Structural Classification of Proteins
home mail help root up expand collapse

Superfamily: Ribonuclease H-like

consists of one domain of this fold
link to SUPERFAMILY database - Superfamily

Lineage:

  1. Root: scop
  2. Class: Alpha and beta proteins (a/b) [51349]
    Mainly parallel beta sheets (beta-alpha-beta units)
  3. Fold: Ribonuclease H-like motif [53066]
    3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
  4. Superfamily: Ribonuclease H-like [53098]
    consists of one domain of this fold
    link to SUPERFAMILY database - Superfamily

Families:

  1. Ribonuclease H [53099] (11)
    1. RNase H (RNase HI) [53100]
      1. Escherichia coli [TaxId: 562] [53101] (37) picpic
        SQ P0A7Y4
      2. Thermus thermophilus [TaxId: 274] [53102] (1) picpic
      3. synthetic, Escherichia coli/Thermus thermophilus chimera [69532] (1) picpic
    2. Class II ribonuclease H (RNase HII) [53103]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53104] (1) picpic
      2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [64093] (2) picpic
      3. Archaeon Thermococcus kodakaraensis [TaxId: 311400] [64094] (2) picpic
      4. Archaeon Pyrococcus horikoshii [TaxId: 53953] [110639] (2) picpic
        SQ O59351
      5. Thermotoga maritima [TaxId: 2336] [142489] (1) picpic
        SQ Q9X017 1-221
    3. HIV RNase H (Domain of reverse transcriptase) [53105]
      1. Human immunodeficiency virus type 1 [TaxId: 11676] [53106] (88) picpic
        SQ P04585 159-692 # chain A coverage; chain B is shorter: 162-582 ! SQ P03366 186-725 # chain A coverage; chain B coverage: 156-584 ! SQ P04585 158-698 # chain A coverage; chain B is shorter: 159-595
      2. Human immunodeficiency virus type 2 [TaxId: 11709] [82443] (1) picpic
    4. BH0863-like Ribonuclease H [142490]
      new class of RNase H
      1. Bacillus halodurans [TaxId: 86665] [142491] (15) picpic
        SQ Q9KEI9 61-193! SQ Q9KEI9 62-193
        BH0863
  2. Retroviral integrase, catalytic domain [53107] (3)
    1. Retroviral integrase, catalytic domain [53108]
      1. Rous sarcoma virus RSV [TaxId: 11886] [53109] (21) picpic
      2. Human immunodeficiency virus type 1 [TaxId: 11676] [53110] (19) picpic
      3. Simian immunodeficiency virus [TaxId: 11723] [53111] (1) picpic
  3. mu transposase, core domain [53112] (1)
    1. mu transposase, core domain [53113]
      1. Bacteriophage mu [TaxId: 10677] [53114] (2) picpic
  4. Transposase inhibitor (Tn5 transposase) [53115] (1)
    1. Transposase inhibitor (Tn5 transposase) [53116]
      contains additional all-alpha subdomains in both N- and C-terminal regions
      1. Escherichia coli [TaxId: 562] [53117] (6) picpic
  5. DnaQ-like 3'-5' exonuclease [53118] (26)
    contains Pfam 00929
    1. Exonuclease domain of prokaryotic DNA polymerase [53119]
      part of Klenow fragment, KF
      1. Escherichia coli [TaxId: 562] [53120] (14) picpic
      2. Thermus aquaticus [TaxId: 271] [53121] (13) picpic
      3. Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422] [53122] (45) picpic
        SQ Q45458 298-876 # 88% sequence identity ! SQ Q5KWC1 299-878 # 99% sequence identity; Geobacillus kaustophilus TaxID:1462
    2. Exonuclease domain of T7 DNA polymerase [53123]
      1. Bacteriophage T7 [TaxId: 10760] [53124] (16) picpic
        SQ P00581
    3. Exonuclease domain of family B DNA polymerases [53125]
      elaborated with additional structures and the N-terminal subdomain
      1. Escherichia coli [TaxId: 562] [102482] (1) picpic
        DNA polymerase II, additional N-terminal subdomain has an OB-fold with a ferredoxin-like fold insertion
      2. Bacteriophage T4 [TaxId: 10665] [53126] (2) picpic
        additional N-terminal subdomain contains rudimental OB-fold
      3. Bacteriophage RB69 [TaxId: 12353] [53127] (27) picpic
        additional N-terminal subdomain contains rudimental OB-fold and rudimental ferredoxin-like fold
      4. Archaeon Thermococcus gorgonarius [TaxId: 71997] [53128] (3) picpic
        additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
      5. Archaeon Thermococcus sp., 9on-7 [TaxId: 35749] [53129] (1) picpic
        additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
      6. Archaeon Desulfurococcus tok [TaxId: 108142] [53130] (2) picpic
        additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
      7. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [53131] (2) picpic
        SQ P56689 1-758 # 93% sequence identity; Thermococcus kodakarensis KOD1 TaxID: 69014
        additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
      8. Sulfolobus solfataricus [TaxId: 2287] [117647] (1) picpic
        SQ P26811 40-864
    4. N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III [82444]
      1. Escherichia coli [TaxId: 562] [82445] (5) picpic
    5. Exonuclease I [53132]
      also includes an alpha+beta domain with SH3-like like motif and non-globular C-terminal all-alpha region
      1. Escherichia coli [TaxId: 562] [53133] (1) picpic
      2. Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333] [159630] (3) picpic
    6. Oligoribonuclease [89719]
      1. Haemophilus influenzae [TaxId: 727] [89720] (1) picpic
        HI1715
      2. Escherichia coli [TaxId: 562] [142492] (6) picpic
        SQ P0A784 1-180
    7. Hypothetical protein AT5G06450 [102483]
      forms a ring-shaped hexamer; function unknown
      1. Thale-cress (Arabidopsis thaliana) [TaxId: 3702] [102484] (7) picpic
    8. Exonuclease ERI1 [117648]
      1. Human (Homo sapiens) [TaxId: 9606] [117649] (1) picpic
        SQ Q8IV48 122-321
    9. Exonuclease domain of phi29 DNA polymerase [117650]
      1. Bacteriophage phi-29 [TaxId: 10756] [117651] (18) picpic
        SQ P03680
    10. Interferon-stimulated gene 20 kDa protein, ISG20 [117652]
      1. Human (Homo sapiens) [TaxId: 9606] [117653] (1) picpic
        SQ Q96AZ6 6-178
    11. Exosome complex exonuclease RRP6 [142493]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142494] (4) picpic
        SQ Q12149 129-420
    12. Ribonuclease D, catalytic domain [142495]
      1. Escherichia coli [TaxId: 562] [142496] (1) picpic
        SQ P09155 1-193
    13. Ribonuclease T [142497]
      1. Pseudomonas aeruginosa [TaxId: 287] [142498] (2) picpic
        SQ Q9HY82 19-220
    14. Three prime repair exonuclease 2, TREX2 [142499]
      1. Human (Homo sapiens) [TaxId: 9606] [142500] (2) picpic
        SQ Q9BQ50 44-271
    15. Three prime repair exonuclease 1, TREX1 [159631]
      1. Mouse (Mus musculus) [TaxId: 10090] [159632] (18) picpic
        SQ Q91XB0 5-234! SQ Q91XB0 9-234
  6. RuvC resolvase [53134] (1)
    1. RuvC resolvase [53135]
      Holliday junction-specific endonuclease
      1. Escherichia coli [TaxId: 562] [53136] (1) picpic
  7. Mitochondrial resolvase ydc2 catalytic domain [69533] (1)
    1. Mitochondrial resolvase ydc2 catalytic domain [69534]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [69535] (1) picpic
  8. Putative Holliday junction resolvase RuvX [102485] (3)
    1. Hypothetical protein YqgF (RuvX) [102486]
      1. Escherichia coli [TaxId: 562] [102487] (3) picpic
    2. Hypothetical protein YrrK (RuvX) [102488]
      1. Bacillus subtilis [TaxId: 1423] [102489] (1) picpic
    3. Hypothetical protein, YqgF homologue [102490]
      1. Thermus thermophilus [TaxId: 274] [102491] (1) picpic
  9. CAF1-like ribonuclease [102492] (2)
    1. Pop2 RNase D domain [102493]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102494] (1) picpic
    2. CCR4-NOT transcription complex subunit 7, CAF1 [159633]
      1. Human (Homo sapiens) [TaxId: 9606] [159634] (1) picpic
        SQ Q9UIV1 11-262
  10. PIWI domain [110640] (3)
    Pfam 02171
    1. Argonaute homologue PF0537 [110641]
      includes the middle domain
      1. Pyrococcus furiosus [TaxId: 2261] [110642] (3) picpic
        SQ Q8U3D2
    2. Argonaute homologue Aq_1447 [142501]
      includes the middle domain
      1. Aquifex aeolicus [TaxId: 63363] [142502] (6) picpic
        SQ O67434 315-706
    3. Hypothetical protein AF1318 [142503]
      1. Archaeoglobus fulgidus [TaxId: 2234] [142504] (5) picpic
        SQ O28951 11-427
  11. TM1739-like [142505] (1)
    Pfam 04251; DUF430; particular similarity to the PIWI domain family
    1. Hypothetical protein TM1739 [142506]
      1. Thermotoga maritima [TaxId: 2336] [142507] (2) picpic
        SQ Q9X261 1-301
  12. Hermes transposase-like [142508] (1)
    1. Transposase Hermes, catalytic domain [142509]
      1. House fly (Musca domestica) [TaxId: 7370] [142510] (1) picpic
        SQ Q25442 163-609
  13. Tex RuvX-like domain-like [159635] (1)
    1. Transcriptional accessory factor Tex [159636]
      1. Pseudomonas aeruginosa [TaxId: 287] [159637] (3) picpic
        SQ Q9HTY8 325-473
  14. Prp8 beta-finger domain-like [159638] (2)
    1. Pre-mRNA-splicing factor 8, Prp8 [159639]
      1. Human (Homo sapiens) [TaxId: 9606] [159640] (3) picpic
        SQ Q6P2Q9 1760-2016! SQ Q6P2Q9 1771-1989
      2. Saccharomyces cerevisiae [TaxId: 4932] [159641] (5) picpic
        SQ P33334 1833-2087! SQ P33334 1835-2087
Enter search key:
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