SCOP 1.75: Superfamily a.4.1: Homeodomain-like

Lineage for Superfamily a.4.1: Homeodomain-like

1. Root: SCOP 1.75

2. Class a: All alpha proteins [46456] (284 folds)

3. Fold a.4: DNA/RNA-binding 3-helical bundle [46688] (14 superfamilies)
   core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down

4. Superfamily a.4.1: Homeodomain-like [46689] (19 families)
   consists only of helices

Families:

1. a.4.1.1: Homeodomain [46690] (40 proteins)
   Pfam PF00046

2. a.4.1.2: Recombinase DNA-binding domain [46728] (5 proteins)

3. a.4.1.3: Myb/SANT domain [46739] (15 proteins)

4. a.4.1.4: DNA-binding domain of telomeric protein [46745] (2 proteins)
   part of Pfam PF00249 (Myb/SANT domain)

5. a.4.1.5: Paired domain [46748] (3 proteins)
   duplication: consists of two domains of this fold

6. a.4.1.6: DNA-binding domain of rap1 [46753] (1 protein)
   duplication: consist of two domains of this fold

7. a.4.1.7: Centromere-binding [46756] (2 proteins)
   duplication: tandem repeat of two similar domains

8. a.4.1.8: AraC type transcriptional activator [46759] (2 proteins)
   duplication: consists of two structural repeats bipartite HTH protein

9. a.4.1.9: Tetracyclin repressor-like, N-terminal domain [46764] (34 proteins)

10. a.4.1.11: GARP response regulators [81683] (1 protein)
    plant myb-related DNA-binding motif

11. a.4.1.12: FIS-like [100918] (4 proteins)

12. a.4.1.13: SLIDE domain [100998] (1 protein)
    myb-related probable DNA-binding motif

13. a.4.1.14: Middle operon regulator, Mor [109659] (1 protein)
    contains extra N-terminal dimerisation subdomain: alpha-hairpin (27-72) dimer is a four-helical bundle with right-handed twist

14. a.4.1.15: Psq domain [140213] (1 protein)
    Pfam PF05225

15. a.4.1.16: Alr1493-like [140216] (1 protein)
    Pfam PF04255; DUF433; contains extra C-terminal helix and N-terminal dimerisation interlock subdomain ((47405))

16. a.4.1.17: Nanomeric phage protein-like [140219] (1 protein)
    contains additional N and C-terminal helices and the C-terminal beta-strand forming an intersubunit beta-barrel with a channel

17. a.4.1.18: SWIRM domain [140222] (3 proteins)
    Pfam PF04433; contains extra N-terminal helix

18. a.4.1.19: Cgl2762-like [158260] (1 protein)
    Pfam PF01527; Transposase 8

19. a.4.1.20: RpiR-like [158263] (1 protein)
    Pfam PF01418; contains two extra helices, one at each termini; overall arrangment of five helices is similar to the helical core of the lambda integrase-like catalytic domain ((56350))

More info for Superfamily a.4.1: Homeodomain-like

Timeline for Superfamily a.4.1: Homeodomain-like:

• Superfamily a.4.1: Homeodomain-like first appeared (with stable ids) in SCOP 1.55
  
• Superfamily a.4.1: Homeodomain-like appears in SCOP 1.73
  
• Superfamily a.4.1: Homeodomain-like appears in SCOPe 2.01
  
• Superfamily a.4.1: Homeodomain-like appears in the current release, SCOPe 2.08