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Difference between revisions of "Syn/anti lateral protonation"

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Line 23: Line 23:
 
! '''Anomeric specificity'''
 
! '''Anomeric specificity'''
 
! '''Mechanism'''
 
! '''Mechanism'''
−
! '''''syn/anti'''''
+
! '''''Syn/anti'' protonator'''
 
! '''Example PDB ID'''
 
! '''Example PDB ID'''
 
! '''Enzyme'''
 
! '''Enzyme'''
Line 110: Line 110:
 
| 1ovw
 
| 1ovw
 
| endo-1,4-glucanase
 
| endo-1,4-glucanase
−
 
 
| ''Fusarium oxysporum''
 
| ''Fusarium oxysporum''
−
| thio-Glc<sub>5</sub>
+
| Michaelis thio-Glc<sub>5</sub>
 
| Glu202
 
| Glu202
 
| Glu197
 
| Glu197
Line 137: Line 136:
 
| inverting
 
| inverting
 
| ''syn''
 
| ''syn''
−
| 3tf4,4tf4
+
| 3tf4, 4tf4
 
| cellulase
 
| cellulase
 
| ''Thermomonospora fusca''
 
| ''Thermomonospora fusca''
 
| product
 
| product
 
| Glu424
 
| Glu424
−
| Asp55,Asp58
+
| Asp55, Asp58
 
| <cite>Irwin1998</cite>
 
| <cite>Irwin1998</cite>
 
|-
 
|-
Line 242: Line 241:
 
| Glu147
 
| Glu147
 
| <cite>Allouch2004</cite>
 
| <cite>Allouch2004</cite>
 +
|-
 +
| [[GH18]]
 +
| K
 +
| (β/α)<sub>8</sub>
 +
| beta
 +
| retaining
 +
| ''anti''
 +
| 1ffr
 +
| chitinase A
 +
| ''Serratia marcescens''
 +
| Michaelis (NAG)<sub>6</sub>
 +
| Glu315
 +
| internal
 +
| <cite>Papanikolau2001</cite>
 +
|-
 +
| [[GH20]]
 +
| K
 +
| (β/α)<sub>8</sub>
 +
| beta
 +
| retaining
 +
| ''anti''
 +
| 1c7s
 +
| chitobiase
 +
| ''Serratia marcescens''
 +
| Michaelis chitobiose
 +
| Glu540
 +
| internal
 +
| <cite>Prag2000</cite>
 +
|-
 +
| [[GH22]]
 +
| none
 +
| lysozyme type
 +
| beta
 +
| retaining
 +
| ''syn''
 +
| 1h6m
 +
| lysozyme C
 +
| ''Gallus gallus''
 +
| Chit-2-F-chitosyl
 +
| Glu35
 +
| Asp52
 +
| <cite>Vocadlo2001</cite>
 +
|-
 +
| [[GH23]]
 +
| none
 +
| lysozyme type
 +
| beta
 +
| inverting
 +
| ''syn''
 +
| 1lsp
 +
| lysozyme G
 +
| ''Cygnus atratus''
 +
| Bulgecin A
 +
| Glu73
 +
| internal
 +
| <cite>Karlsen1996</cite>
 +
|-
 +
| [[GH24]]
 +
| I
 +
| α + β
 +
| beta
 +
| inverting
 +
| ''syn''
 +
| 148l
 +
| lysozyme E
 +
| ''Bacteriophage T4''
 +
| chitobiosyl
 +
| Glu11
 +
| Glu26
 +
| <cite>Baldwin1993</cite>
 +
|-
 +
| [[GH26]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta
 +
| retaining
 +
| ''anti''
 +
| 1gw1
 +
| mannanase A
 +
| ''Cellvibrio japonicus''
 +
| (Man<sub>2</sub>)-2-F-mannosyl
 +
| Glu212
 +
| Glu320
 +
| <cite>Ducros2002</cite>
 +
|-
 +
| [[GH27]]
 +
| D
 +
| (β/α)<sub>8</sub>
 +
| alpha
 +
| retaining
 +
| ''anti''
 +
| 1ktc
 +
| α-N-acetyl galactosaminidase
 +
| ''Gallus gallus''
 +
| NAGal
 +
| Asp201
 +
| Asp410
 +
| <cite>Garman2002</cite>
 +
|-
 +
| [[GH29]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| alpha
 +
| retaining
 +
| ''syn''
 +
| 1hl9
 +
| α-L-fucosidase
 +
| ''Thermotoga maritima''
 +
| 2-F-fucopyranosyl
 +
| Glu266
 +
| Asp224
 +
| <cite>Sulzenbacher2004</cite>
 +
|-
 +
| [[GH31]]
 +
| D
 +
| (β/α)<sub>8</sub>
 +
| alpha
 +
| retaining
 +
| ''anti''
 +
| 1xsk
 +
| α-xylosidase
 +
| ''Escherechia coli''
 +
| 5-F-xylosyl
 +
| Asp482
 +
| Asp416
 +
| <cite>Lovering2005</cite>
 +
|-
 +
| [[GH33]]
 +
| E
 +
| 6-fold β-propeller
 +
| alpha
 +
| retaining
 +
| ''anti''
 +
| 1s0k
 +
| trans-sialidase
 +
| ''Trypanosoma cruzi''
 +
| 2-F,3-F-sialosyl
 +
| Asp59
 +
| Tyr342
 +
| <cite>Amaya2004</cite>
 
|}
 
|}
−
 
 
== References ==
 
== References ==
  
Line 265: Line 403:
 
# Aleshin1996 pmid=8679589
 
# Aleshin1996 pmid=8679589
 
# Allouch2004 pmid=15062085
 
# Allouch2004 pmid=15062085
−
 
+
# Papanikolau2001 pmid=11560481
 +
# Prag2000 pmid=10884356
 +
# Vocadlo2001 pmid=11518970
 +
# Karlsen1996 pmid=15299731
 +
# Baldwin1993 pmid=8259514
 +
# Ducros2002 pmid=12203498
 +
# Garman2002 pmid=12005440
 +
# Sulzenbacher2004 pmid=14715651
 +
# Lovering2005 pmid=15501829
 +
# Amaya2004 pmid=15130470
 
</biblio>
 
</biblio>
  
 
[[Category:Definitions and explanations]]
 
[[Category:Definitions and explanations]]

Revision as of 14:56, 15 November 2009


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 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 1h2j 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]
GH33 E 6-fold β-propeller alpha retaining anti 1s0k trans-sialidase Trypanosoma cruzi 2-F,3-F-sialosyl Asp59 Tyr342 [27]

References

Error fetching PMID 15642336:
Error fetching PMID 9223646:
Error fetching PMID 11732897:
Error fetching PMID 11709165:
Error fetching PMID 12595701:
Error fetching PMID 12744312:
Error fetching PMID 8952478:
Error fetching PMID 11884144:
Error fetching PMID 9537366:
Error fetching PMID 9537990:
Error fetching PMID 10220321:
Error fetching PMID 10200171:
Error fetching PMID 10331869:
Error fetching PMID 8679589:
Error fetching PMID 15062085:
Error fetching PMID 11560481:
Error fetching PMID 10884356:
Error fetching PMID 11518970:
Error fetching PMID 15299731:
Error fetching PMID 8259514:
Error fetching PMID 12203498:
Error fetching PMID 12005440:
Error fetching PMID 14715651:
Error fetching PMID 15501829:
Error fetching PMID 15130470:

  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. Error fetching PMID 15642336: [Nerinckx2005]
  3. Error fetching PMID 9223646: [Wiesmann1997]
  4. Error fetching PMID 11732897: [Juers2001]
  5. Error fetching PMID 11709165: [Hrmova2001]
  6. Error fetching PMID 12595701: [Varrot_A2003]
  7. Error fetching PMID 12744312: [Varrot_B2003]
  8. Error fetching PMID 8952478: [Sulzenbacher1996]
  9. Error fetching PMID 11884144: [Guerin2002]
  10. Error fetching PMID 9537366: [Irwin1998]
  11. Error fetching PMID 9537990: [Notenboom1998]
  12. Error fetching PMID 10220321: [Sidhu1999]
  13. Error fetching PMID 10200171: [Sulzenbacher1999]
  14. Error fetching PMID 10331869: [Uitdehaag1999]
  15. Mikami B, Adachi M, Kage T, Sarikaya E, Nanmori T, Shinke R, and Utsumi S. (1999). Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose. Biochemistry. 1999;38(22):7050-61. DOI:10.1021/bi9829377 | PubMed ID:10353816 [Mikami1999]
  16. Error fetching PMID 8679589: [Aleshin1996]
  17. Error fetching PMID 15062085: [Allouch2004]
  18. Error fetching PMID 11560481: [Papanikolau2001]
  19. Error fetching PMID 10884356: [Prag2000]
  20. Error fetching PMID 11518970: [Vocadlo2001]
  21. Error fetching PMID 15299731: [Karlsen1996]
  22. Error fetching PMID 8259514: [Baldwin1993]
  23. Error fetching PMID 12203498: [Ducros2002]
  24. Error fetching PMID 12005440: [Garman2002]
  25. Error fetching PMID 14715651: [Sulzenbacher2004]
  26. Error fetching PMID 15501829: [Lovering2005]
  27. Error fetching PMID 15130470: [Amaya2004]

All Medline abstracts: PubMed

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