Lineage for Class e: Multi-domain proteins (alpha and beta)

  1. Root: SCOP 1.71
  2. 617324Class e: Multi-domain proteins (alpha and beta) [56572] (48 folds)

Folds:

  1. 617325e.1: Serpins [56573] (1 superfamily)
    contains a cluster of helices and a beta-sandwich
  2. 617463e.2: Replication terminator protein (Tus) [56595] (1 superfamily)
    contains a cluster of helices and a beta-sandwich
  3. 617469e.3: beta-lactamase/transpeptidase-like [56600] (1 superfamily)
    contains a cluster of helices and an alpha+beta sandwich
  4. 617815e.5: Heme-dependent catalase-like [56633] (1 superfamily)
    contains an (8,10) beta-barrel and an all-alpha domain
  5. 617949e.6: Acyl-CoA dehydrogenase NM domain-like [56644] (1 superfamily)
    2 domains: (1) all-alpha: 5 helices; (2) contains an open beta-sheet barrel: n*=5, S*=8; complex topology
  6. 618023e.7: Carbohydrate phosphatase [56654] (1 superfamily)
    N-terminal domain is an alpha+beta, C-terminal domain is an alpha/beta with mixed beta-sheet
  7. 618192e.8: DNA/RNA polymerases [56671] (1 superfamily)
    divided into morphological domains including "palm", "thumb" and "fingers"; the catalytic "palm" domain is conserved to all members
  8. 618660e.10: Prokaryotic type I DNA topoisomerase [56711] (1 superfamily)
    4 domains: (1) Toprim alpha/beta; (2&4) "winged helix"-like; (3) barrel: n=6, S=8
  9. 618688e.11: Type II DNA topoisomerase [56718] (1 superfamily)
    4 domains: (1) toprim alpha/beta; (2) "winged helix"-like; (3) alpha+beta; (4) all-alpha
  10. 618698e.12: DNA topoisomerase IV, alpha subunit [56725] (1 superfamily)
    2 domains: (1) toprim alpha/beta; (2) "winged helix"-like
  11. 618705e.13: DNA primase core [56730] (1 superfamily)
    2 domains: (1) alpha+beta; (2) toprim alpha/beta
  12. 618729e.15: Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56740] (1 superfamily)
    2 domains: alpha+beta and all-beta
  13. 618747e.17: D-aminoacid aminotransferase-like PLP-dependent enzymes [56751] (1 superfamily)
    2 domains: (1) alpha+beta: beta3-alpha2-beta2; (2) alpha/beta, a part of its mixed sheet forms barrel: n=6, S=8
  14. 618805e.18: Nickel-iron hydrogenase, large subunit [56761] (1 superfamily)
    3 domains: (1) all-alpha; (2&3) alpha+beta
  15. 618837e.19: Nickel-iron hydrogenase, small subunit [56769] (1 superfamily)
    2 domains: (1) alpa/beta; (2) Fe-S cluster-bound
  16. 618869e.22: Dehydroquinate synthase-like [56795] (1 superfamily)
    2 domains: (1) alpha/beta of a Rossmann-fold topology, binds NAD (2) multihelical array
  17. 618928e.23: Acetyl-CoA synthetase-like [56800] (1 superfamily)
    4 domains: (1&2) duplication: share the same alpha/beta fold; (3) beta-barrel; (4) alpha+beta
  18. 618964e.24: Ribosomal protein L1 [56807] (1 superfamily)
    2 domains: (1) alpha+beta; (2) alpha/beta (interrupts domain 1)
  19. 618978e.25: Sec1/munc18-like (SM) proteins [56814] (1 superfamily)
    3 domains: (1 and 2) alpha+beta; (3) mostly alpha, inserted in domain 2
  20. 618992e.26: Prismane protein-like [56820] (1 superfamily)
    3 domains: (1) spectrin repeat-like 3-helical bundle; (2 and 3) alpha/beta: Rossmann-fold topology
  21. 619045e.27: Upper collar protein gp10 (connector protein) [56825] (1 superfamily)
    2 domains: (1) alpha-helical bundle; (2) beta-barrel (n=5, S=8)
  22. 619089e.28: Reovirus inner layer core protein p3 [56830] (1 superfamily)
    large protein without apparent domain division; has a number of all-alpha regions and one all beta domain near the C-end
  23. 619101e.29: beta and beta-prime subunits of DNA dependent RNA-polymerase [64483] (1 superfamily)
    Multidomain subunits of complex domain organization
  24. 619143e.32: Phase 1 flagellin [64517] (1 superfamily)
    3 domains: (1) alpha-helical bundle; (2&3) complex all-beta folds
  25. 619150e.34: NSP3 homodimer [69902] (1 superfamily)
    2 domains: (1) all-alpha, (2) alpha+beta; asymmetric homodimer with each domain intertwining with its counterpart
  26. 619163e.35: Membrane penetration protein mu1 [69907] (1 superfamily)
    4 domains: three intertwined predominately alpha domains and one jelly-roll beta-sandwich
  27. 619171e.37: Siroheme synthase middle domains-like [75614] (1 superfamily)
    2 domains: (1) alpha+beta, 2 layers; (2) 3/4-helical bundle, right-handed twist, left-handed superhelix
  28. 619187e.38: Release factor [75619] (1 superfamily)
    4 domains: (1) 3-helical bundle; (2) alpha+beta of ferredoxin-like fold (3 and 4) alpha+beta of dsRDB-like fold
  29. 619198e.39: YebC-like [75624] (1 superfamily)
    3 domains: (1) 3-helical bundle; (2 and 3 ) alpha+beta of different folds: domain 3 has a ferredoxin-like fold and is inserted in domain 2
  30. 619210e.40: Cullin homology domain [75631] (1 superfamily)
    3 domains: (1) 4-helical bundle; (2) alpha+beta; (3) "winged helix"-like
  31. 619218e.41: Adenylylcyclase toxin (the edema factor) [81299] (1 superfamily)
    3 domains: (1&2) alpha+beta, with domain 2 being inserted in domain 1; (3) all-alpha
  32. 619242e.42: L-A virus major coat protein [82855] (1 superfamily)
    large protein without apparent domain division
  33. 619249e.43: Subunits of heterodimeric actin filament capping protein Capz [90095] (1 superfamily)
    3 domains: (1) protozoan pheromone-like alpha-helical bundle; (2) rubredoxin-like domain lacking metal-binding site; (3) alpha+beta heterodimerisation domain: alpha-beta(5)-alpha
  34. 619261e.44: 2-methylcitrate dehydratase PrpD [103377] (1 superfamily)
    consists of an all-alpha and alpha+beta domains
  35. 619268e.45: Antivirulence factor [103382] (1 superfamily)
    contains a helical bundle with a buried helix and an alpha+beta insert domain
  36. 619274e.46: Virulence-associated V antigen [103387] (1 superfamily)
    consists of an all-alpha and alpha+beta domains connected by antiparallel coiled coil
  37. 619280e.47: 39 kda initiator binding protein, IBP39, C-terminal domains [103408] (1 superfamily)
    2 closely associated domains: (1) all-alpha, EF-hand like; (2) alpha+beta, Frataxin-like
  38. 619290e.48: Major capsid protein VP5 [103416] (1 superfamily)
    large protein without apparent domain division
  39. 619297e.49: Recombination protein RecR [111303] (1 superfamily)
    consists of three domains: alpha-helical dimerisation domain (res. 1-53) with HhH motif; 'treble cleft' C4 zinc-finger domain (54-76); and Toprim domain (76-199; segment-swapped dimer)
  40. 619306e.50: Hypothetical protein At2g17340 [111320] (1 superfamily)
    2 domains; d1: [all-alpha; 3-helical bundle, similar to the immunoglobulin/albumin-binding domain-like fold (scop_cf 46996)]; d2: [alpha/beta; 3 layers, a/b/a; 6-stranded mixed beta-sheet, order: 321456, strand 6 is antiparallel to the rest]
  41. 619312e.51: Urocanase [111325] (1 superfamily)
    3 domains; d1: alpha+beta [alpha(2)-beta(3); mixed sheet: 213]; d2: alpha/beta of the NAD(P)-binding Rossmann-fold superfamily (scop_sf 51735, most similar to scop_fa 51883 and scop_fa 51736); d3: alpha+beta of the glutamine synthetase/guanido kinase fold (scop_cf 55930); d1 and d3 form a single beta-sheet
  42. 619326e.52: NAD kinase [111330] (1 superfamily)
    2 domains: d1 [alpha/beta; related to the PFK N-terminal domain (scop_sf 53784)]; d2 [all-beta; atypical beta-sandwich made of 4 structural repeats of beta(3) unit]
  43. 619342e.53: QueA-like [111336] (1 superfamily)
    2 domains; d1 (1-64,174-335) [alpha/beta; 3 layers, a/b/a; mixed beta sheet of 9 strands, order: 219863457; strands 1, 5 and 8 are antiparallel to the rest]; d2 (65-142) [all-beta; barrel, closed (n=6, S=10); greek-key; topologically similar to the split barrel fold (scop_cf 50474)
  44. 619351e.54: CbiD-like [111341] (1 superfamily)
    2 domains; (1) alpha+beta (res 1-192), a circularly permuted rS5 domain 2-like fold (scop_cf 54210); (2) alpha/beta with parallel beta-sheet of 4 strands, order 2134
  45. 619357e.55: Rap/Ran-GAP [111346] (1 superfamily)
    consists of two domains; d1: alpha+beta (78-190; alpha-beta(4)-alpha-beta-alpha; 3 layers; antiparallel beta-sheet of 5 strands; order 51234); d2: alpha/beta similar to the G-domain fold (191-381; scop_fa 52592)
  46. 619366e.56: YaeB-like [118195] (1 superfamily)
    2 domains; d1: [beta-barrel (n=6, S=10), similar to the Reductase/isomerase/elongation factor common domain fold (scop_cf 50412), provides homodimerisation interface]; d2: [alpha+beta (disordered)]
  47. 619373e.57: Vacuolar ATP synthase subunit C [118202] (1 superfamily)
    2 alpha+beta (sub)domains [each has a ferredoxin-like fold; scop_cf 54861], connected with 3-helical bundle; duplication: two repeats of beta-alpha-beta-[alpha coiled-coil]-beta-alpha-beta motif
  48. 619379e.58: Viral ssDNA binding protein [118207] (1 superfamily)
    2 domains; d1: [large alpha+beta domain subdivided into the 'head', 'neck' and 'shoulders' regions; in the 'neck', there is an OB-fold interrupted by large insertions]; d2: [all-alpha, 6 helices; orthogonal array]

More info for Class e: Multi-domain proteins (alpha and beta)

Timeline for Class e: Multi-domain proteins (alpha and beta):