SCOPe Funding Alert: SCOPe support from the NIH ended in April 2016. John-Marc Chandonia is the primary maintainer and has continued to develop SCOPe using vacation time. Three proposals to the NIH for continued funding have been unsuccessful. If our current NIH proposal is not funded, SCOPe will shut down permanently in Summer 2017 as Dr. Chandonia will need to seek a new position.

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

  1. Root: SCOPe 2.05
  2. 1949014Class e: Multi-domain proteins (alpha and beta) [56572] (68 folds)

Folds:

  1. 1949015e.1: Serpins [56573] (1 superfamily)
    contains a cluster of helices and a beta-sandwich
  2. 1949276e.2: Replication terminator protein (Tus) [56595] (1 superfamily)
    contains a cluster of helices and a beta-sandwich
  3. 1949285e.3: beta-lactamase/transpeptidase-like [56600] (1 superfamily)
    contains a cluster of helices and an alpha+beta sandwich
  4. 1950591e.5: Heme-dependent catalase-like [56633] (1 superfamily)
    contains an (8,10) beta-barrel and an all-alpha domain
  5. 1950935e.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. 1951217e.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. 1951566e.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. 1953196e.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. 1953229e.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. 1953291e.12: DNA topoisomerase IV, alpha subunit [56725] (1 superfamily)
    2 domains: (1) toprim alpha/beta; (2) "winged helix"-like
  11. 1953298e.13: DNA primase core [56730] (1 superfamily)
    2 domains: (1) alpha+beta; (2) toprim alpha/beta
  12. 1953326e.15: Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56740] (1 superfamily)
    2 domains: alpha+beta and all-beta
  13. 1953348e.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. 1953511e.18: HydB/Nqo4-like [56761] (1 superfamily)
    3 domains: (1) all-alpha; (2&3) alpha+beta
  15. 1953691e.19: HydA/Nqo6-like [56769] (1 superfamily)
    2 domains: (1) alpa/beta; (2) Fe-S cluster-bound
  16. 1953870e.22: Dehydroquinate synthase-like [56795] (1 superfamily)
    2 domains: (1) alpha/beta of a Rossmann-fold topology, binds NAD (2) multihelical array
  17. 1953994e.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. 1954161e.24: Ribosomal protein L1 [56807] (1 superfamily)
    2 domains: (1) alpha+beta; (2) alpha/beta (interrupts domain 1)
  19. 1954192e.25: Sec1/munc18-like (SM) proteins [56814] (1 superfamily)
    3 domains: (1 and 2) alpha+beta; (3) mostly alpha, inserted in domain 2
  20. 1954209e.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. 1954300e.27: Upper collar protein gp10 (connector protein) [56825] (1 superfamily)
    2 domains: (1) alpha-helical bundle; (2) beta-barrel (n=5, S=8)
  22. 1954344e.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. 1954356e.29: beta and beta-prime subunits of DNA dependent RNA-polymerase [64483] (1 superfamily)
    Multidomain subunits of complex domain organization
  24. 1954526e.32: Phase 1 flagellin [64517] (1 superfamily)
    3 domains: (1) alpha-helical bundle; (2&3) complex all-beta folds
  25. 1954533e.34: NSP3 homodimer [69902] (1 superfamily)
    2 domains: (1) all-alpha, (2) alpha+beta; asymmetric homodimer with each domain intertwining with its counterpart
  26. 1954546e.35: Membrane penetration protein mu1 [69907] (1 superfamily)
    4 domains: three intertwined predominately alpha domains and one jelly-roll beta-sandwich
  27. 1954554e.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. 1954570e.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. 1954595e.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. 1954610e.40: Cullin homology domain [75631] (1 superfamily)
    3 domains: (1) 4-helical bundle; (2) alpha+beta; (3) "winged helix"-like
  31. 1954623e.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. 1954647e.42: L-A virus major coat protein [82855] (1 superfamily)
    large protein without apparent domain division
  33. 1954654e.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. 1954689e.44: 2-methylcitrate dehydratase PrpD [103377] (1 superfamily)
    consists of an all-alpha and alpha+beta domains
  35. 1954696e.45: Antivirulence factor [103382] (1 superfamily)
    contains a helical bundle with a buried helix and an alpha+beta insert domain
  36. 1954705e.46: Virulence-associated V antigen [103387] (1 superfamily)
    consists of an all-alpha and alpha+beta domains connected by antiparallel coiled coil
  37. 1954714e.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. 1954724e.48: Major capsid protein VP5 [103416] (1 superfamily)
    large protein without apparent domain division
  39. 1954731e.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. 1954754e.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. 1954769e.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. 1954794e.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. 1954864e.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. 1954878e.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. 1954884e.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. 1954893e.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. 1954900e.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. 1954906e.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. 1954913e.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. 1954920e.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. 1954942e.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. 1954948e.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. 1954972e.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. 1954982e.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. 1954989e.65: VPA0735-like [160934] (1 superfamily)
    consists of a cluster of helices and two beta-sandwich domains of similar topology; probable duplication
  56. 1955000e.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. 1955006e.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. 1955013e.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. 1955020e.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. 1955034e.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. 1955049e.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. 1955055e.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. 1955062e.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. 1955069e.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. 1955078e.75: Flu NP-like [161002] (1 superfamily)
    consists of alpha+beta and all-alpha domains; biological unit is a trimer
  66. 1955118e.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. 1955157e.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. 1955170e.78: DNA gyrase B, C-terminal domain-like [254116] (1 superfamily)
    2 domains: (1) toprim alpha/beta; (2) alpha+beta "tail" domain

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

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