CAZypedia needs your help!
We have many unassigned pages in need of Authors and Responsible Curators. See a page that's out-of-date and just needs a touch-up? - You are also welcome to become a CAZypedian. Here's how.
Scientists at all career stages, including students, are welcome to contribute.
Learn more about CAZypedia's misson here and in this article.
Totally new to the CAZy classification? Read this first.

Syn/anti lateral protonation

From CAZypedia
Jump to navigation Jump to search
Under construction icon-blue-48px.png

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 provides 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 of syn/anti protonation examples

Note

This table contains only one example per GH-family of a ligand-complexed protein structure where the syn positioning (close to the ring-oxygen of the sugar moiety at subsite -1) or anti positioning (at the opposite side of the ring-oxygen, close to C-2) of the proton donor can be clearly observed. Where available, the selected examples are Michaelis-type complexes with the ligand spanning the -1/+1 subsites, since these have an intact glycosidic or thioglycosidic bond or are N-analogs of the substrate (e.g. acarbose). In some examples, the proton donor has been mutated (e.g., to the corresponding amide or to an alanine), and in those cases one may wish to look at a superposition of the given PDB example with the structure of the native enzyme. If a Michaelis-type complex is not yet available, the second and third example choices, respectively, are trapped glycosyl-enzyme intermediates or product complexes with subsite -1 correctly occupied.

Please also be aware that this is a large table with many data, so some (hopefully few) errors may have sneaked in.

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 Reference
GH1 A (β/α)8 beta retaining anti 2cer β-glycosidase S Sulfolobus solfataricus P2 phenethyl glucoimidazol Glu206 Glu387 [3]
GH2 A (β/α)8 beta retaining anti 2vzu exo-β-glucosaminidase Amicolatopsis orientalis PNP-β-d-glucosamine Glu469 Glu541 [4]
GH3 none (β/α)8 beta retaining anti 1iex exo-1,3-1,4-glucanase Hordeum vulgare thiocellobiose Glu491 Asp285 [5]
GH5 A (β/α)8 beta retaining anti 1h2j endo-β-1,4-glucanase Bacillus agaradhaerens 2',4'-DNP-2-F-cellobioside Glu129 Glu228 [6]
GH6 none (β/α)8 beta inverting syn 1qjw cellobiohydrolase 2 Hypocrea jecorina (Glc)2-S-(Glc)2 Asp221 debated [7]
GH7 B β-jelly roll beta retaining syn 1ovw endo-1,4-glucanase Fusarium oxysporum thio-(Glc)5 Glu202 Glu197 [8]
GH8 M (α/α)6 beta inverting anti 1kwf endo-1,4-glucanase Clostridium thermocellum cellopentaose Glu95 Asp278 [9]
GH9 none (α/α)6 beta inverting syn 1rq5 cellobiohydrolase Clostridium thermocellum cellotetraose Glu795 Asp383 [10]
GH10 A (β/α)8 beta retaining anti 2d24 β-1,4-xylanase Streptomyces olivaceoviridis E-86 xylopentaose Glu128 Glu236 [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 1w2u endoglucanase Humicola grisea thiocellotetraose Glu205 Glu120 [13]
GH13 H (β/α)8 alpha retaining anti 1cxk β-cyclodextrin glucanotransferase Bacillus circulans maltononaose Glu257 Asp229 [14]
GH14 none (β/α)8 alpha inverting syn 1itc β-amylase Bacillus cereus maltopentaose 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 β-agarase A Zobellia galactanivorans oligoagarose Glu152 Glu147 [17]
GH17 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1
GH18 K (β/α)8 beta retaining anti 1ffr chitinase A Serratia marcescens (NAG)6 Glu315 internal [18]
GH20 K (β/α)8 beta retaining anti 1c7s chitobiase Serratia marcescens 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 2',4'-DNP-2-F-cellotrioside Glu212 Glu320 [23]
GH27 D (β/α)8 alpha retaining anti 1ktc α-N-acetyl galactosaminidase Gallus gallus NAGal Asp201 Asp410 [24]
GH28 N β-helix alpha inverting anti 2uvf exo-polygalacturonosidase Yersinia enterocolitica ATCC9610D digalacturonic acid Asp402 Asp381 Asp403 [25]
GH29 none (β/α)8 alpha retaining syn 1hl9 α-l-fucosidase Thermotoga maritima 2-F-fuco- pyranosyl Glu266 Asp224 [26]
GH30 A (β/α)8 beta retaining anti 2v3d glucocerebrosidase 1 Homo sapiens N-butyl-deoxynojirimycin Glu235 Glu340 [27]
GH31 D (β/α)8 alpha retaining anti 2qmj maltase-glucoamylase Homo sapiens acarbose Asp542 Asp443 [28]
GH32 J 5-fold β-propeller beta retaining anti 2add fructan β-(2,1)-fructosidase Cichorium intybus sucrose Glu201 Asp22 [29]
GH33 E 6-fold β-propeller alpha retaining anti 1s0i trans-sialidase Trypanosoma cruzi sialyl-lactose Asp59 Tyr342 [30]
GH34 E 6-fold β-propeller alpha retaining anti 2bat neuraminidase Influenza A virus sialic acid Asp151 Tyr406 [31]
GH35 A (β/α)8 beta retaining anti 1xc6 β-galactosidase Penicillium sp. d-galactose Glu200 Glu299 [32]
GH37 G (α/α)6 alpha inverting anti 2jf4 trehalase Escherechia coli validoxylamine Asp312 Glu496 [33]
GH38 none (β/α)7 alpha retaining anti 1qwn α-mannosidase II Drosophila melanogaster 5-F-β-l-gulosyl Asp341 Asp204 [34]
GH39 A (β/α)8 beta retaining anti 1uhv β-xylosidase Thermoanaerobacterium saccharolyticum 2-F-xylosyl Glu160 Glu277 [35]
GH42 A (β/α)8 beta retaining anti 1kwk β-galactosidase Thermus thermophylus A4 d-galactose Glu141 Glu312 [36]
GH44 none (β/α)8 beta retaining anti 2eqd endoglucanase Clostridium thermocellum cellooctaose Glu186 Glu359 [37]
GH45 none 6-strand. β-barrel beta inverting syn 4eng endo-1,4-glucanase Humicola insolens cellohexaose Asp121 Asp10 [38]
GH46 I α + β beta inverting predicted syn by clan see at GH24
GH47 none (α/α)7 alpha inverting anti 1x9d α-mannosidase I Homo sapiens Me-2-S-(α-Man)-2-thio-α-Man Asp463 Glu599 [39], [40]
GH48 M (α/α)6 beta inverting predicted anti by clan see at GH8
GH49 N β-helix alpha inverting predicted anti by clan see at GH28
GH50 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1
GH51 A (β/α)8 alpha retaining anti 1qw9 α-l-arabino- furanosidase Geobacillus stearothermophilus PNP-l-arabino-furanoside Glu175 Glu294 [41]
GH53 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1
GH54 none β-sandwich alpha retaining anti 1wd4 α-l-arabino- furanosidase B Aspergillus kawachii l-arabinofuranose Asp297 Glu221 [42]
GH55 none β-helix beta inverting anti 3eqo β-1,3-glucanase Phanerochaete chrysosporium K-3 d-gluconolacton Glu633 unknown [43]
GH56 none (β/α)7 beta retaining anti 1fcv hyaluronidase Apis mellifera (hyaluron.)4 Glu113 internal [44]
GH57 none (β/α)7 alpha retaining anti 1kly glucanotransferase Thermococcus litoralis acarbose Asp214 Glu123 [45]
GH59 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1
GH63 G (α/α)6 alpha inverting predicted anti by clan see at GH37
GH65 L (α/α)6 alpha inverting predicted syn by clan see at GH15
GH67 none (β/α)8 alpha inverting syn 1gql α-glucuronidase Cellvibrio japonicus Ueda107 d-glucuronic acid Glu292 unknown [46]
GH68 J 5-fold β-propeller beta retaining anti 1pt2 levansucrase Bacillus subtilis sucrose Glu342 Asp86 [47]
GH70 H (β/α)8 alpha retaining predicted anti by clan see e.g. at GH13
GH72 A (β/α)8 beta retaining anti 2w62 β-1,3-glucano- transferase Saccharomyces cerevisiae S288C laminaripentaose Glu176 Glu275 [48]
GH74 none 7-fold β-propeller beta inverting syn 2ebs cellobiohydrolase (OXG-RCBH) Geotrichum sp. m128 xyloglucan heptasaccharide Asp465 Asp35 [49]
GH77 H (β/α)8 alpha retaining anti 1esw amylomaltase Thermus aquaticus acarbose Asp395 Asp293 [50]
GH79 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1
GH80 I α + β beta inverting predicted syn by clan see at GH24
GH83 E 6-fold β-propeller alpha retaining predicted anti by clan see e.g. at GH33
GH84 none (β/α)8 beta retaining anti 2chn β-N-acetyl- glucosaminidase Bacteroides thetaiota- omicron VPI-5482 NAG-thiazoline Glu242 internal [51]
GH85 K (β/α)8 beta retaining anti 2w92 endo-β-N-acetyl- glucosaminidase D Streptococcus pneumoniae TIGR4 NAG-thiazoline Glu337 internal [52]
GH86 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1
GH89 none (β/α)8 alpha retaining anti 2vcb α-N-acetyl- glucosaminidase Clostridium perfringens PUGNAc Glu483 Glu601 [53]
GH92 none (α/α)6 + β-sandw. alpha inverting anti 2ww1 α-1,2-mannosidase Bacteroides thetaiota- omicron VPI-5482 thiomannobioside Glu533 Asp644 Asp642 [54]
GH93 E 6-fold β-propeller alpha retaining predicted anti by clan see e.g. at GH33
GH94 none (α/α)6 beta inverting syn 1v7x chitobiose phosphorylase Vibrio proteolyticus GlcNAc Asp492 phosphate [55]
GH95 none (α/α)6 alpha inverting anti 2ead α-1,2-l-fucosidase Bifidobacterium bifidum Fuc-α-1,2-Gal Glu566 Asn423 Asp766 [56]
GH97 none (β/α)8 alpha retaining + inverting anti 2zq0 α-glucosidase Bacteroides thetaiota- omicron VPI-5482 acarbose Glu532 Glu508 [57]
GH102 none double-ψ β-barrel beta retaining syn 2pi8 lytic transglycosylase A Escherechia coli chitohexaose Asp308 none [58]
GH113 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1

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. Gloster TM, Roberts S, Perugino G, Rossi M, Moracci M, Panday N, Terinek M, Vasella A, and Davies GJ. (2006). Structural, kinetic, and thermodynamic analysis of glucoimidazole-derived glycosidase inhibitors. Biochemistry. 2006;45(39):11879-84. DOI:10.1021/bi060973x | PubMed ID:17002288 [Gloster2006]
  4. van Bueren AL, Ghinet MG, Gregg K, Fleury A, Brzezinski R, and Boraston AB. (2009). The structural basis of substrate recognition in an exo-beta-D-glucosaminidase involved in chitosan hydrolysis. J Mol Biol. 2009;385(1):131-9. DOI:10.1016/j.jmb.2008.10.031 | PubMed ID:18976664 [van_Bueren2009]
  5. Hrmova M, Varghese JN, De Gori R, Smith BJ, Driguez H, and Fincher GB. (2001). Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase. Structure. 2001;9(11):1005-16. DOI:10.1016/s0969-2126(01)00673-6 | PubMed ID:11709165 [Hrmova2001]
  6. Varrot A and Davies GJ. (2003). Direct experimental observation of the hydrogen-bonding network of a glycosidase along its reaction coordinate revealed by atomic resolution analyses of endoglucanase Cel5A. Acta Crystallogr D Biol Crystallogr. 2003;59(Pt 3):447-52. DOI:10.1107/s0907444902023405 | PubMed ID:12595701 [Varrot2003]
  7. Zou Jy, Kleywegt GJ, Ståhlberg J, Driguez H, Nerinckx W, Claeyssens M, Koivula A, Teeri TT, and Jones TA. (1999). Crystallographic evidence for substrate ring distortion and protein conformational changes during catalysis in cellobiohydrolase Ce16A from trichoderma reesei. Structure. 1999;7(9):1035-45. DOI:10.1016/s0969-2126(99)80171-3 | PubMed ID:10508787 [Zhou1999]
  8. Sulzenbacher G, Mackenzie LF, Wilson KS, Withers SG, Dupont C, and Davies GJ. (1999). The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 A resolution. Biochemistry. 1999;38(15):4826-33. DOI:10.1021/bi982648i | PubMed ID:10200171 [Sulzenbacher1999]
  9. Guérin DM, Lascombe MB, Costabel M, Souchon H, Lamzin V, Béguin P, and Alzari PM. (2002). Atomic (0.94 A) resolution structure of an inverting glycosidase in complex with substrate. J Mol Biol. 2002;316(5):1061-9. DOI:10.1006/jmbi.2001.5404 | PubMed ID:11884144 [Guerin2002]
  10. Schubot FD, Kataeva IA, Chang J, Shah AK, Ljungdahl LG, Rose JP, and Wang BC. (2004). Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum. Biochemistry. 2004;43(5):1163-70. DOI:10.1021/bi030202i | PubMed ID:14756552 [Schubot2004]
  11. Suzuki R, Fujimoto Z, Ito S, Kawahara S, Kaneko S, Taira K, Hasegawa T, and Kuno A. (2009). Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86. J Biochem. 2009;146(1):61-70. DOI:10.1093/jb/mvp047 | PubMed ID:19279191 [Suzuki2009]
  12. Sidhu G, Withers SG, Nguyen NT, McIntosh LP, Ziser L, and Brayer GD. (1999). Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase. Biochemistry. 1999;38(17):5346-54. DOI:10.1021/bi982946f | PubMed ID:10220321 [Sidhu1999]
  13. Sandgren M, Berglund GI, Shaw A, Ståhlberg J, Kenne L, Desmet T, and Mitchinson C. (2004). Crystal complex structures reveal how substrate is bound in the -4 to the +2 binding sites of Humicola grisea Cel12A. J Mol Biol. 2004;342(5):1505-17. DOI:10.1016/j.jmb.2004.07.098 | PubMed ID:15364577 [Sandgren2004]
  14. Uitdehaag JC, Mosi R, Kalk KH, van der Veen BA, Dijkhuizen L, Withers SG, and Dijkstra BW. (1999). X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the alpha-amylase family. Nat Struct Biol. 1999;6(5):432-6. DOI:10.1038/8235 | PubMed ID:10331869 [Uitdehaag1999]
  15. Miyake H, Kurisu G, Kusunoki M, Nishimura S, Kitamura S, and Nitta Y. (2003). Crystal structure of a catalytic site mutant of beta-amylase from Bacillus cereus var. mycoides cocrystallized with maltopentaose. Biochemistry. 2003;42(19):5574-81. DOI:10.1021/bi020712x | PubMed ID:12741813 [Miyake2003]
  16. Aleshin AE, Stoffer B, Firsov LM, Svensson B, and Honzatko RB. (1996). Crystallographic complexes of glucoamylase with maltooligosaccharide analogs: relationship of stereochemical distortions at the nonreducing end to the catalytic mechanism. Biochemistry. 1996;35(25):8319-28. DOI:10.1021/bi960321g | PubMed ID:8679589 [Aleshin1996]
  17. Allouch J, Helbert W, Henrissat B, and Czjzek M. (2004). Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose. Structure. 2004;12(4):623-32. DOI:10.1016/j.str.2004.02.020 | PubMed ID:15062085 [Allouch2004]
  18. Papanikolau Y, Prag G, Tavlas G, Vorgias CE, Oppenheim AB, and Petratos K. (2001). High resolution structural analyses of mutant chitinase A complexes with substrates provide new insight into the mechanism of catalysis. Biochemistry. 2001;40(38):11338-43. DOI:10.1021/bi010505h | PubMed ID:11560481 [Papanikolau2001]
  19. Prag G, Papanikolau Y, Tavlas G, Vorgias CE, Petratos K, and Oppenheim AB. (2000). Structures of chitobiase mutants complexed with the substrate Di-N-acetyl-d-glucosamine: the catalytic role of the conserved acidic pair, aspartate 539 and glutamate 540. J Mol Biol. 2000;300(3):611-7. DOI:10.1006/jmbi.2000.3906 | PubMed ID:10884356 [Prag2000]
  20. Vocadlo DJ, Davies GJ, Laine R, and Withers SG. (2001). Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate. Nature. 2001;412(6849):835-8. DOI:10.1038/35090602 | PubMed ID:11518970 [Vocadlo2001]
  21. Karlsen S, Hough E, Rao ZH, and Isaacs NW. (1996). Structure of a bulgecin-inhibited g-type lysozyme from the egg white of the Australian black swan. A comparison of the binding of bulgecin to three muramidases. Acta Crystallogr D Biol Crystallogr. 1996;52(Pt 1):105-14. DOI:10.1107/S0907444995008468 | PubMed ID:15299731 [Karlsen1996]
  22. Baldwin EP, Hajiseyedjavadi O, Baase WA, and Matthews BW. (1993). The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme. Science. 1993;262(5140):1715-8. DOI:10.1126/science.8259514 | PubMed ID:8259514 [Baldwin1993]
  23. Ducros VM, Zechel DL, Murshudov GN, Gilbert HJ, Szabó L, Stoll D, Withers SG, and Davies GJ. (2002). Substrate distortion by a beta-mannanase: snapshots of the Michaelis and covalent-intermediate complexes suggest a B(2,5) conformation for the transition state. Angew Chem Int Ed Engl. 2002;41(15):2824-7. DOI:10.1002/1521-3773(20020802)41:15<2824::AID-ANIE2824>3.0.CO;2-G | PubMed ID:12203498 [Ducros2002]
  24. Garman SC, Hannick L, Zhu A, and Garboczi DN. (2002). The 1.9 A structure of alpha-N-acetylgalactosaminidase: molecular basis of glycosidase deficiency diseases. Structure. 2002;10(3):425-34. DOI:10.1016/s0969-2126(02)00726-8 | PubMed ID:12005440 [Garman2002]
  25. Abbott DW and Boraston AB. (2007). The structural basis for exopolygalacturonase activity in a family 28 glycoside hydrolase. J Mol Biol. 2007;368(5):1215-22. DOI:10.1016/j.jmb.2007.02.083 | PubMed ID:17397864 [Abbott2007]
  26. Sulzenbacher G, Bignon C, Nishimura T, Tarling CA, Withers SG, Henrissat B, and Bourne Y. (2004). Crystal structure of Thermotoga maritima alpha-L-fucosidase. Insights into the catalytic mechanism and the molecular basis for fucosidosis. J Biol Chem. 2004;279(13):13119-28. DOI:10.1074/jbc.M313783200 | PubMed ID:14715651 [Sulzenbacher2004]
  27. Brumshtein B, Greenblatt HM, Butters TD, Shaaltiel Y, Aviezer D, Silman I, Futerman AH, and Sussman JL. (2007). Crystal structures of complexes of N-butyl- and N-nonyl-deoxynojirimycin bound to acid beta-glucosidase: insights into the mechanism of chemical chaperone action in Gaucher disease. J Biol Chem. 2007;282(39):29052-29058. DOI:10.1074/jbc.M705005200 | PubMed ID:17666401 [Brumshtein2007]
  28. Sim L, Quezada-Calvillo R, Sterchi EE, Nichols BL, and Rose DR. (2008). Human intestinal maltase-glucoamylase: crystal structure of the N-terminal catalytic subunit and basis of inhibition and substrate specificity. J Mol Biol. 2008;375(3):782-92. DOI:10.1016/j.jmb.2007.10.069 | PubMed ID:18036614 [Sim2008]
  29. Verhaest M, Lammens W, Le Roy K, De Ranter CJ, Van Laere A, Rabijns A, and Van den Ende W. (2007). Insights into the fine architecture of the active site of chicory fructan 1-exohydrolase: 1-kestose as substrate vs sucrose as inhibitor. New Phytol. 2007;174(1):90-100. DOI:10.1111/j.1469-8137.2007.01988.x | PubMed ID:17335500 [Verhaest2007]
  30. Amaya MF, Watts AG, Damager I, Wehenkel A, Nguyen T, Buschiazzo A, Paris G, Frasch AC, Withers SG, and Alzari PM. (2004). Structural insights into the catalytic mechanism of Trypanosoma cruzi trans-sialidase. Structure. 2004;12(5):775-84. DOI:10.1016/j.str.2004.02.036 | PubMed ID:15130470 [Amaya2004]
  31. Varghese JN, McKimm-Breschkin JL, Caldwell JB, Kortt AA, and Colman PM. (1992). The structure of the complex between influenza virus neuraminidase and sialic acid, the viral receptor. Proteins. 1992;14(3):327-32. DOI:10.1002/prot.340140302 | PubMed ID:1438172 [Varghese1992]
  32. Rojas AL, Nagem RA, Neustroev KN, Arand M, Adamska M, Eneyskaya EV, Kulminskaya AA, Garratt RC, Golubev AM, and Polikarpov I. (2004). Crystal structures of beta-galactosidase from Penicillium sp. and its complex with galactose. J Mol Biol. 2004;343(5):1281-92. DOI:10.1016/j.jmb.2004.09.012 | PubMed ID:15491613 [Rojas2004]
  33. Gibson RP, Gloster TM, Roberts S, Warren RA, Storch de Gracia I, García A, Chiara JL, and Davies GJ. (2007). Molecular basis for trehalase inhibition revealed by the structure of trehalase in complex with potent inhibitors. Angew Chem Int Ed Engl. 2007;46(22):4115-9. DOI:10.1002/anie.200604825 | PubMed ID:17455176 [Gibson2007]
  34. Numao S, Kuntz DA, Withers SG, and Rose DR. (2003). Insights into the mechanism of Drosophila melanogaster Golgi alpha-mannosidase II through the structural analysis of covalent reaction intermediates. J Biol Chem. 2003;278(48):48074-83. DOI:10.1074/jbc.M309249200 | PubMed ID:12960159 [Numao2003]
  35. Yang JK, Yoon HJ, Ahn HJ, Lee BI, Pedelacq JD, Liong EC, Berendzen J, Laivenieks M, Vieille C, Zeikus GJ, Vocadlo DJ, Withers SG, and Suh SW. (2004). Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase. J Mol Biol. 2004;335(1):155-65. DOI:10.1016/j.jmb.2003.10.026 | PubMed ID:14659747 [Yang2004]
  36. Hidaka M, Fushinobu S, Ohtsu N, Motoshima H, Matsuzawa H, Shoun H, and Wakagi T. (2002). Trimeric crystal structure of the glycoside hydrolase family 42 beta-galactosidase from Thermus thermophilus A4 and the structure of its complex with galactose. J Mol Biol. 2002;322(1):79-91. DOI:10.1016/s0022-2836(02)00746-5 | PubMed ID:12215416 [Hidaka2002]
  37. Kitago Y, Karita S, Watanabe N, Kamiya M, Aizawa T, Sakka K, and Tanaka I. (2007). Crystal structure of Cel44A, a glycoside hydrolase family 44 endoglucanase from Clostridium thermocellum. J Biol Chem. 2007;282(49):35703-11. DOI:10.1074/jbc.M706835200 | PubMed ID:17905739 [Kitago2007]
  38. Davies GJ, Dodson G, Moore MH, Tolley SP, Dauter Z, Wilson KS, Rasmussen G, and Schülein M. (1996). Structure determination and refinement of the Humicola insolens endoglucanase V at 1.5 A resolution. Acta Crystallogr D Biol Crystallogr. 1996;52(Pt 1):7-17. DOI:10.1107/S0907444995009280 | PubMed ID:15299721 [Davies1996]
  39. Karaveg K, Siriwardena A, Tempel W, Liu ZJ, Glushka J, Wang BC, and Moremen KW. (2005). Mechanism of class 1 (glycosylhydrolase family 47) {alpha}-mannosidases involved in N-glycan processing and endoplasmic reticulum quality control. J Biol Chem. 2005;280(16):16197-207. DOI:10.1074/jbc.M500119200 | PubMed ID:15713668 [Karaveg2005]
  40. Cantú D, Nerinckx W, and Reilly PJ. (2008). Theory and computation show that Asp463 is the catalytic proton donor in human endoplasmic reticulum alpha-(1-->2)-mannosidase I. Carbohydr Res. 2008;343(13):2235-42. DOI:10.1016/j.carres.2008.05.026 | PubMed ID:18619586 [Nerinckx2008]
  41. Hövel K, Shallom D, Niefind K, Belakhov V, Shoham G, Baasov T, Shoham Y, and Schomburg D. (2003). Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase. EMBO J. 2003;22(19):4922-32. DOI:10.1093/emboj/cdg494 | PubMed ID:14517232 [Hoevel2003]
  42. Miyanaga A, Koseki T, Matsuzawa H, Wakagi T, Shoun H, and Fushinobu S. (2004). Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose. J Biol Chem. 2004;279(43):44907-14. DOI:10.1074/jbc.M405390200 | PubMed ID:15292273 [Miyanaga2004]
  43. Ishida T, Fushinobu S, Kawai R, Kitaoka M, Igarashi K, and Samejima M. (2009). Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J Biol Chem. 2009;284(15):10100-9. DOI:10.1074/jbc.M808122200 | PubMed ID:19193645 [Ishida2009]
  44. Marković-Housley Z, Miglierini G, Soldatova L, Rizkallah PJ, Müller U, and Schirmer T. (2000). Crystal structure of hyaluronidase, a major allergen of bee venom. Structure. 2000;8(10):1025-35. DOI:10.1016/s0969-2126(00)00511-6 | PubMed ID:11080624 [Markovic-Housley2000]
  45. Imamura H, Fushinobu S, Yamamoto M, Kumasaka T, Jeon BS, Wakagi T, and Matsuzawa H. (2003). Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor. J Biol Chem. 2003;278(21):19378-86. DOI:10.1074/jbc.M213134200 | PubMed ID:12618437 [Imamura2003]
  46. Nurizzo D, Nagy T, Gilbert HJ, and Davies GJ. (2002). The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A. Structure. 2002;10(4):547-56. DOI:10.1016/s0969-2126(02)00742-6 | PubMed ID:11937059 [Nurizzo2002]
  47. Meng G and Fütterer K. (2003). Structural framework of fructosyl transfer in Bacillus subtilis levansucrase. Nat Struct Biol. 2003;10(11):935-41. DOI:10.1038/nsb974 | PubMed ID:14517548 [Meng2003]
  48. Hurtado-Guerrero R, Schüttelkopf AW, Mouyna I, Ibrahim AF, Shepherd S, Fontaine T, Latgé JP, and van Aalten DM. (2009). Molecular mechanisms of yeast cell wall glucan remodeling. J Biol Chem. 2009;284(13):8461-9. DOI:10.1074/jbc.M807990200 | PubMed ID:19097997 [Hurtado-Gerrero2009]
  49. Yaoi K, Kondo H, Hiyoshi A, Noro N, Sugimoto H, Tsuda S, Mitsuishi Y, and Miyazaki K. (2007). The structural basis for the exo-mode of action in GH74 oligoxyloglucan reducing end-specific cellobiohydrolase. J Mol Biol. 2007;370(1):53-62. DOI:10.1016/j.jmb.2007.04.035 | PubMed ID:17498741 [Yaoi2007]
  50. Przylas I, Terada Y, Fujii K, Takaha T, Saenger W, and Sträter N. (2000). X-ray structure of acarbose bound to amylomaltase from Thermus aquaticus. Implications for the synthesis of large cyclic glucans. Eur J Biochem. 2000;267(23):6903-13. DOI:10.1046/j.1432-1033.2000.01790.x | PubMed ID:11082203 [Przylas2000]
  51. Dennis RJ, Taylor EJ, Macauley MS, Stubbs KA, Turkenburg JP, Hart SJ, Black GN, Vocadlo DJ, and Davies GJ. (2006). Structure and mechanism of a bacterial beta-glucosaminidase having O-GlcNAcase activity. Nat Struct Mol Biol. 2006;13(4):365-71. DOI:10.1038/nsmb1079 | PubMed ID:16565725 [Dennis2006]
  52. Abbott DW, Macauley MS, Vocadlo DJ, and Boraston AB. (2009). Streptococcus pneumoniae endohexosaminidase D, structural and mechanistic insight into substrate-assisted catalysis in family 85 glycoside hydrolases. J Biol Chem. 2009;284(17):11676-89. DOI:10.1074/jbc.M809663200 | PubMed ID:19181667 [Abbott2009]
  53. Ficko-Blean E, Stubbs KA, Nemirovsky O, Vocadlo DJ, and Boraston AB. (2008). Structural and mechanistic insight into the basis of mucopolysaccharidosis IIIB. Proc Natl Acad Sci U S A. 2008;105(18):6560-5. DOI:10.1073/pnas.0711491105 | PubMed ID:18443291 [Ficko-Blean2008]
  54. Zhu et al. (2010) Nature Chemical Biology in the press; DOI: 10.1038/nchembio.278 direct link.

    [Zhu2009]
  55. Hidaka M, Honda Y, Kitaoka M, Nirasawa S, Hayashi K, Wakagi T, Shoun H, and Fushinobu S. (2004). Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold. Structure. 2004;12(6):937-47. DOI:10.1016/j.str.2004.03.027 | PubMed ID:15274915 [Hidaka2004]
  56. Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, and Kato R. (2007). Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum. J Biol Chem. 2007;282(25):18497-18509. DOI:10.1074/jbc.M702246200 | PubMed ID:17459873 [Nagae2007]
  57. Kitamura M, Okuyama M, Tanzawa F, Mori H, Kitago Y, Watanabe N, Kimura A, Tanaka I, and Yao M. (2008). Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron. J Biol Chem. 2008;283(52):36328-37. DOI:10.1074/jbc.M806115200 | PubMed ID:18981178 [Kitamura2008]
  58. 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