Class: Alpha and beta proteins (a/b)

Mainly parallel beta sheets (beta-alpha-beta units)

Lineage:

1. Root: scop
2. Class: Alpha and beta proteins (a/b)
   Mainly parallel beta sheets (beta-alpha-beta units)

Folds:

1. TIM beta/alpha-barrel (23)
   contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
   the first six superfamilies have similar phosphate-binding sites
2. NAD(P)-binding Rossmann-fold domains (1)
   core: 3 layers, a/b/a; parallel beta-sheet of 6 strands, order 321456
   The nucleotide-binding modes of this and the next two folds/superfamilies are similar
3. FAD/NAD(P)-binding domain (1)
   core: 3 layers, b/b/a; central parallel beta-sheet of 5 strands, order 32145; top antiparallel beta-sheet of 3 strands, meander
4. Nucleotide-binding domain (1)
   3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
5. N-terminal domain of MurD (UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase) (1)
   3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; incomplete Rossmann-like fold; binds UDP group
6. Cellulases (1)
   variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=7, S=8; strand order 1234567
7. PFL-like glycyl radical enzymes (1)
   contains: barrel, closed; n=10, S=10; accommodates a hairpin loop inside the barrel
8. The "swivelling" beta/beta/alpha domain (5)
   3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology
   this domain is thought to be mobile in all proteins known to contain it
9. Barstar-like (2)
   2 layers, a/b; parallel beta-sheet of 3 strands, order 123
10. Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) (2)
    2 curved layers, a/b; parallel beta-sheet; order 1234...N
11. Outer arm dynein light chain 1 (1)
    (beta-beta-alpha)n superhelix
12. Ribosomal proteins L15p and L18e (1)
    core: three turns of irregular (beta-beta-alpha)n superhelix
13. SpoIIaa-like (2)
    core: 4 turns of a (beta-alpha)n superhelix
14. ClpP/crotonase (1)
    core: 4 turns of (beta-beta-alpha)n superhelix
15. BRCT domain (1)
    3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
16. beta-subunit of the lumazine synthase/riboflavin synthase complex (1)
    3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
17. Caspase-like (1)
    3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
18. DNA glycosylase (1)
    3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
19. Catalytic domain of malonyl-CoA ACP transacylase (1)
    3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
20. Initiation factor IF2/eIF5b, domain 3 (1)
    3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
21. Ribosomal protein L13 (1)
    3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 3214
22. Ribosomal protein L4 (1)
    3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 1423
23. Flavodoxin-like (16)
    3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345
24. Methylglyoxal synthase-like (1)
    3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
25. Ferredoxin reductase-like, C-terminal NADP-linked domain (1)
    3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
26. Adenine nucleotide alpha hydrolase-like (3)
    core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145
27. Pyrimidine nucleoside phosphorylase central domain (1)
    3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
28. N-terminal domain of DNA photolyase (1)
    3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
29. ETFP adenine nucleotide-binding domain-like (1)
    3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 32145
30. Biotin carboxylase N-terminal domain-like (1)
    3 layers: a/b/a; parallel or mixed beta-sheet of 4 to 6 strands
    possible rudiment form of Rossmann-fold domain
31. DHS-like NAD/FAD-binding domain (1)
    3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; Rossmann-like
32. Tubulin, GTPase domain (1)
    3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
33. Cysteine hydrolase (1)
    3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
34. Halotolerance protein Hal3 (1)
    3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
35. Glucosamine 6-phosphate deaminase/isomerase (1)
    3 layers: a/b/a; parallel beta-sheet of 6 strands, order 324561
36. Thiamin diphosphate-binding fold (THDP-binding) (1)
    3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213465
37. P-loop containing nucleotide triphosphate hydrolases (1)
    3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes
38. Fructose permease, subunit IIb (1)
    3 layers: a/b/a, parallel beta-sheet of 6 strands, order 324156
39. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) (1)
    3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567
40. Methylesterase CheB, C-terminal domain (1)
    3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3421567
41. Subtilisin-like (1)
    3 layers: a/b/a, parallel beta-sheet of 7 strands, order 2314567; left-handed crossover connection between strands 2 & 3
42. Arginase/deacetylase (1)
    3 layers: a/b/a, parallel beta-sheet of 8 strands, order 21387456
43. CoA-dependent acyltransferases (1)
    core: 2 layers, a/b; mixed beta-sheet of 6 strands, order 324561; strands 3 & 6 are antiparallel to the rest
44. Phosphotyrosine protein phosphatases I-like (2)
    3 layers: a/b/a; parallel beta-sheet of 4 strands, order 2134
45. (Phosphotyrosine protein) phosphatases II (1)
    core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1432
46. Rhodanese/Cell cycle control phosphatase (1)
    3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
47. Thioredoxin fold (3)
    core: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 is antiparallel to the rest
48. Transketolase C-terminal domain-like (1)
    3 layers: a/b/a; mixed beta-sheet of 5 strands, order 13245, strand 1 is antiparallel to the rest
49. Pyruvate kinase C-terminal domain-like (2)
    3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145, strand 5 is antiparallel to the rest
50. Leucine aminopeptidase, N-terminal domain (1)
    3 layers: a/b/a; mixed beta-sheet of 5 strands, order 23145; strand 2 is antiparallel to the rest
51. Anticodon-binding domain-like (4)
    3 layers: a/b/a; mixed beta-sheet of five strands, order 21345; strand 4 is antiparallel to the rest
52. Restriction endonuclease-like (3)
    core: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, in some families, 5 are antiparallel to the rest
53. Resolvase-like (2)
    Core: 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest
54. IIA domain of mannose transporter, IIA-Man (1)
    3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest
55. Ribonuclease H-like motif (7)
    3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
56. Phosphorylase/hydrolase-like (6)
    core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops
57. Molybdenumm cofactor biosynthesis protein MogA (1)
    3 layers: a/b/a; mixed beta-sheet of 5 strands; order: 21354, strand 5 is antiparallel to the rest; permutation of the Phosphorylase/hydrolase-like fold
58. Aminoacid dehydrogenase-like, N-terminal domain (1)
    3 layers: a/b/a; mixed beta-sheet of 5 strands; 12435, strand 2 is antiparallel to the rest
59. Glutamate ligase domain (1)
    3 layers: a/b/a; mixed beta-sheet of 6 strands, order 126345; strand 1 is antiparallel to the rest
60. Phosphoglycerate mutase-like (1)
    core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 324156; strand 5 is antiparallel to the rest
61. PRTase-like (1)
    core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
62. Integrin A (or I) domain (1)
    core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
63. Glutaconate-CoA transferase subunits (1)
    core: 3 layers: a/b/a; parallel or mixed b-sheet of 6 strands, order 432156; part of sheet is folded upon itself and forms a barrel-like structure
64. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III (1)
    3 layers: a/b/a; mixed beta-sheet of 6 strands, order 231456; strand 3 is antiparallel to the rest
65. Formyltransferase (1)
    3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest
66. S-adenosyl-L-methionine-dependent methyltransferases (1)
    core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest
67. PLP-dependent transferases (1)
    main domain: 3 layers: a/b/a, mixed beta-sheet of 7 strands, order 3245671; strand 7 is antiparallel to the rest
68. Nucleotide-diphospho-sugar transferases (1)
    3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214657; strand 6 is antiparallel to the rest
69. alpha/beta-Hydrolases (1)
    core: 3 layers, a/b/a; mixed beta-sheet of 8 strands, order 12435678, strand 2 is antiparallel to the rest
70. Nucleoside hydrolase (1)
    core: 3 layers, a/b/a ; mixed beta-sheet of 8 strands, order 32145687; strand 7 is antiparallel to the rest
71. Dihydrofolate reductases (1)
    3 layers: a/b/a; mixed beta-sheet of 8 strands, order 34251687; strand 8 is antiparallel to the rest
72. Ribokinase-like (2)
    core: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest
    potential superfamily: members of this fold have similar functions but different ATP-binding sites
73. Carbamate kinase-like (1)
    3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 34215786; strand 8 is antiparallel to the rest
74. Class II aldolase (1)
    3 layers: a/b/a; mixed (mostly antiparallel) beta-sheet of 9 strands, order 432159876; left-handed crossover between strands 4 and 5
75. Cytosolic phospholipase A2 catalytic domain (1)
    3 layers: a/b/a; mixed beta-sheet of 9 strands, order 654321789; strands 4, 6 and 8 are antiparallel to the rest
76. Phosphatase/sulphatase (1)
    3 layers: a/b/a; mixed beta-sheet of 10 strands, order 564371892A, (A=10) strand 9 is antiparallel to the rest
77. Isocitrate & isopropylmalate dehydrogenases (1)
    consists of two intertwined (sub)domains related by pseudodyad; duplication
    3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213A945867 (A=10); strands from 5 to 9 are antiparallel to the rest
78. ATC-like (2)
    consists of two similar domains related by pseudodyad; duplication
    core: 3 layers, a/b/a, parallel beta-sheet of 4 strands, order 2134
79. Tryptophan synthase beta subunit-like PLP-dependent enzymes (1)
    consists of two similar domains related by pseudodyad; duplication
    core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 3214
80. SIS domain (1)
    consists of two similar domains related by pseudodyad; duplication
    3 layers: a/b/a; parallel beta-sheet of 5 strands, order 21345
81. Formate dehydrogenase/DMSO reductase, domains 1-3 (1)
    contains of two similar intertwined domains related by pseudodyad; duplication
    core: 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
82. Aldehyde reductase (dehydrogenase), ALDH (1)
    consists of two similar domains with 3 layers (a/b/a) each; duplication
    core: parallel beta-sheet of 5 strands, order 32145
83. Aconitase, first 3 domains (1)
    consists of three similar domains with 3 layers (a/b/a) each; duplication
    core: parallel beta-sheet of 5 strands, order 32145
84. Phosphoglucomutase, first 3 domains (1)
    consists of three similar domains with 3 layers (a/b/a) each; duplication
    core: mixed beta-sheet of 4 strands, order 2134, strand 4 is antiparallel to the rest
85. L-fucose isomerase, N-terminal and second domains (1)
    consists of two domains of similar topology, 3 layers (a/b/a) each
    Domain 1 (1-173) has parallel beta-sheet of 5 strands, order 21345
    Domain 2 (174-355) has parallel beta-sheet of 4 strands, order 2134
86. Phosphoglycerate kinase (1)
    consists of two non-similar domains, 3 layers (a/b/a) each
    Domain 1 has parallel beta-sheet of 6 strands, order 342156
    Domain 2 has parallel beta-sheet of 6 strands, order 321456
87. UDP-Glycosyltransferase/glycogen phosphorylase (1)
    consists of two non-similar domains with 3 layers (a/b/a) each
    domain 1: parallel beta-sheet of 7 strands, order 3214567
    domain 2: parallel beta-sheet of 6 strands, order 321456
88. Glutaminase/Asparaginase (1)
    consists of two non-similar alpha/beta domains, 3 layers (a/b/a) each
    Domain 1 has mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest; left-handed crossover connection between strands 4 and 5
    Domain 2 has parallel beta-sheet of 4 strands, order 1234
89. Phosphofructokinase (1)
    consists of two non-similar domains, 3 layers (a/b/a) each
    Domain 1 has mixed sheet of 7 strands, order 3214567; strands 3 & 7 are antiparallel to the rest
    Domain 2 has parallel sheet of 4 strands, order 2314
90. Cobalt precorrin-4 methyltransferase CbiF (1)
    consists of two non-similar domains
    Domain 1 has antiparallel sheet of 5 strands, order 32415
    Domain 2 has mixed sheet of 5 strands, order 12534; strands 4 & 5 are antiparallel to the rest
91. Phosphoenolpyruvate carboxykinase (ATP-oxaloacetate carboxy-liase) (1)
    consists of two alpa/beta domains
    duplication: the domains share an unusual fold of 2 helices and 6-stranded mixed sheet; beta(2)-alpha-beta(4)-alpha; order 312465, strands 1 and 5 are antiparallel to the rest
92. Chelatase-like (2)
    duplication: tandem repeat of two domains; 3 layers (a/b/a); parallel beta-sheet of 4 strands, order 2134
93. Periplasmic binding protein-like I (1)
    consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
    parallel beta-sheet of 6 strands, order 213456
94. Periplasmic binding protein-like II (1)
    consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
    mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest
95. Thiolase-like (1)
    consists of two similar domains related by pseudodyad; duplication
    3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32451; strands 1 & 5 are antiparallel to the rest
96. Fe-only hydrogenase (1)
    consist of two intertwined domains; contains partial duplication
97. Cytidine deaminase (1)
    consists of two very similar domains with 3 layers (a/b/a)each; duplication
    mixed beta-sheet of 4 strands, order 2134; strand 2 is antiparallel to the rest