        SQ Q76G20
    19. S1-domain of Ribonuclease E [110198]
      1. Escherichia coli [TaxId: 562] [110199] (3) picpic
        SQ P21513 35-125
    20. Probable GTPase EngC (YjeQ), N-terminal domain [110200]
      1. Thermotoga maritima [TaxId: 2336] [110201] (1) picpic
        SQ Q9X242 # TM1717
      2. Bacillus subtilis [TaxId: 1423] [117197] (1) picpic
        SQ O34530
    21. Cold shock domain protein E1 (UNR) [117198]
      1. Human (Homo sapiens) [TaxId: 9606] [117199] (1) picpic
        SQ O75534 15-90
    22. S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) [117200]
      1. Human (Homo sapiens) [TaxId: 9606] [117201] (1) picpic
        SQ Q14690 173-278
    23. Exoribonuclease 2, RNB [159089]
      RNase II; contains 3 S1-like domains in addition to an OB-fold embedded in the catalytic domain
      1. Escherichia coli [TaxId: 562] [159090] (18) picpic
        SQ P30850 1-82! SQ P30850 4-82! SQ P30850 5-82! SQ P30850 558-643! SQ P30850 558-644! SQ P30850 83-172
    24. S1-domain of exosome component 3 (RRP40) [159091]
      1. Saccharomyces cerevisiae [TaxId: 4932] [159092] (1) picpic
        SQ Q08285 62-151
      2. Human (Homo sapiens) [TaxId: 9606] [159093] (1) picpic
        SQ Q9NQT5 108-195
    25. Ribonuclease II family protein DR0020 [159094]
      1. Deinococcus radiodurans [TaxId: 1299] [159095] (4) picpic
        SQ Q9RYD0 404-461
    26. S1-domain of Ribosomal RNA-processing protein 4, RRP4 [159096]
      1. Human (Homo sapiens) [TaxId: 9606] [159097] (1) picpic
        SQ Q13868 73-167
    27. Exosome component 1, EXOSC1 [159098]
      3'-5' exoribonuclease CSL4 homolog
      1. Human (Homo sapiens) [TaxId: 9606] [159099] (1) picpic
        SQ Q9Y3B2 61-185
    28. S1-domain of exosome complex RNA-binding protein 1, ECR1 [159100]
      1. Aeropyrum pernix [TaxId: 56636] [159101] (1) picpic
        SQ Q9YC02 60-147
      2. Sulfolobus solfataricus [TaxId: 2287] [159102] (2) picpic
        SQ Q9UXC4 66-152
      3. Archaeoglobus fulgidus [TaxId: 2234] [159103] (3) picpic
        SQ O29758 53-135
    29. Exosome complex exonuclease RRP44 [159104]
      member or the RNase II family; contains 3 S1-like domains; two of them are in tandem N-terminally to the catalytic domain and one is C-terminally to the catalytic domain that also contains an OB-fold
      1. Saccharomyces cerevisiae [TaxId: 4932] [159105] (3) picpic
        SQ Q08162 252-399! SQ Q08162 400-494! SQ Q08162 911-998
    30. Tex S1-domain [159106]
      1. Pseudomonas aeruginosa [TaxId: 287] [159107] (3) picpic
        SQ Q9HTY8 637-730
  7. TRAM domain [101768] (3)
    Pfam 01938
    1. rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain [101769]
      1. Escherichia coli [TaxId: 562] [101770] (3) picpic
    2. Hypothetical protein MM1357 [141311]
      1. Methanosarcina mazei [TaxId: 2209] [141312] (1) picpic
        SQ Q8PX65 1-68
    3. Hypothetical protein MMP0076 [141313]
      1. Methanococcus maripaludis [TaxId: 39152] [141314] (1) picpic
        SQ Q6M142 1-69
  8. Hypothetical protein MTH1 (MT0001), insert domain [74955] (1)
    1. Hypothetical protein MTH1 (MT0001), insert domain [74956]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [74957] (1) picpic
  9. DNA ligase/mRNA capping enzyme postcatalytic domain [50307] (6)
    1. RNA guanylyltransferase (mRNA capping enzyme) [50308]
      1. Chlorella virus PBCV-1 [TaxId: 10506] [50309] (3) picpic
    2. mRNA capping enzyme alpha subunit [89330]
      1. Yeast (Candida albicans) [TaxId: 5476] [89331] (1) picpic
    3. ATP-dependent DNA ligase [50310]
      1. Bacteriophage T7 [TaxId: 10760] [50311] (1) picpic
      2. Chlorella virus PBCV-1 [TaxId: 10506] [50312] (7) picpic
    4. NAD+-dependent DNA ligase [50313]
      1. Thermus filiformis [TaxId: 276] [50314] (2) picpic
    5. DNA ligase I (LIG1) [117202]
      1. Human (Homo sapiens) [TaxId: 9606] [117203] (1) picpic
        SQ P18858 262-901
  10. Phage ssDNA-binding proteins [50315] (5)
    barrel, open; n*=5, S*=8; the members' structures vary greater that those from cellular organisms
    1. Gene V protein [50316]
      1. Enterobacteria phage M13, including coliphage f1 [TaxId: 10870] [50317] (19) picpic
      2. Pseudomonas phage Pf3 [TaxId: 10872] [50318] (1) picpic
    2. Gene 32 protein (gp32) core [50319]
      contains a Zn-finger subdomain, res. 63-111
      1. Bacteriophage T4 [TaxId: 10665] [50320] (1) picpic
      2. Enterobacteria phage RB69 [TaxId: 12353] [159108] (3) picpic
        SQ Q7Y265 32-241
    3. gp2.5 [63774]
      1. Bacteriophage T7 [TaxId: 10760] [63775] (1) picpic
  11. DNA replication initiator (cdc21/cdc54) N-terminal domain [89332] (1)
    1. DNA replication initiator (cdc21/cdc54) N-terminal domain [89333]
      MCM complex protein; dodecamer assembly; includes the N-terminal all-alpha subdomain and inserted Zn-finger
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [89334] (1) picpic
  12. RNA polymerase subunit RBP8 [50321] (1)
    duplication; contains tandem repeat of two incomplete OB-folds; forms a single barrel; n=8, S=10
    1. RNA polymerase subunit RBP8 [50322]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50323] (31) picpic
        SQ P20436
  13. RecO N-terminal domain-like [117204] (1)
    N-terminal part of Pfam 02565
    1. Recombinational repair protein RecO, N-terminal domain [117205]
      1. Deinococcus radiodurans [TaxId: 1299] [117206] (1) picpic
        SQ Q9RW50 # DR0819
  14. TIP49 domain [141315] (1)
    N-terminal part of Pfam 06068; the RuvA-like OB-fold domain in RuvB-like eukaryotic proteins
    1. RuvB-like 2 protein, RUVBL2 (TIP49b) [141316]
      1. Human (Homo sapiens) [TaxId: 9606] [141317] (1) picpic
        SQ Q9Y230 131-212
  15. SSO2064-like [159109] (1)
    Pfam 01796; DUF35; contains extra N-terminal zinc finger subdomain of the rubredoxin-like fold
    1. Hypothetical protein SSO2064 [159110]
      1. Sulfolobus solfataricus [TaxId: 2287] [159111] (2) picpic
        SQ Q97WQ4 8-144
  16. RNB domain-like [159112] (3)
    Pfam 00773; RNase II catalytic domain; decorated OB-fold domain with extra C-terminal structures forming the active site
    1. Exosome complex exonuclease RRP44 [159113]
      1. Saccharomyces cerevisiae [TaxId: 4932] [159114] (1) picpic
        SQ Q08162 495-910
    2. Ribonuclease II family protein DR0020 [159115]
      Includes extra N-terminal all-alpha subdomain
      1. Deinococcus radiodurans [TaxId: 1299] [159116] (4) picpic
        SQ Q9RYD0 3-403
    3. Exoribonuclease 2, RNB [159117]
      RNase II
      1. Escherichia coli [TaxId: 562] [159118] (6) picpic
        SQ P30850 173-557
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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