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Difference between revisions of "Glycoside Hydrolase Family 66"

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* [[Author]]: [[User:Ryuichiro Suzuki|Ryuichiro Suzuki]]
* [[Author]]: ^^^Ryuichiro Suzuki^^^
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|none, (β/α)
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== Substrate specificities ==
 
== Substrate specificities ==
Glycoside hydrolases of GH66 contains exo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases.   
+
[[Glycoside hydrolases]] of family GH66 include [[endo]]-acting dextranases (Dex; EC [{{EClink}}3.2.1.11 3.2.1.11]) and cycloisomaltooligosaccharide glucanotransferases (CITase; EC [{{EClink}}2.4.1.248 2.4.1.248]).  
 +
Family GH66 enzymes are classified into the following three types: Type I Dexs, Type II Dexs with low CITase activity, and Type III CITases <cite>Kim2012A Kim2012B</cite>.
 +
 
 +
Dex enzymes hydrolyze α-1,6-linkages of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dex enzymes from oral streptococci have been studied since the 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into families [[GH49]] and GH66.  
 +
 
 +
CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus'' sp. T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region is a family 35 carbohydrate-binding module ([[CBM35]]) domain <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.
 +
 
  
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>.
+
GH66 enzymes are [[retaining]] enzymes, as first shown by structural analysis of cyclic dextrins formed by transglycosylation from a-1,6-glucan by ''Bacillus'' sp. T-3040 CITase-T3040 <cite>Oguma1993</cite>. This has been supported by subsequent structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. GH66 enzymes appear to operate through a [[classical Koshland retaining mechanism]]. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (''Bt''Dex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>. Dexs from family [[GH49]] are inverting enzymes.
 +
 
 
== Catalytic Residues ==
 
== Catalytic Residues ==
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from ''Bacillus circulans'' T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase from ''Paenibacillus'' sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.
+
Catalytic residues of several GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The [[catalytic nucleophile]] is aspartic acid and the [[general acid/base]] is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from ''Streptococcus mutans'' (''Sm''Dex) <cite>Nsuzu2012 Igarashi2002</cite>, Asp340 and Glu412 in Dex from ''Paenibacillus'' sp. (''Ps''Dex) <cite>Kim2012A</cite>, Asp270 and Glu342 in CITase-T3040  <cite>SuzukiR2012, Nsuzu2014</cite>, and Asp269 and Glu341 in CITase-598K <cite>SuzukiR2012</cite>.
 +
 
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.
+
Crystal structures of a truncated mutant of ''Streptococcus mutans'' ''Sm''Dex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of a GH66 enzyme <cite>Nsuzu2012</cite>. Three structures, ligand free (PDB ID [{{PDBlink}}3vmn 3vmn]), in complex with IG3 (PDB ID [{{PDBlink}}3vmo 3vmo]), and in complex with 4’,5’-epoxypentyl α-D-glucopyranoside (PDB ID [{{PDBlink}}3vmp 3vmp]), have been solved <cite>Nsuzu2012</cite>. The catalytic domain of ''Sm''Dex is a (β/α)<sub>8</sub>-barrel fold, accompanied by N-terminal immunoglobulin-like β-sandwich fold and C-terminal β-sandwich structure containing two Greek key motifs. These three domains are the common structural components in GH66 enzymes.
 +
 
 +
A structure for a GH66 CITase-T3040 (PDB ID [{{PDBlink}}3wnk 3wnk]-[{{PDBlink}}3wno 3wno]) has been reported <cite>Nsuzu2014</cite>. CITase-T3040 has a similar domain arrangement to that of ''Sm''Dex, but a [[CBM35]] domain is inserted into the catalytic module, which assists substrate uptake and production of the dominant cyclooctylisomaltoside (CI-8).
 +
 
 
== Family Firsts ==
 
== Family Firsts ==
;First stereochemistry determination:.
+
;First stereochemistry determination: ''Bacillus'' sp. T-3040 CITase-T3040 by structural analysis of transglycosylation products using <sup>1</sup>H-NMR and <sup>13</sup>C-NMR spectroscopy <cite>Oguma1993</cite>.
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.
+
;First [[catalytic nucleophile]] identification: ''Streptococcus mutans'' ''Sm''Dex and ''Paenibacillus'' sp. ''Ps''Dex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.
+
;First [[general acid/base]] residue identification: ''Sm''Dex and ''Ps''Dex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .
+
;First 3-D structure: Truncated mutant of ''Sm''Dex <cite>Nsuzu2012</cite>.
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
 +
#Staat1974 pmid=4816468
 +
#Hamada1975 pmid=1205620
 +
#Ellis1977 pmid=14177
 
#Funane2008 pmid=19060390
 
#Funane2008 pmid=19060390
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of ''Bacillus'' and ''Paenibacillus'' bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. ''Biosci Biotechnol Biochem''. '''72''', 3277-3280.  [DOI: 10.1271/bbb.80384]
 
</biblio>
 
<biblio>
 
 
#SuzukiR2012 pmid=22542750
 
#SuzukiR2012 pmid=22542750
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from ''Paenibacillus'' sp. 598K. ''Biochim''. ''Biophys''. ''Acta'' '''1824''', 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]
+
#Funane2011 pmid=21193067
</biblio>
 
<biblio>
 
 
#Kim2012A pmid=22461618
 
#Kim2012A pmid=22461618
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. ''J''. ''Biol''. ''Chem''. '''287''', 19927-19935 [DOI: 10.1074/jbc.M111.339036]
 
</biblio>
 
<biblio>
 
 
#Kim2012B pmid=22776355
 
#Kim2012B pmid=22776355
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. ''FEBS J''. '''279''', 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]
+
#Nsuzu2012 pmid=22337884
 +
#Igarashi2002 pmid=12030973
 +
#Oguma1993 Oguma T, Horiuchi T, and Kobayashi M. ''Novel Cyclic Dextrins, Cycloisomaltooligosaccharides, from Bacillus sp. T-3040 Culture''. Biosci Biotechnol Biochem. 1993 57(7):1225-1227. [http://dx.doi.org/10.1271/bbb.57.1225 DOI:10.1271/bbb.57.1225]
 +
#Nsuzu2014 pmid=24616103
 
</biblio>
 
</biblio>
<biblio>
 
#Nsuzu2011 pmid=22139161
 
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from ''Streptococcus mutans''. ''Acta Crystallogr''. ''F Struct''. ''Biol''. ''Cryst''. ''Commun''. '''67''', 1542–1544 [DOI: 10.1107/S1744309111038425]
 
</biblio>
 
<biblio>
 
#Nsuzu2012 pmid=22337884
 
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by ''Streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J''. ''Biol''. ''Chem''. '''287''', 19916-19926. [DOI: 10.1074/jbc.M112.342444]
 
</biblio> 
 
  
 
[[Category:Glycoside Hydrolase Families|GH066]]
 
[[Category:Glycoside Hydrolase Families|GH066]]

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Glycoside Hydrolase Family GH66
Clan none, (β/α)8
Mechanism retaining
Active site residues known
CAZy DB link
http://www.cazy.org/GH66.html


Substrate specificities

Glycoside hydrolases of family GH66 include endo-acting dextranases (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferases (CITase; EC 2.4.1.248). Family GH66 enzymes are classified into the following three types: Type I Dexs, Type II Dexs with low CITase activity, and Type III CITases [1, 2].

Dex enzymes hydrolyze α-1,6-linkages of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dex enzymes from oral streptococci have been studied since the 1970s [3, 4, 5]. Dexs are classified into families GH49 and GH66.

CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 [6]. CITases produce CIs from IG4 and larger IGs [7]. CITase from Bacillus sp. T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from Paenibacillus sp. 598K (CITase-598K) was CI-7 [7, 8]. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region is a family 35 carbohydrate-binding module (CBM35) domain [8]. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered [1, 2].


Kinetics and Mechanism

GH66 enzymes are retaining enzymes, as first shown by structural analysis of cyclic dextrins formed by transglycosylation from a-1,6-glucan by Bacillus sp. T-3040 CITase-T3040 [9]. This has been supported by subsequent structural [10] and chemical rescue studies [1]. GH66 enzymes appear to operate through a classical Koshland retaining mechanism. The kcat and KM values of Dex from Bacteroides thetaiotaomicron VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s-1 and 0.029 mM, respectively [2]. Both CITase-T3040 and CITase-598K showed the same KM value for dextran 40 (0.18 mM) [7]. The kcat values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s-1 and 5.8 s-1, respectively [7]. Dexs from family GH49 are inverting enzymes.

Catalytic Residues

Catalytic residues of several GH66 enzymes have been identified by mutational and structural studies [1, 7, 10, 11]. The catalytic nucleophile is aspartic acid and the general acid/base is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from Streptococcus mutans (SmDex) [10, 11], Asp340 and Glu412 in Dex from Paenibacillus sp. (PsDex) [1], Asp270 and Glu342 in CITase-T3040 [7, 12], and Asp269 and Glu341 in CITase-598K [7].

Three-dimensional structures

Crystal structures of a truncated mutant of Streptococcus mutans SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of a GH66 enzyme [10]. Three structures, ligand free (PDB ID 3vmn), in complex with IG3 (PDB ID 3vmo), and in complex with 4’,5’-epoxypentyl α-D-glucopyranoside (PDB ID 3vmp), have been solved [10]. The catalytic domain of SmDex is a (β/α)8-barrel fold, accompanied by N-terminal immunoglobulin-like β-sandwich fold and C-terminal β-sandwich structure containing two Greek key motifs. These three domains are the common structural components in GH66 enzymes.

A structure for a GH66 CITase-T3040 (PDB ID 3wnk-3wno) has been reported [12]. CITase-T3040 has a similar domain arrangement to that of SmDex, but a CBM35 domain is inserted into the catalytic module, which assists substrate uptake and production of the dominant cyclooctylisomaltoside (CI-8).

Family Firsts

First stereochemistry determination
Bacillus sp. T-3040 CITase-T3040 by structural analysis of transglycosylation products using 1H-NMR and 13C-NMR spectroscopy [9].
First catalytic nucleophile identification
Streptococcus mutans SmDex and Paenibacillus sp. PsDex by structural study [10] and chemical rescue approach [1], respectively.
First general acid/base residue identification
SmDex and PsDex by structural study [10] and chemical rescue approach [1], respectively.
First 3-D structure
Truncated mutant of SmDex [10].

References

  1. Kim YM, Kiso Y, Muraki T, Kang MS, Nakai H, Saburi W, Lang W, Kang HK, Okuyama M, Mori H, Suzuki R, Funane K, Suzuki N, Momma M, Fujimoto Z, Oguma T, Kobayashi M, Kim D, and Kimura A. (2012). Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. J Biol Chem. 2012;287(24):19927-35. DOI:10.1074/jbc.M111.339036 | PubMed ID:22461618 [Kim2012A]
  2. Kim YM, Yamamoto E, Kang MS, Nakai H, Saburi W, Okuyama M, Mori H, Funane K, Momma M, Fujimoto Z, Kobayashi M, Kim D, and Kimura A. (2012). Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. FEBS J. 2012;279(17):3185-91. DOI:10.1111/j.1742-4658.2012.08698.x | PubMed ID:22776355 [Kim2012B]
  3. Staat RH and Schachtele CF. (1974). Evaluation of dextranase production by the cariogenic bacterium Streptococcus mutans. Infect Immun. 1974;9(2):467-9. DOI:10.1128/iai.9.2.467-469.1974 | PubMed ID:4816468 [Staat1974]
  4. Hamada S, Mizuno J, Murayama Y, Ooshima Y, and Masuda N. (1975). Effect of dextranase on the extracellular polysaccharide synthesis of Streptococcus mutans; chemical and scanning electron microscopy studies. Infect Immun. 1975;12(6):1415-25. DOI:10.1128/iai.12.6.1415-1425.1975 | PubMed ID:1205620 [Hamada1975]
  5. Ellis DW and Miller CH. (1977). Extracellular dextran hydrolase from Streptococcus mutans strain 6715. J Dent Res. 1977;56(1):57-69. DOI:10.1177/00220345770560011301 | PubMed ID:14177 [Ellis1977]
  6. Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, and Kobayashi M. (2008). Isolation of Bacillus and Paenibacillus bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. Biosci Biotechnol Biochem. 2008;72(12):3277-80. DOI:10.1271/bbb.80384 | PubMed ID:19060390 [Funane2008]
  7. Suzuki R, Terasawa K, Kimura K, Fujimoto Z, Momma M, Kobayashi M, Kimura A, and Funane K. (2012). Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K. Biochim Biophys Acta. 2012;1824(7):919-24. DOI:10.1016/j.bbapap.2012.04.001 | PubMed ID:22542750 [SuzukiR2012]
  8. Funane K, Kawabata Y, Suzuki R, Kim YM, Kang HK, Suzuki N, Fujimoto Z, Kimura A, and Kobayashi M. (2011). Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040. Biochim Biophys Acta. 2011;1814(3):428-34. DOI:10.1016/j.bbapap.2010.12.009 | PubMed ID:21193067 [Funane2011]
  9. Oguma T, Horiuchi T, and Kobayashi M. Novel Cyclic Dextrins, Cycloisomaltooligosaccharides, from Bacillus sp. T-3040 Culture. Biosci Biotechnol Biochem. 1993 57(7):1225-1227. DOI:10.1271/bbb.57.1225

    [Oguma1993]
  10. Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K, and Kimura A. (2012). Structural elucidation of dextran degradation mechanism by streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem. 2012;287(24):19916-26. DOI:10.1074/jbc.M112.342444 | PubMed ID:22337884 [Nsuzu2012]
  11. Igarashi T, Morisaki H, Yamamoto A, and Goto N. (2002). An essential amino acid residue for catalytic activity of the dextranase of Streptococcus mutans. Oral Microbiol Immunol. 2002;17(3):193-6. DOI:10.1034/j.1399-302x.2002.170310.x | PubMed ID:12030973 [Igarashi2002]
  12. Suzuki N, Fujimoto Z, Kim YM, Momma M, Kishine N, Suzuki R, Suzuki S, Kitamura S, Kobayashi M, Kimura A, and Funane K. (2014). Structural elucidation of the cyclization mechanism of α-1,6-glucan by Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase. J Biol Chem. 2014;289(17):12040-12051. DOI:10.1074/jbc.M114.547992 | PubMed ID:24616103 [Nsuzu2014]

All Medline abstracts: PubMed