Structural Classification of Proteins

Class: Multi-domain proteins (alpha and beta)

: Folds consisting of two or more domains belonging to different classes

Lineage:

Root: scop
Class: Multi-domain proteins (alpha and beta) [56572]
Folds consisting of two or more domains belonging to different classes

Folds:

Serpins [56573] (1)
contains a cluster of helices and a beta-sandwich
1. Serpins [56574] (1)
  1. Serpins [56575] (17)
FdhE-like [144019] (1)
consists on the N-terminal five-helical bundle, a tandem repeat of two rubredoxin-like domains and the C-terminal helix packed together
1. FdhE-like [144020] (1)
  1. FdhE-like [144021] (1)
    Pfam 04216
Replication terminator protein (Tus) [56595] (1)
contains a cluster of helices and a beta-sandwich
1. Replication terminator protein (Tus) [56596] (1)
  1. Replication terminator protein (Tus) [56597] (1)
2-methylcitrate dehydratase PrpD [103377] (1)
consists of an all-alpha and alpha+beta domains
1. 2-methylcitrate dehydratase PrpD [103378] (1)
  1. 2-methylcitrate dehydratase PrpD [103379] (1)
Antivirulence factor [103382] (1)
contains a helical bundle with a buried helix and an alpha+beta insert domain
1. Antivirulence factor [103383] (1)
  1. Antivirulence factor [103384] (1)
Virulence-associated V antigen [103387] (1)
consists of an all-alpha and alpha+beta domains connected by antiparallel coiled coil
1. Virulence-associated V antigen [103388] (1)
  1. Virulence-associated V antigen [103389] (1)
Heme-dependent catalase-like [56633] (1)
contains an (8,10) beta-barrel and an all-alpha domain
1. Heme-dependent catalase-like [56634] (2)
  1. Heme-dependent catalases [56635] (9)
  2. Allene oxide synthase [118183] (1)
Acyl-CoA dehydrogenase NM domain-like [56644] (1)
2 domains: (1) all-alpha: 5 helices; (2) contains an open beta-sheet barrel: n*=5, S*=8; complex topology
1. Acyl-CoA dehydrogenase NM domain-like [56645] (2)
  flavoprotein: binds FAD; constituent families differ in the numbers of C-terminal domains (four-helical bundles)
  1. Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains [56646] (12)
  2. acyl-CoA oxidase N-terminal domains [75600] (2)
Carbohydrate phosphatase [56654] (1)
N-terminal domain is an alpha+beta, C-terminal domain is an alpha/beta with mixed beta-sheet
1. Carbohydrate phosphatase [56655] (2)
  1. Inositol monophosphatase/fructose-1,6-bisphosphatase-like [56656] (14)
  2. GlpX-like bacterial fructose-1,6-bisphosphatase [90087] (1)
    similar to the other family in overall domain architecture but each domain has a permuted topology
DNA/RNA polymerases [56671] (1)
divided into morphological domains including "palm", "thumb" and "fingers"; the catalytic "palm" domain is conserved to all members
1. DNA/RNA polymerases [56672] (6)
  "palm" domain has a ferredoxin-like fold, related to that of an adenylyl cyclase domain
  1. DNA polymerase I [56673] (12)
  2. Lesion bypass DNA polymerase (Y-family), catalytic domain [100888] (5)
    contains a distinct 'fingers' domain possibly related to the C-terminal subdomain of hypothetical protein Ta1206 (1qw2)
  3. Reverse transcriptase [56686] (3)
  4. T7 RNA polymerase [56691] (1)
  5. RNA-dependent RNA-polymerase [56694] (10)
  6. dsRNA phage RNA-dependent RNA-polymerase [64480] (1)
beta and beta-prime subunits of DNA dependent RNA-polymerase [64483] (1)
Multidomain subunits of complex domain organization
1. beta and beta-prime subunits of DNA dependent RNA-polymerase [64484] (2)
  The catalytic site is formed by the association of two double-psi beta-barrel domains, one from each subunit
  1. RNA-polymerase beta [64485] (3)
  2. RNA-polymerase beta-prime [64490] (3)
Adenylylcyclase toxin (the edema factor) [81299] (1)
3 domains: (1&2) alpha+beta, with domain 2 being inserted in domain 1; (3) all-alpha
1. Adenylylcyclase toxin (the edema factor) [81298] (1)
  Domain 1 has topological and active site similarity to the Nucleotidyltransferases (eg. 1kny N-domain); domain 3 binds calmodulin
  1. Adenylylcyclase toxin (the edema factor) [69887] (1)
    decorated with many insertions and the C-terminal domain
Prokaryotic type I DNA topoisomerase [56711] (1)
4 domains: (1) Toprim alpha/beta; (2&4) "winged helix"-like; (3) barrel: n=6, S=8
1. Prokaryotic type I DNA topoisomerase [56712] (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
  1. Prokaryotic type I DNA topoisomerase [56713] (3)
    domain 4 contains the catalytic tyrosine residue
Type II DNA topoisomerase [56718] (1)
4 domains: (1) toprim alpha/beta; (2) "winged helix"-like; (3) alpha+beta; (4) all-alpha
1. Type II DNA topoisomerase [56719] (1)
  1. Type II DNA topoisomerase [56720] (2)
    domain 2 contains the catalytic tyrosine residue
DNA topoisomerase IV, alpha subunit [56725] (1)
2 domains: (1) toprim alpha/beta; (2) "winged helix"-like
1. DNA topoisomerase IV, alpha subunit [56726] (1)
  1. DNA topoisomerase IV, alpha subunit [56727] (1)
    domain 2 contains the catalytic tyrosine residue
DNA primase core [56730] (1)
2 domains: (1) alpha+beta; (2) toprim alpha/beta
1. DNA primase core [56731] (2)
  1. DNA primase DnaG catalytic core [56732] (1)
  2. Primase fragment of primase-helicase protein [90090] (1)
Recombination protein RecR [111303] (1)
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)
1. Recombination protein RecR [111304] (1)
  1. Recombination protein RecR [111305] (1)
    three sequential domains correspond to Pfam 00633, Pfam 02132 and Pfam 01751, respectively
Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56740] (1)
2 domains: alpha+beta and all-beta
1. Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56741] (1)
  1. Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56742] (2)
D-aminoacid aminotransferase-like PLP-dependent enzymes [56751] (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-aminoacid aminotransferase-like PLP-dependent enzymes [56752] (1)
  1. D-aminoacid aminotransferase-like PLP-dependent enzymes [56753] (5)
HydB/Nqo4-like [56761] (1)
3 domains: (1) all-alpha; (2&3) alpha+beta
1. HydB/Nqo4-like [56762] (2)
  1. Nickel-iron hydrogenase, large subunit [56763] (5)
  2. Nqo4-like [144028] (1)
    Pfam 00346; Respiratory-chain NADH dehydrogenase, 49 Kd subunit
HydA/Nqo6-like [56769] (1)
2 domains: (1) alpa/beta; (2) Fe-S cluster-bound
1. HydA/Nqo6-like [56770] (2)
  1. Nickel-iron hydrogenase, small subunit [56771] (5)
  2. Nq06-like [144031] (1)
    Pfam 01058
Dehydroquinate synthase-like [56795] (1)
2 domains: (1) alpha/beta of a Rossmann-fold topology, binds NAD (2) multihelical array
1. Dehydroquinate synthase-like [56796] (2)
  1. Dehydroquinate synthase, DHQS [56797] (2)
  2. Iron-containing alcohol dehydrogenase [69892] (6)
    Pfam 00465
Siroheme synthase middle domains-like [75614] (1)
2 domains: (1) alpha+beta, 2 layers; (2) 3/4-helical bundle, right-handed twist, left-handed superhelix
1. Siroheme synthase middle domains-like [75615] (1)
  1. Siroheme synthase middle domains-like [75616] (2)
Acetyl-CoA synthetase-like [56800] (1)
4 domains: (1&2) duplication: share the same alpha/beta fold; (3) beta-barrel; (4) alpha+beta
1. Acetyl-CoA synthetase-like [56801] (1)
  1. Acetyl-CoA synthetase-like [56802] (7)
Ribosomal protein L1 [56807] (1)
2 domains: (1) alpha+beta; (2) alpha/beta (interrupts domain 1)
1. Ribosomal protein L1 [56808] (1)
  1. Ribosomal protein L1 [56809] (4)
Release factor [75619] (1)
4 domains: (1) 3-helical bundle; (2) alpha+beta of ferredoxin-like fold (3 and 4) alpha+beta of dsRDB-like fold
1. Release factor [75620] (1)
  1. Release factor [75621] (2)
    Pfam 00472
YaeB-like [118195] (1)
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)]
1. YaeB-like [118196] (1)
  1. YaeB-like [118197] (1)
    Pfam 01980
YebC-like [75624] (1)
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
1. YebC-like [75625] (1)
  1. YebC-like [75626] (3)
Cullin homology domain [75631] (1)
3 domains: (1) 4-helical bundle; (2) alpha+beta; (3) "winged helix"-like
1. Cullin homology domain [75632] (1)
  1. Cullin homology domain [75633] (1)
Sec1/munc18-like (SM) proteins [56814] (1)
3 domains: (1 and 2) alpha+beta; (3) mostly alpha, inserted in domain 2
1. Sec1/munc18-like (SM) proteins [56815] (1)
  1. Sec1/munc18-like (SM) proteins [56816] (3)
Prismane protein-like [56820] (1)
3 domains: (1) spectrin repeat-like 3-helical bundle; (2 and 3) alpha/beta: Rossmann-fold topology
1. Prismane protein-like [56821] (3)
  1. Carbon monoxide dehydrogenase [64514] (3)
  2. Hybrid cluster protein (prismane protein) [56822] (2)
    contains extra N-terminal 3-helical bundle domain
  3. Acetyl-CoA synthase [82852] (2)
    4 domains: structures and assembly of domains 1 and 2 are similar to those of domains 1 and 3 of the CODH subunit; (3 and 4) alpha+beta
Subunits of heterodimeric actin filament capping protein Capz [90095] (1)
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
1. Subunits of heterodimeric actin filament capping protein Capz [90096] (2)
  1. Capz alpha-1 subunit [90097] (1)
  2. Capz beta-1 subunit [90100] (1)
beta-lactamase/transpeptidase-like [56600] (1)
contains a cluster of helices and an alpha+beta sandwich
1. beta-lactamase/transpeptidase-like [56601] (3)
  1. beta-Lactamase/D-ala carboxypeptidase [56602] (36)
  2. Glutaminase [90084] (2)
    Pfam 04960
  3. Dac-like [144040] (3)
    Pfam 02113; D-Ala-D-Ala carboxypeptidase 3 (S13) family; contains a large insertion comprising two subdomains: (d1) aplha+beta with topological similarity to one subunit of the DTD-like family (scop_fa 69501) and (d2) six-stranded beta-sandwich with a crossed-loop topology
Upper collar protein gp10 (connector protein) [56825] (1)
2 domains: (1) alpha-helical bundle; (2) beta-barrel (n=5, S=8)
1. Upper collar protein gp10 (connector protein) [56826] (1)
  1. Upper collar protein gp10 (connector protein) [56827] (1)
Phase 1 flagellin [64517] (1)
3 domains: (1) alpha-helical bundle; (2&3) complex all-beta folds
1. Phase 1 flagellin [64518] (1)
  1. Phase 1 flagellin [64519] (1)
39 kda initiator binding protein, IBP39, C-terminal domains [103408] (1)
2 closely associated domains: (1) all-alpha, EF-hand like; (2) alpha+beta, Frataxin-like
1. 39 kda initiator binding protein, IBP39, C-terminal domains [103409] (1)
  1. 39 kda initiator binding protein, IBP39, C-terminal domains [103410] (1)
AF1104-like [111320] (1)
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]
1. AF1104-like [111321] (1)
  1. AF1104-like [111322] (3)
    Pfam 01937
Urocanase [111325] (1)
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
1. Urocanase [111326] (1)
  1. Urocanase [111327] (2)
    Pfam 01175
NAD kinase [111330] (1)
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]
1. NAD kinase [111331] (1)
  1. NAD kinase [111332] (2)
    Pfam 01513
QueA-like [111336] (1)
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)
1. QueA-like [111337] (1)
  1. QueA-like [111338] (2)
    Pfam 02547
CbiD-like [111341] (1)
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
1. CbiD-like [111342] (1)
  1. CbiD-like [111343] (1)
    Pfam 01888
Rap/Ran-GAP [111346] (1)
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)
1. Rap/Ran-GAP [111347] (1)
  1. Rap/Ran-GAP [111348] (1)
    Pfam 02145
Vacuolar ATP synthase subunit C [118202] (1)
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
1. Vacuolar ATP synthase subunit C [118203] (1)
  1. Vacuolar ATP synthase subunit C [118204] (1)
    Pfam 03223
Thermophilic metalloprotease-like [144051] (1)
consists of two domains; d1: alpha/beta (3 layers, a/b/a; parralel beta-sheet, order 2134); d2: pseudo beta-barrel capped by helices
1. Thermophilic metalloprotease-like [144052] (1)
  1. Thermophilic metalloprotease (M29) [144053] (2)
    Pfam 02073
ImpE-like [144058] (1)
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 (scop_fa 54161)
1. ImpE-like [144059] (1)
  1. ImpE-like [144060] (1)
    Pfam 07024
Heme iron utilization protein-like [144063] (1)
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
1. Heme iron utilization protein-like [144064] (2)
  1. HemS/ChuS-like [144065] (2)
    Pfam 05171; Haemin-degrading proteins; duplication: consists of thandem repeat of this fold joined at the 'free' ends of their PH-like barrels
  2. ChuX-like [144070] (1)
    Pfam 06228; DUF1008; single-domain subunits form a dimer similar to the HemS/ChuS subunits
NSP3 homodimer [69902] (1)
2 domains: (1) all-alpha, (2) alpha+beta; asymmetric homodimer with each domain intertwining with its counterpart
1. NSP3 homodimer [69903] (1)
  1. NSP3 homodimer [69904] (1)
E2F-DP heterodimerization region [144073] (1)
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
1. E2F-DP heterodimerization region [144074] (2)
  1. DP dimerization segment [144075] (1)
    Pfam 08781
  2. E2F dimerization segment [144078] (1)
    PfamB 001971
Membrane penetration protein mu1 [69907] (1)
4 domains: three intertwined predominately alpha domains and one jelly-roll beta-sandwich
1. Membrane penetration protein mu1 [69908] (1)
  1. Membrane penetration protein mu1 [69909] (1)
Reovirus inner layer core protein p3 [56830] (1)
large protein without apparent domain division; has a number of all-alpha regions and one all beta domain near the C-end
1. Reovirus inner layer core protein p3 [56831] (2)
  1. Orbivirus core [56832] (1)
  2. Phytoreovirus core [103413] (1)
L-A virus major coat protein [82855] (1)
large protein without apparent domain division
1. L-A virus major coat protein [82856] (1)
  1. L-A virus major coat protein [82857] (1)
Major capsid protein VP5 [103416] (1)
large protein without apparent domain division
1. Major capsid protein VP5 [103417] (1)
  1. Major capsid protein VP5 [103418] (1)
Viral ssDNA binding protein [118207] (1)
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]
1. Viral ssDNA binding protein [118208] (1)
  1. Viral ssDNA binding protein [118209] (1)
    Pfam 00747