Structural Classification of Proteins

Fold: TIM beta/alpha-barrel

: contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
the first seven superfamilies have similar phosphate-binding sites

Lineage:

Root: scop
Class: Alpha and beta proteins (a/b) [51349]
Mainly parallel beta sheets (beta-alpha-beta units)
Fold: TIM beta/alpha-barrel [51350]
contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
the first seven superfamilies have similar phosphate-binding sites

Superfamilies:

Triosephosphate isomerase (TIM) [51351] (1)
uperfamily
1. Triosephosphate isomerase (TIM) [51352] (18)
Ribulose-phoshate binding barrel [51366] (6)
uperfamily
1. Histidine biosynthesis enzymes [51367] (6)
  structural evidence for the gene duplication within the barrel fold
2. D-ribulose-5-phosphate 3-epimerase [51372] (5)
3. Decarboxylase [51375] (13)
4. Tryptophan biosynthesis enzymes [51381] (12)
5. NanE-like [117362] (2)
  Pfam 04131
6. PdxS-like [141755] (1)
  Pfam 01680; SOR/SNZ
Thiamin phosphate synthase [51391] (1)
uperfamily
1. Thiamin phosphate synthase [51392] (2)
Pyridoxine 5'-phosphate synthase [63892] (1)
uperfamily
1. Pyridoxine 5'-phosphate synthase [63893] (1)
FMN-linked oxidoreductases [51395] (1)
uperfamily
1. FMN-linked oxidoreductases [51396] (30)
Inosine monophosphate dehydrogenase (IMPDH) [51412] (1)
The phosphate moiety of substrate binds in the 'common' phosphate-binding site
uperfamily
1. Inosine monophosphate dehydrogenase (IMPDH) [51413] (8)
PLP-binding barrel [51419] (2)
circular permutation of the canonical fold: begins with an alpha helix and ends with a beta-strand
uperfamily
1. Alanine racemase-like, N-terminal domain [51420] (9)
2. "Hypothetical" protein ybl036c [51427] (1)
NAD(P)-linked oxidoreductase [51430] (1)
uperfamily
1. Aldo-keto reductases (NADP) [51431] (20)
  Common fold covers whole protein structure
(Trans)glycosidases [51445] (14)
uperfamily
1. Amylase, catalytic domain [51446] (54)
  members of the family may contain various insert subdomains
  in alpha-amylases and closer relatives this domain is usually followed by a common all-beta domain
2. beta-glycanases [51487] (54)
  consist of a number of sequence families
3. Putative alpha-L-fucosidase, catalytic domain [102079] (1)
  glycosyl hydrolase family 29; contains additional beta-barrel with a topological similarity to the C-terminal domain of alpha amylases
4. Family 1 of glycosyl hydrolase [51521] (15)
5. Type II chitinase [51534] (22)
  glycosylase family 18
6. 1,4-beta-N-acetylmuraminidase [63912] (3)
  Glycosyl hydrolase family 25; probably have evolved from a type II chitinase ancestor
  permutation of the common fold; strand 8 is antiparallel to the rest of the barrel
7. beta-N-acetylhexosaminidase catalytic domain [51550] (5)
  Glycosyl hydrolase family 20, GH20
8. alpha-D-glucuronidase/Hyaluronidase catalytic domain [82253] (4)
  Glycosyl hydrolase family 67, GH67; structurally related to GH20; contains extra C-terminal alpha-helical subdomain
9. NagZ-like [51553] (2)
  Pfam 00933; Glycosyl hydrolase family 3 domain
10. Bee venom hyaluronidase [69387] (1)
  distorted barrel lacks the second strand
11. Outer surface protein, N-terminal domain [110354] (1)
  corresponds to the N-terminal part of Pfam 05913
12. YicI catalytic domain-like [117372] (2)
13. Glycosyl hydrolases family 35 catalytic domain [117375] (1)
  Pfam 01301
14. TM1410-like [141796] (1)
  Pfam 03537
Metallo-dependent hydrolases [51556] (18)
the beta-sheet barrel is similarly distorted and capped by a C-terminal helix
has transition metal ions bound inside the barrel
uperfamily
1. Adenosine/AMP deaminase [51557] (4)
2. Dihydroorotase [63917] (1)
3. Cytosine deaminase catalytic domain [69390] (1)
4. alpha-subunit of urease, catalytic domain [51560] (3)
5. Hydantoinase (dihydropyrimidinase), catalytic domain [75073] (9)
6. SAH/MTA deaminase-like [82258] (5)
7. Isoaspartyl dipeptidase, catalytic domain [89489] (1)
8. N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain [82261] (3)
9. D-aminoacylase, catalytic domain [82264] (1)
10. TatD Mg-dependent DNase-like [82267] (4)
11. Phosphotriesterase-like [51564] (4)
12. Renal dipeptidase [75079] (1)
13. Uronate isomerase-like [75082] (2)
  contains all-alpha subdomain inserted after the first strand
14. Adenine deaminase-like [141816] (1)
15. PP1699/LP2961-like [141819] (5)
  Pfam 04909; Amidohydrolase; stand-alone domain
16. DR0824-like [159397] (1)
17. Imidazolonepropionase-like [159400] (4)
18. Zn-dependent arginine carboxypeptidase-like [159408] (3)
Aldolase [51569] (8)
Common fold covers whole protein structure
uperfamily
1. Class I aldolase [51570] (37)
  the catalytic lysine forms schiff-base intermediate with substrate
  possible link between the aldolase superfamily and the phosphate-binding beta/alpha barrels
2. Class II FBP aldolase [51591] (3)
  metal-dependent
3. 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) [51594] (5)
  hybrid of classes I and II aldolase
4. Class I DAHP synthetase [51599] (6)
5. HMGL-like [89494] (3)
  Pfam 00682
6. NeuB-like [110368] (2)
  Pfam 03102
7. GatZ-like [141837] (1)
  Pfam 08013
8. Class-II DAHP synthetase [141840] (1)
  Pfam 01474
Enolase C-terminal domain-like [51604] (2)
binds metal ion (magnesium or manganese) in conserved site inside barrel
N-terminal alpha+beta domain is common to this superfamily
uperfamily
1. Enolase [51605] (8)
2. D-glucarate dehydratase-like [51609] (20)
Phosphoenolpyruvate/pyruvate domain [51621] (7)
uperfamily
1. Pyruvate kinase [51622] (6)
2. Pyruvate phosphate dikinase, C-terminal domain [51629] (3)
3. Phosphoenolpyruvate carboxylase [51632] (1)
4. Phosphoenolpyruvate mutase/Isocitrate lyase-like [88704] (6)
  forms a swapped dimer
5. HpcH/HpaI aldolase [51638] (4)
  forms a swapped dimer; contains a PK-type metal-binding site
6. Ketopantoate hydroxymethyltransferase PanB [89503] (3)
7. Mll9387-like [159416] (1)
  Pfam 09370; TIM-barrel signal transduction protein; forms a swapped dimer similar to the Phosphoenolpyruvate mutase/Isocitrate lyase-like and HpcH/HpaI aldolase families
Malate synthase G [51645] (1)
uperfamily
1. Malate synthase G [51646] (2)
RuBisCo, C-terminal domain [51649] (1)
uperfamily
1. RuBisCo, large subunit, C-terminal domain [51650] (12)
  N-terminal domain is alpha+beta
Xylose isomerase-like [51658] (7)
different families share similar but non-identical metal-binding sites
uperfamily
1. Endonuclease IV [51659] (2)
2. IolI-like [75090] (3)
3. Hypothetical protein YgbM (EC1530) [75093] (1)
4. L-rhamnose isomerase [51662] (1)
5. Xylose isomerase [51665] (12)
6. UxuA-like [110377] (1)
  Pfam 03786
7. KguE-like [141854] (1)
  part of Pfam 01261
Bacterial luciferase-like [51679] (4)
consists of clearly related families of somewhat different folds
uperfamily
1. Bacterial luciferase (alkanal monooxygenase) [51680] (2)
  typical (beta/alpha)8-barrel fold
  heterodimer of two similar chains
2. Non-fluorescent flavoprotein (luxF, FP390) [51683] (2)
  incomplete beta/alpha barrel with mixed beta-sheet of 7 strands
3. F420 dependent oxidoreductases [51687] (3)
4. Ssud-like monoxygenases [82275] (2)
Nicotinate/Quinolinate PRTase C-terminal domain-like [51690] (2)
incomplete beta/alpha barrel with parallel beta-sheet of 7 strands
uperfamily
1. NadC C-terminal domain-like [51691] (6)
2. Monomeric nicotinate phosphoribosyltransferase C-terminal domain [110910] (3)
PLC-like phosphodiesterases [51695] (3)
uperfamily
1. Mammalian PLC [51696] (2)
2. Bacterial PLC [51699] (2)
3. Glycerophosphoryl diester phosphodiesterase [89508] (4)
  Pfam 03009
Cobalamin (vitamin B12)-dependent enzymes [51703] (4)
uperfamily
1. Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain [51704] (2)
  the subunits are clearly related but only one (alpha) is active
2. Glutamate mutase, large subunit [51707] (1)
3. Diol dehydratase, alpha subunit [51710] (2)
4. D-lysine 5,6-aminomutase alpha subunit, KamD [117392] (1)
  most similar to the glutamate mutase subunit; contains second cofactor, PLP
tRNA-guanine transglycosylase [51713] (1)
uperfamily
1. tRNA-guanine transglycosylase [51714] (2)
Dihydropteroate synthetase-like [51717] (2)
uperfamily
1. Dihydropteroate synthetase [51718] (4)
2. Methyltetrahydrofolate-utiluzing methyltransferases [51723] (2)
UROD/MetE-like [51726] (2)
uperfamily
1. Uroporphyrinogen decarboxylase, UROD [51727] (2)
2. Cobalamin-independent methionine synthase [110384] (1)
  Pfam 01717; duplication; consists of two related domains
FAD-linked oxidoreductase [51730] (2)
distinct cofactor-binding mode from both FMN- and NAD(P)-linked TIM-barrel oxidoreductases; families are related by a circular permutation
uperfamily
1. Methylenetetrahydrofolate reductase [51731] (2)
2. Proline dehydrohenase domain of bifunctional PutA protein [82279] (1)
Monomethylamine methyltransferase MtmB [75098] (1)
uperfamily
1. Monomethylamine methyltransferase MtmB [75099] (1)
Homocysteine S-methyltransferase [82282] (1)
uperfamily
1. Homocysteine S-methyltransferase [82283] (3)
  Pfam 02574
(2r)-phospho-3-sulfolactate synthase ComA [102110] (1)
uperfamily
1. (2r)-phospho-3-sulfolactate synthase ComA [102111] (2)
Radical SAM enzymes [102114] (3)
common Fe-S cluster and SAM binding sites are embedded into complete or incomplete beta/alpha-barrel
uperfamily
1. Biotin synthase [102115] (1)
  regular (beta/alpha)8 barrel
2. Oxygen-independent coproporphyrinogen III oxidase HemN [102118] (1)
  open beta/alpha barrel decorated with additional structures
3. MoCo biosynthesis proteins [110388] (1)
  open alpha/beta-barrel with a specific second FeS cluster-binding region corresponding to Pfam 06463
GlpP-like [110391] (1)
uperfamily
1. GlpP-like [110392] (1)
  Pfam 04309
CutC-like [110395] (1)
uperfamily
1. CutC-like [110396] (1)
  Pfam 03932
ThiG-like [110399] (1)
shares the common phosphate-binding site with other superfamilies
uperfamily
1. ThiG-like [110400] (2)
  Pfam 05690
TM1631-like [117396] (1)
uperfamily
1. TM1631-like [117397] (2)
  Pfam 01904; DUF72
EAL domain-like [141868] (1)
variant of the beta/alpha-barrel fold with strand 1 being antiparallel to the rest
uperfamily
1. EAL domain [141869] (1)
  Pfam 00563