Class: Multi-domain proteins (alpha and beta)

Folds consisting of two or more domains belonging to different classes

Lineage:

1. Root: scop
2. Class: Multi-domain proteins (alpha and beta)
   Folds consisting of two or more domains belonging to different classes

Folds:

1. Serpins (1)
   contains a cluster of helices and a beta-sandwich
   1. Serpins (1)
2. Replication terminator protein (Tus) (1)
   contains a cluster of helices and a beta-sandwich
   1. Replication terminator protein (Tus) (1)
3. beta-Lactamase/D-ala carboxypeptidase (1)
   contains a cluster of helices and an alpha+beta sandwich
   1. beta-Lactamase/D-ala carboxypeptidase (1)
4. ADP ribosyl cyclase (1)
   contains a cluster of helices and an alpha/beta domain
   1. ADP ribosyl cyclase (1)
5. Heme-linked catalases (1)
   contains an (8,10) beta-barrel and an all-alpha domain
   1. Heme-linked catalases (1)
6. Acyl-CoA dehydrogenase (flavoprotein), N-terminal and middle domains (1)
   1. Acyl-CoA dehydrogenase (flavoprotein), N-terminal and middle domains (1)
7. Sugar phosphatases (1)
   N-terminal domain is an alpha+beta, C-terminal domain is an alpha/beta with mixed beta-sheet
   1. Sugar phosphatases (1)
8. DNA/RNA polymerases (1)
   1. DNA/RNA polymerases (4)
      "palm" domain has a ferredoxin-like fold, related to that of an adenylyl cyclase domain
9. Nucleotidyltransferases (1)
   common catalytic domain is alpha+beta; 2 layers: a/b; mixed sheet
   1. Nucleotidyltransferases (3)
10. Prokaryotic type I DNA topoisomerase (1)
    4 domains: (1) Toprim alpha/beta; (2&4) "winged helix"-like; (3) barrel: n=6, S=8
    1. Prokaryotic type I DNA topoisomerase (1)
       duplication: the protein chain passing through the domains 2-4 makes two structural repeats
       The active site is formed by the toprim and "winged helix" domains (domains 1 and 4); these two domains are also found in the type II topoisomerase (DNA gyrase A) and in the alpha subunit of topoisomerase IV
11. Type II DNA topoisomerase (1)
    4 domains: (1) toprim alpha/beta; (2) "winged helix"-like; (3) alpha+beta; (4) all-alpha
    1. Type II DNA topoisomerase (1)
12. DNA topoisomerase IV, alpha subunit (1)
    2 domains: (1) toprim alpha/beta; (2) "winged helix"-like
    1. DNA topoisomerase IV, alpha subunit (1)
13. DNA primase DnaG catalytic core (1)
    3 domains: (1) toprim alpha+beta; (2) alpha/beta; (3) all-alpha
    1. DNA primase DnaG catalytic core (1)
14. DNA repair protein MutM (Fpg) (1)
    3 domains: (1) beta-sandwich; (2) all-alpha (HhH-like motifs?; (3) zinc finger
    1. DNA repair protein MutM (Fpg) (1)
15. Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment (1)
    2 domains: alpha+beta and all-beta
    1. Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment (1)
16. DNA primase (1)
    3 domains: two alpha+beta domains and one all-alpha domain
    1. DNA primase (1)
17. D-amino acid aminotransferase-like PLP-dependent enzymes (1)
    2 domains: (1) alpha+beta: beta3-alpha2-beta2; (2) alpha/beta, a part of its mixed sheet forms barrel: n=6, S=8
    1. D-amino acid aminotransferase-like PLP-dependent enzymes (1)
18. Nickel-iron hydrogenase, large subunit (1)
    3 domains: (1) all-alpha; (2&3) alpha+beta
    1. Nickel-iron hydrogenase, large subunit (1)
19. Nickel-iron hydrogenase, small subunit (1)
    2 domains: (1) alpa/beta; (2) Fe-S cluster-bound
    1. Nickel-iron hydrogenase, small subunit (1)
20. Heat shock protein 70kD (HSP70), C-terminal, substrate-binding fragment (1)
    2 domains: (1) beta-sandwich: 8 strands in 2 sheets; (2) alpha-helical bundle
    1. Heat shock protein 70kD (HSP70), C-terminal, substrate-binding fragment (1)
21. HAD-like (1)
    2 domains: (1) alpha/beta with a Rossmann-fold topology, (2) 4-helical bundle
    1. HAD-like (3)
22. Dehydroquinate synthase, DHQS (1)
    2 domains: (1) alpha/beta of a Rossmann-fold topology, binds NAD (2) multihelical array
    1. Dehydroquinate synthase, DHQS (1)
23. Firefly luciferase-like (1)
    4 domains: (1&2) duplication: share the same alpha/beta fold; (3) beta-barrel; (4) alpha+beta
    1. Firefly luciferase-like (1)
24. Ribosomal protein L1 (1)
    2 domains: (1) alpha+beta; (2) alpha/beta (interrupts domain 1)
    1. Ribosomal protein L1 (1)
25. Neuronal Sec1, NSec1 (1)
    3 domains: (1 and 2) alpha+beta; (3) mostly alpha, inserted in domain 2
    1. Neuronal Sec1, NSec1 (1)
26. Hybrid cluster protein (prismane protein) (1)
    4 domains: (1 and 2) spectrin repeat-like 3-helical bundles; (3 and 4) alpha/beta: Rossmann-fold topology
    1. Hybrid cluster protein (prismane protein) (1)
27. Upper collar protein gp10 (connector protein) (1)
    2 domains: (1) alpha-helical bundle; (2) beta-barrel (n=5, S=8)
    1. Upper collar protein gp10 (connector protein) (1)
28. BTV inner layer core protein vp3 (1)
    large protein without apparent domain division; has a number of all-alpha regions and one all beta domain near the C-end
    1. BTV inner layer core protein vp3 (1)