SCOPe 2.08: Superfamily c.55.3: Ribonuclease H-like

Lineage for Superfamily c.55.3: Ribonuclease H-like

1. Root: SCOPe 2.08

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

3. Fold c.55: Ribonuclease H-like motif [53066] (7 superfamilies)
   3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest

4. Superfamily c.55.3: Ribonuclease H-like [53098] (18 families)
   consists of one domain of this fold

Families:

1. c.55.3.1: Ribonuclease H [53099] (5 proteins)

2. c.55.3.2: Retroviral integrase, catalytic domain [53107] (2 proteins)
   Pfam PF00665

3. c.55.3.3: mu transposase, core domain [53112] (1 protein)
   automatically mapped to Pfam PF02914

4. c.55.3.4: Transposase inhibitor (Tn5 transposase) [53115] (1 protein)

5. c.55.3.5: DnaQ-like 3'-5' exonuclease [53118] (17 proteins)
   contains Pfam PF00929

6. c.55.3.6: RuvC resolvase [53134] (2 proteins)
   automatically mapped to Pfam PF02075

7. c.55.3.7: Mitochondrial resolvase ydc2 catalytic domain [69533] (1 protein)
   automatically mapped to Pfam PF09159

8. c.55.3.8: Putative Holliday junction resolvase RuvX [102485] (3 proteins)
   automatically mapped to Pfam PF03652

9. c.55.3.9: CAF1-like ribonuclease [102492] (3 proteins)

10. c.55.3.11: TM1739-like [142505] (1 protein)
    Pfam PF04251; DUF430; particular similarity to the PIWI domain family

11. c.55.3.12: Hermes transposase-like [142508] (1 protein)

12. c.55.3.13: Tex RuvX-like domain-like [159635] (1 protein)

13. c.55.3.14: Prp8 beta-finger domain-like [159638] (1 protein)
    automatically mapped to Pfam PF12134

14. c.55.3.15: PIWI domain C-terminal [310608] (4 proteins)
    PubMed 15565169 notes that both halves of PIWI are usually a single evolutionary unit; however, fragments have been characterized separately. The N-terminal half is (c.44.3.1)

15. c.55.3.16: RuvC-like domain from CRISPR-associated protein Cas9 [345969] (1 protein)
    Homology to RuvC noted in PubMed 21756346
    Pfam PF18541

16. c.55.3.17: Ribonuclease H-like domain of RAG1 [418811] (1 protein)
    Middle of Pfam PF12940

17. c.55.3.18: RuvC-like domain from CRISPR-associated protein Cas12a / Cpf1 [418836] (1 protein)
    Pfam PF18516

18. c.55.3.0: automated matches [191357] (1 protein)
    not a true family

More info for Superfamily c.55.3: Ribonuclease H-like

Timeline for Superfamily c.55.3: Ribonuclease H-like:

• Superfamily c.55.3: Ribonuclease H-like first appeared (with stable ids) in SCOP 1.55
  
• Superfamily c.55.3: Ribonuclease H-like appears in SCOPe 2.07