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A Database of TIM barrel Enzymes

Introduction:

The eight-stranded a /b barrel (TIM barrel) is by far the most common tertiary fold observed in high resolution protein crystal structures. It is estimated that 10% of all known enzymes have this domain (Farber et.al.,). The members of this large family of proteins catalyze very different reactions. Such diversity in function has made this family an attractive target for protein engineering. Moreover, the evolutionary history of this protein family has been the subject of rigorous debate. Arguments have been made in favor of both convergent and divergent evolution. Because of the lack of sequence homology, the ancestry of this molecule is still a mystery. In this study, an analysis has been attempted on proteins which were found to have the a/b structural motif to study their structural features like conformational preferences, functional significance, topological features such as solvent accessibility, residue preference, salt bridges, sequence similarity etc.This database is a collection of sequence, structural, functional and conformational information about all enzymes that have the TIM barrel (alpha8/beta8) topology (where the beta strand order is parallel:1,2,3,4,5,6,7,8)

The TIM dataset:

The database currently contains 85 enzymes devided into either functional or structural classes. Click on the TIM barrel enzyme link for details about the enzyme. The global statistics are given below.
 
1) 1-3 b glucanase (1ghs)  (2.3 Å) 45) Arabino-heptulosonate-7-phosphate synthase (1qr7)(2.6 Å)
2) Yeast Hypothetical protein  (1b54)(2.1 Å) 46) Old yellow enzyme (1oya)(2.0 Å)
3) 1,4 a D-glucan maltotetrahydrolase (2amg)(2.2 Å) 47) Concanavalin B (1cnv)(1.68 Å)
4) 1-3, 1-4 b glucanase (1aq0)(2.0 Å) 48) 3-dehydroquinate dehydratase (1qfe)(2.1 Å)
5) FR-1 Protein (1frb)(1.7 Å) 49) Oligo 1-6 glucosidase (1uok)(2.0 Å)
6) Orotidine 5? monophosphate decarboxylase (1dbt)(2.4 Å) 50) Glutamate Mutase (1cb7)(2.0 Å)
7) Adenosine deaminase (1a4m)(1.95 Å) 51) N-5-phosphoryl anthranilate isomerase (1pii)(2.0 Å)
8) b-glycosidase (1bgg)(2.3 Å) 52) Phosphotriesterase (1psc)(2.0 Å)
9) D-ribulose-5-phosphate 3-epimerase (1rpx)(2.3 Å) 53) Endo-b-1-4-xylanase (1bg4)(1.5 Å)
10) Cyclodextrin glycosyl transferase (1ciu)(2.3 Å) 54) Tryptophan synthase ( a  subunit) (2wsy)(2.3 Å)
11) Triosephosphate Isomerase (1tpf)(1.8 Å) 55) Pyruvate kinase (1pkl)(2.35 Å)
12) Phosphoenol pyruvate carboxylase (1fiy)(2.8 Å) 56) N-acetyl neuraminate lyase (1nal)(2.2 Å)
13) Dihydropicolinate Synthase (1dhp)(2.5 Å) 57) 2-Dehydro-3-Deoxy-Galactarate Aldolase (1dxe) (1.9 Å)
14) Ornithine decarboxylase (7odc)(1.6 Å) 58) RUBISCO (large subunit) (1bur) (1.8 Å)
15) Endo-b-N-acetyl glucose aminidase (2ebn)(2.0 Å) 59) chitinase A (1ctn)(2.3 Å)
16) Flavocytochrome B2 (1fcb) (2.4 Å) 60) Indole-3 glycerol phosphate synthase (1a53)(2.0 Å)
17) b mannanase (1bqc)(1.5 Å) 61) Trimethylamine dehydrogenase (2tmd) (2.4 Å)
18) Thiamin phosphate synthase (2tps)(1.25 Å) 62) Isocitrate Lyase (1f61)(2.0Å)
19) Fructose bis-phosphate aldolase (1f2j)(1.9 Å) 63) Di hydro orotate dehydrogenase (2dor)(2.0 Å)
20) Aldehyde reductase (2alr)(2.0 Å) 64) Urease  (c subunit) (1fwj)(2.2 Å)
21) Quinolinate phosphoribosyl transferase (1qpo)(2.4 Å) 65) Methylmalonyl CoA mutase (4req)(2.2 Å)
22) Glycholate oxidase (1gox) (2.0 Å) 66) Uroporphyrinogen decarboxylase (1uro)(1.8 Å)
23) Transaldolase B (1onr)(1.8 Å) 67) Xylose isomerase (1xya)(1.81 Å)
24) D-glucarate dehydratase (1bqg)(2.3 Å) 68) Aldose reductase (1ads)(1.6 Å)
25) Exo-1-4-b-D- glycanase (2exo)(1.8 Å) 69) tRNA- Guanine transglycosylase (1pud)(1.85 Å)
26) Isoamylase (1bf2)(2.0 Å) 70) a-amylase (1aqm)(1.85 Å)
27) Inosine monophosphate dehydrogenase (1ak5)(2.3 Å) 71) Endocellulase E1 (1ece)(2.4 Å)
28) Phosphoenol pyruvate mutase (1pym) () 72) 2-5-diketo D-gluconic acid reductase (1a80)(2.1 Å)
29) Dihydropteroate synthase (1aj0)(2.0 Å) 73) Phosphoinositide-Specific Phospholipase C, Isozyme d1 (1djx)(2.3 Å)
30) Potassium channel b subunit (1qrq)(2.8Å) 74) Luciferase (flavin mono oxygenase) (1luc)(1.5 Å)
31) Mandelate racemase (1mns) (2.0 Å) 75) 3-deoxy-D-manno-Octulosonate 8 phosphate synthase (1d9e)(2.4 Å)
32) Enolase (7enl)(2.2 Å) 76) CHO reductase (1c9w)(2.4 Å)
33) Myrosinase (thioglucoside glucohydratase) (2myr)(1.6 Å) 77) Rhamnose isomerase (1de5)(2.2 Å)
34) Alanine racemase (1bd0)(1.6 Å) 78) Tetrahydromethanopterin reductase (1ezw)(1.65 Å)
35) Hevamine (2hvm)(1.8 Å) 79) His A protein (1qo2) (1.85 Å)
36) 5-Amino laevulinate dehydratase (1aw5)(2.3 Å) 80) propane Diol dehydratase (1egm)(1.85 Å)
37) Muconate cyclo isomerase (1muc)(1.85 Å) 81) Malate synthase G (1d8c)(2.00 Å)
38) Chloromuconate isomerase (2chr)(3.0 Å) 82) His F protein (1thf) (1.45 Å)
39) Methylene tetrahydrofolate reductase (1b5t)(2.5 Å) 83)beta amylase (1bya)(2.2 Å)
40) Chitobiase (1c7s)(1.8 Å) 84) Methyltetrahydrofolate corrinoid / iron sulfur protein methyltransferase (1f6y)(2.2 Å)
41) Pyruvate phosphate dikinase (2dik)(2.5 Å)
42) 3-alpha-hydroxy steroid dehydrogenase (1afs)(2.5 Å)
43) Narbonin (1nar)(1.8 Å)
44) Endonuclease IV (1qtw)(1.02 Å)

Statistics of the TIM barrel database:

1. Conformational characterization:

2. Composition of the database:

3. Residue preferences in different regions of the TIM barrel ezymes:


Version 1.0
Last Updated:24 july 2001
Maintained by S. Kumar Singh and M. Madan Babu

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