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Difference between revisions of "Syn/anti lateral protonation"

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| fructan β-(2,1)-fructosidase
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| ''Cichorium intybus''
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# Verhaest2007 pmid=17335500
 
# Amaya2004 pmid=15130470
 
# Amaya2004 pmid=15130470
 
# Varghese1992 pmid=1438172
 
# Varghese1992 pmid=1438172

Revision as of 14:56, 4 January 2010


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This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.


Overview

This page will provide a table (and eventually a full lexicon article) on the spatial positioning of the catalytic general acid residue in the active sites of glycoside hydrolases. The table below updates those found in the seminal paper on this concept by Heightman and Vasella [1], and the more recent summary by Nerinckx et al. [2].

Table

This table can be re-sorted by clicking on the icons in the header (javascript must be turned on in your browser). To reset the page to be sorted by GH family, click the page tab above the page title.

Family Clan Structure fold Anomeric specificity Mechanism Syn/anti protonator Example PDB ID Enzyme Organism Ligand General acid Nucleophile or General base Primary reference
GH1 A (β/α)8 beta retaining anti 4pbg 6-phospho-beta-galactosidase Lactococcus lactis product Glu160 Glu375 [3]
GH2 A (β/α)8 beta retaining anti 1jz0 beta-galactosidase Escherechia coli 2-F-galactosyl Glu461 Glu537 [4]
GH3 none (β/α)8 beta retaining anti 1iew exo-1,3-1,4-glucanase Hordeum vulgare 2-F-glucosyl Glu491 Asp285 [5]
GH5 A (β/α)8 beta retaining anti 1iew endo-1,4-glucanase Bacillus agaradhaerans 2-F-glucosyl Glu129 Glu228 [6]
GH6 none (β/α)8 beta inverting syn 1ocn cellobiohydrolase Humicola insolens Glc-isofagomine Asp226 debated [7]
GH7 B β-jelly roll beta retaining syn 1ovw endo-1,4-glucanase Fusarium oxysporum Michaelis thio-Glc5 Glu202 Glu197 [8]
GH8 M (α/α)6 beta inverting anti 1kwf endo-1,4-glucanase Clostridium thermocellum Michaelis Glu95 Asp278 [9]
GH9 none (α/α)6 beta inverting syn 3tf4, 4tf4 cellulase Thermomonospora fusca product Glu424 Asp55, Asp58 [10]
GH10 A (β/α)8 beta retaining anti 2xyl xylanase B (Cex) Cellulomonas fimi Xyl-2-F-xylosyl Glu127 Glu233 [11]
GH11 C β-jelly roll beta retaining syn 1bvv xylanase Bacillus circulans Xyl-2-F-xylosyl Glu172 Glu78 [12]
GH12 C β-jelly roll beta retaining syn 2nlr endo-1,4-glucanase Streptomyces lividans Glc2-2-F-glucosyl Glu203 Glu120 [13]
GH13 H (β/α)8 alpha retaining anti 1ckx beta-cyclodextrin glucanotransferase Bacillus circulans Michaelis Glu257 Asp229 [14]
GH14 none (β/α)8 alpha inverting syn 1b9z beta-amylase Bacillus cereus product Glu172 Glu367 [15]
GH15 L (α/α)6 alpha inverting syn 1gah glucoamylase Aspergillus awamori acarbose Glu179 Glu400 [16]
GH16 B β-jelly roll beta retaining syn 1urx beta-agarase A Zobellia galactanivorans product Glu152 Glu147 [17]
GH18 K (β/α)8 beta retaining anti 1ffr chitinase A Serratia marcescens Michaelis (NAG)6 Glu315 internal [18]
GH20 K (β/α)8 beta retaining anti 1c7s chitobiase Serratia marcescens Michaelis chitobiose Glu540 internal [19]
GH22 none lysozyme type beta retaining syn 1h6m lysozyme C Gallus gallus Chit-2-F-chitosyl Glu35 Asp52 [20]
GH23 none lysozyme type beta inverting syn 1lsp lysozyme G Cygnus atratus Bulgecin A Glu73 internal [21]
GH24 I α + β beta inverting syn 148l lysozyme E Bacteriophage T4 chitobiosyl Glu11 Glu26 [22]
GH26 A (β/α)8 beta retaining anti 1gw1 mannanase A Cellvibrio japonicus (Man2)-2-F-mannosyl Glu212 Glu320 [23]
GH27 D (β/α)8 alpha retaining anti 1ktc α-N-acetyl galactosaminidase Gallus gallus NAGal Asp201 Asp410 [24]
GH29 none (β/α)8 alpha retaining syn 1hl9 α-L-fucosidase Thermotoga maritima 2-F-fucopyranosyl Glu266 Asp224 [25]
GH31 D (β/α)8 alpha retaining anti 1xsk α-xylosidase Escherechia coli 5-F-xylosyl Asp482 Asp416 [26]
GH32 J 5-fold β-propeller alpha retaining anti 2add fructan β-(2,1)-fructosidase Cichorium intybus sucrose Glu201 Asp22 [27]
GH33 E 6-fold β-propeller alpha retaining anti 1s0k trans-sialidase Trypanosoma cruzi 2-F,3-F-sialosyl Asp59 Tyr342 [28]
GH34 E 6-fold β-propeller alpha retaining anti 2bat neuraminidase Influenza A virus sialic acid Asp151 Tyr406 [29]
GH37 G (α/α)6 alpha inverting anti 2jf4 trehalase Escherechia coli validoxylamine Asp312 Glu496 [30]
GH38 none (β/α)7 alpha retaining anti 1qwn α-mannosidase II Drosophila melanogaster 5-F-β-L-gulosyl Asp341 Asp204 [31]
GH39 A (β/α)8 beta retaining anti 1uhv β-xylosidase Thermoanaerobacterium saccharolyticum 2-F-xylosyl Glu160 Glu277 [32]
GH42 A (β/α)8 beta retaining anti 1kwk β-galactosidase Thermus thermophylus A4 galactose Glu141 Glu312 [33]
GH44 none (β/α)8 beta retaining anti 2eqd endoglucanase Clostridium thermocellum cellooctaose Glu186 Glu359 [34]
GH45 none six-stranded β-barrel beta inverting syn 4eng endo-1,4-glucanase Humicola insolens product Asp121 Asp10 [35]
GH47 none (α/α)7 alpha inverting anti 1x9d α-mannosidase I Homo sapiens Michaelis Asp463 Glu599 [36], [37]
GH51 A (β/α)8 alpha retaining anti 1pz2 α-L-arabinofuranosidase Geobacillus stearothermophilus L-arabinofuranosyl Glu175 Glu294 [38]
GH54 none β-sandwich alpha retaining anti 1wd4 α-L-arabinofuranosidase B Aspergillus kawachii L-arabinofuranose Asp297 Glu221 [39]
GH56 none (β/α)7 beta retaining anti 1fcv hyaluronidase Apis mellifera (hyaluron.)4 Glu113 internal [40]
GH57 none (β/α)7 alpha retaining anti 1kly glucanotransferase Thermococcus litoralis acarbose Asp214 Glu123 [41]
GH67 none (β/α)8 alpha inverting syn 1gql α-glucuronidase Cellvibrio japonicus Ueda107 glucuronic acid Glu292 unknown [42]
GH68 J 5-fold β-propeller beta retaining anti 1pt2 levansucrase Bacillus subtilis sucrose Glu342 Asp86 [43]
GH74 none 7-fold β-propeller beta inverting syn 2ebs cellobiohydrolase (OXG-RCBH) Geotrichum sp. m128 xyloglucan heptasaccharide Asp465 Asp35 [44]
GH77 H (β/α)8 alpha retaining anti 1esw amylomaltase Thermus aquaticus acarbose Asp395 Asp293 [45]
GH90 none (β)-helix alpha inverting anti 1tyw endo-α-L-1,3-rhamnosidase Enterobacteris phage P22 epitope fragment Asp395 Asp392 [46]
GH94 none (α/α)6 beta inverting syn 1v7x chitobiose phosphorylase Vibrio proteolyticus GlcNAc Asp492 phosphate [47]
GH95 none (α/α)6 alpha inverting anti 2ead α-1,2-L-fucosidase Bifibacterium bifidum substrate Glu566 Asn423 Asp766 [48]
GH102 none double-psi beta-barrel beta retaining syn 2pi8 lytic transglycosylase A Escherechia coli chitohexaose Asp308 none [49]

References

  1. Heightman, T.D. and Vasella, A.T. (1999) Recent Insights into Inhibition, Structure, and Mechanism of Configuration-Retaining Glycosidases. Angewandte Chemie-International Edition 38(6), 750-770. Article online.

    [HeightmanVasella1999]
  2. Nerinckx W, Desmet T, Piens K, and Claeyssens M. (2005). An elaboration on the syn-anti proton donor concept of glycoside hydrolases: electrostatic stabilisation of the transition state as a general strategy. FEBS Lett. 2005;579(2):302-12. DOI:10.1016/j.febslet.2004.12.021 | PubMed ID:15642336 [Nerinckx2005]
  3. Wiesmann C, Hengstenberg W, and Schulz GE. (1997). Crystal structures and mechanism of 6-phospho-beta-galactosidase from Lactococcus lactis. J Mol Biol. 1997;269(5):851-60. DOI:10.1006/jmbi.1997.1084 | PubMed ID:9223646 [Wiesmann1997]
  4. Juers DH, Heightman TD, Vasella A, McCarter JD, Mackenzie L, Withers SG, and Matthews BW. (2001). A structural view of the action of Escherichia coli (lacZ) beta-galactosidase. Biochemistry. 2001;40(49):14781-94. DOI:10.1021/bi011727i | PubMed ID:11732897 [Juers2001]
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  49. van Straaten KE, Barends TR, Dijkstra BW, and Thunnissen AM. (2007). Structure of Escherichia coli Lytic transglycosylase MltA with bound chitohexaose: implications for peptidoglycan binding and cleavage. J Biol Chem. 2007;282(29):21197-205. DOI:10.1074/jbc.M701818200 | PubMed ID:17502382 [van_Straaten2007]

All Medline abstracts: PubMed