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

  1. Root: SCOPe 2.06
  2. 2217451Class e: Multi-domain proteins (alpha and beta) [56572] (69 folds)

Folds:

  1. 2217452e.1: Serpins [56573] (1 superfamily)
    contains a cluster of helices and a beta-sandwich
  2. 2217731e.2: Replication terminator protein (Tus) [56595] (1 superfamily)
    contains a cluster of helices and a beta-sandwich
  3. 2217740e.3: beta-lactamase/transpeptidase-like [56600] (1 superfamily)
    contains a cluster of helices and an alpha+beta sandwich
  4. 2219093e.5: Heme-dependent catalase-like [56633] (1 superfamily)
    contains an (8,10) beta-barrel and an all-alpha domain
  5. 2219439e.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. 2219721e.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. 2220074e.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. 2221735e.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. 2221768e.11: Type II DNA topoisomerase C-terminal domain-like [56718] (1 superfamily)
    4 domains: (1) toprim alpha/beta; (2) "winged helix"-like; (3) alpha+beta; (4) all-alpha
  10. 2221837e.12: DNA topoisomerase IV, alpha subunit [56725] (1 superfamily)
    2 domains: (1) toprim alpha/beta; (2) "winged helix"-like
  11. 2221844e.13: DNA primase core [56730] (1 superfamily)
    2 domains: (1) alpha+beta; (2) toprim alpha/beta
  12. 2221872e.15: Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56740] (1 superfamily)
    2 domains: alpha+beta and all-beta
  13. 2221894e.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. 2222059e.18: HydB/Nqo4-like [56761] (1 superfamily)
    3 domains: (1) all-alpha; (2&3) alpha+beta
  15. 2222239e.19: HydA/Nqo6-like [56769] (1 superfamily)
    2 domains: (1) alpa/beta; (2) Fe-S cluster-bound
  16. 2222418e.22: Dehydroquinate synthase-like [56795] (1 superfamily)
    2 domains: (1) alpha/beta of a Rossmann-fold topology, binds NAD (2) multihelical array
  17. 2222543e.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. 2222730e.24: Ribosomal protein L1 [56807] (1 superfamily)
    2 domains: (1) alpha+beta; (2) alpha/beta (interrupts domain 1)
  19. 2222761e.25: Sec1/munc18-like (SM) proteins [56814] (1 superfamily)
    3 domains: (1 and 2) alpha+beta; (3) mostly alpha, inserted in domain 2
  20. 2222779e.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. 2222872e.27: Upper collar protein gp10 (connector protein) [56825] (1 superfamily)
    2 domains: (1) alpha-helical bundle; (2) beta-barrel (n=5, S=8)
  22. 2222916e.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. 2222928e.29: beta and beta-prime subunits of DNA dependent RNA-polymerase [64483] (1 superfamily)
    Multidomain subunits of complex domain organization
  24. 2223098e.32: Phase 1 flagellin [64517] (1 superfamily)
    3 domains: (1) alpha-helical bundle; (2&3) complex all-beta folds
  25. 2223105e.34: NSP3 homodimer [69902] (1 superfamily)
    2 domains: (1) all-alpha, (2) alpha+beta; asymmetric homodimer with each domain intertwining with its counterpart
  26. 2223118e.35: Membrane penetration protein mu1 [69907] (1 superfamily)
    4 domains: three intertwined predominately alpha domains and one jelly-roll beta-sandwich
  27. 2223126e.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. 2223142e.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. 2223167e.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. 2223182e.40: Cullin homology domain [75631] (1 superfamily)
    3 domains: (1) 4-helical bundle; (2) alpha+beta; (3) "winged helix"-like
  31. 2223195e.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. 2223219e.42: L-A virus major coat protein [82855] (1 superfamily)
    large protein without apparent domain division
  33. 2223226e.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. 2223261e.44: 2-methylcitrate dehydratase PrpD [103377] (1 superfamily)
    consists of an all-alpha and alpha+beta domains
  35. 2223268e.45: Antivirulence factor [103382] (1 superfamily)
    contains a helical bundle with a buried helix and an alpha+beta insert domain
  36. 2223277e.46: Virulence-associated V antigen [103387] (1 superfamily)
    consists of an all-alpha and alpha+beta domains connected by antiparallel coiled coil
  37. 2223286e.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. 2223296e.48: Major capsid protein VP5 [103416] (1 superfamily)
    large protein without apparent domain division
  39. 2223303e.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. 2223326e.50: AF1104-like [111320] (1 superfamily)
    2 domains; d1: [all-alpha; 3-helical bundle, similar to the immunoglobulin/albumin-binding domain-like fold (46996)]; d2: [alpha/beta; 3 layers, a/b/a; 6-stranded mixed beta-sheet, order: 321456, strand 6 is antiparallel to the rest]
  41. 2223341e.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 (51735); d3: alpha+beta of the glutamine synthetase/guanido kinase fold (55930); d1 and d3 form a single beta-sheet
  42. 2223366e.52: NAD kinase/diacylglycerol kinase-like [111330] (1 superfamily)
    2 domains: d1 [alpha/beta; related to the PFK N-terminal domain (53784)]; d2 [all-beta; atypical beta-sandwich made of 4 structural repeats of beta(3) unit]
  43. 2223436e.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 (50474)
  44. 2223450e.54: CbiD-like [111341] (1 superfamily)
    2 domains; (1) alpha+beta (res 1-192), a circularly permuted rS5 domain 2-like fold (54210); (2) alpha/beta with parallel beta-sheet of 4 strands, order 2134
  45. 2223456e.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; (52592))
  46. 2223465e.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 (50412), provides homodimerisation interface]; d2: [alpha+beta (disordered)]
  47. 2223472e.57: Vacuolar ATP synthase subunit C [118202] (1 superfamily)
    2 alpha+beta (sub)domains [each has a ferredoxin-like fold; (54861)], connected with 3-helical bundle; duplication: two repeats of beta-alpha-beta-[alpha coiled-coil]-beta-alpha-beta motif
  48. 2223479e.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]
  49. 2223486e.59: FdhE-like [144019] (1 superfamily)
    consists on the N-terminal five-helical bundle, a tandem repeat of two rubredoxin-like domains and the C-terminal helix packed together
  50. 2223493e.60: Thermophilic metalloprotease-like [144051] (1 superfamily)
    consists of two domains; d1: alpha/beta (3 layers, a/b/a; parralel beta-sheet, order 2134); d2: pseudo beta-barrel capped by helices
  51. 2223515e.61: ImpE-like [144058] (1 superfamily)
    consists of two domains; d1: right-handed superhelix of five helices; d2: pseudo beta-barrel containing structurally similar part to the "Histone-like" proteins from archaea (54161)
  52. 2223521e.62: Heme iron utilization protein-like [144063] (1 superfamily)
    2 domains; d1 - 3-helical bundle similar to the homeodomain-like fold; d2 - 6-stranded beta-barrel capped by two helices at one end, similar topology to the PH-like fold
  53. 2223546e.63: E2F-DP heterodimerization region [144073] (1 superfamily)
    heterodimeric fold with the N-terminal long helices of both chains forming a parallel coiled coil and their C-terminal folded beta-hairpins interlocking together in a beta-sandwich
  54. 2223556e.64: FlhC-like [160929] (1 superfamily)
    3 domains; d1 & d2 are similar three-helical bundles, with d1 containing an HTH motif; d3: zinc finger of a rubredoxin-like fold
  55. 2223563e.65: VPA0735-like [160934] (1 superfamily)
    consists of a cluster of helices and two beta-sandwich domains of similar topology; probable duplication
  56. 2223574e.66: Api92-like [160939] (1 superfamily)
    2 domains; d1: [alpha+beta with similarity to ferredoxin-like fold]; d2: [6 helices, bundle, one buried central helix], inserted into d1
  57. 2223580e.67: PH0156-like [160944] (1 superfamily)
    2 (sub)domains; d1: [alpha/beta with central mixed beta-sheet, order: 23415876, similarity to the G protein but no P-loop]; d2: [all-alpha, 5 helices, provides dimerization interface]
  58. 2223587e.68: YacF-like [160949] (1 superfamily)
    2 domains; d1: kinked four-helical bundle, inserted in d2: beta-sandwich of 7 strands in two sheets
  59. 2223594e.69: Poly(A) polymerase catalytic subunit-like [160956] (1 superfamily)
    3 domains; d1: all-alpha, contains HhH motif; d2: alpha+beta of nucleotidyltransferase fold (81302); d3: [alpha+beta; beta(3)-alpha-beta(3)-alpha(2); 3 layers: a/b/a; mixed beta-sheet of 6 strands, order 123654, strands 2 and 5 are antiparallel to the rest
  60. 2223608e.70: MalF N-terminal region-like [160963] (1 superfamily)
    consists of 3 N-terminal transmembrane helices, an alpha+beta linker domain and a beta-barrel (n=7; S=8) with one overside loop
  61. 2223623e.71: AF1531-like [160974] (1 superfamily)
    2 domains; d1: incomplete barrel similar to the OB-fold domain of ribosomal L2 protein, d2: six helices, array
  62. 2223629e.72: SSO1389-like [160979] (1 superfamily)
    2 domains; d1: [alpha/beta, central parallel beta-sheet of 6 strands, order 321456, Rossmann-like]; d2: [alpha+beta, cluster of helices and a small 4-stranded beta-sheet]
  63. 2223636e.73: CV3147-like [160990] (1 superfamily)
    2 domains; d1: [alpha/beta; 3 layers, a/b/a, mixed beta-sheet of 8 strands, order 12543876, strands 1, 7 and 8 are antiparallel to the rest]; d2: [pseudo beta-barrel of 6 strands, meander]
  64. 2223643e.74: HI0933 insert domain-like [160995] (1 superfamily)
    2 domains; d1: barrel, closed, n=6, S=12, greek-key; d2: four-helical bundle, inserted in d1
  65. 2223652e.75: Flu NP-like [161002] (1 superfamily)
    consists of alpha+beta and all-alpha domains; biological unit is a trimer
  66. 2223692e.76: Viral glycoprotein ectodomain-like [161007] (1 superfamily)
    complex fold; contains three rigid, mostly-beta domains and an alpha-helical region, acting as a conformatiomal switch ("fusion stalk")
  67. 2223731e.77: PA C-terminal domain-like [254112] (1 superfamily)
    Pfam PF00603; PubMed 18615018; complex fold with N-terminal a+b domain and C-terminal all-a domain
  68. 2223744e.78: DNA gyrase B, C-terminal domain-like [254116] (1 superfamily)
    2 domains: (1) toprim alpha/beta; (2) alpha+beta "tail" domain
  69. 2223766e.79: CRISPR associated protein Cas1-like [310568] (1 superfamily)
    2 domains: N-terminal domain consists of 10 strands and 2 helices; C-terminal domain comprises 10 helices

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

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