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Difference between revisions of "Glycoside Hydrolase Family 130"

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== Substrate specificities ==
 
== Substrate specificities ==
[[GH130]]  contains phosphorylases catalyzing the phosphorolysis of &beta;-mannosidic linkage at the non-reducing end of substrates. 4-''O''-&beta;-D-Mannosyl-D-glucose phosphorylase (EC [{{EClink}}2.4.1.281 2.4.1.281]), &beta;-1,4-mannooligosaccharide phosphorylase (EC [{{EClink}}2.4.1.319 2.4.1.319]), 1,4-&beta;-mannosyl-''N''-acetylglucosamine phosphorylase (EC [{{EClink}}2.4.1.320 2.4.1.320]), 1,2-&beta;-oligomannan phosphorylase, and &beta;-1,2-mannnobiose phosphorylase are members of this family. A GH130 mannoside phosphorylase, unknown human gut bacterium mannoside phosphorylase (UhgbMP), discovered by functional metagenomics of the human gut microbiota, phosphorolyzes 4-''O''-&beta;-D-mannosyl-N,N'-diacetylchitobiose, and exhibits higher synthetic activity to ''N'',''N'''-diacetylchitobiose as an acceptor substrate than ''N''-acetyl-D-glucosamine <cite>Ladeveze2013</cite>.
+
Family [[GH130]]  contains [[phosphorylases]] that catalyze the phosphorolysis of &beta;-mannosidic linkages at the non-reducing end of substrates. 4-''O''-&beta;-D-Mannosyl-D-glucose phosphorylase (EC [{{EClink}}2.4.1.281 2.4.1.281]), &beta;-1,4-mannooligosaccharide phosphorylase (EC [{{EClink}}2.4.1.319 2.4.1.319]), 1,4-&beta;-mannosyl-''N''-acetylglucosamine phosphorylase (EC [{{EClink}}2.4.1.320 2.4.1.320]), 1,2-&beta;-oligomannan phosphorylase, and &beta;-1,2-mannnobiose phosphorylase are members of this family. A GH130 mannoside phosphorylase, unknown human gut bacterium mannoside phosphorylase (UhgbMP), discovered by functional metagenomics of the human gut microbiota, phosphorolyzes 4-''O''-&beta;-D-mannosyl-N,N'-diacetylchitobiose, and exhibits higher synthetic activity when using ''N'',''N'''-diacetylchitobiose as an acceptor substrate compared to ''N''-acetyl-D-glucosamine <cite>Ladeveze2013</cite>.
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==
GH130 phosphorylases phosphorolyze &beta;-mannosidic linkage at the non-reducing end of substrates with net inversion of anomeric configuration. Senoura et al. <cite>Senoura2011</cite> demonstrated that 4-''O''-&beta;-D-mannosyl-D-glucose phosphorylase from ''Bacteroides fragilis'' (BfMGP) produces &alpha;-mannose 1-phosphate and glucose from 4-''O''-&beta;-D-mannosyl-D-glucose and inorganic phosphate. A unique reaction mechanism of GH130 enzymes has been proposed on the basis of the three-dimensional strucuture of BfMGP <cite>Nakae2013</cite>. In contrast to known inverting glycoside phosphorylases, whose general acid catalyst directly donates a proton to glycosidic oxygen, the catalytic Asp of GH130 enzymes (Asp131 in BfMGP) donates a proton to O3 of mannosyl group bound to subsite -1, and a proton is tranferred to the glycosidic oxygen from 3OH group of the mannosyl residue. Inorganic phosphate attacks C1 of the mannosyl residue at the non-reducing end of substrate and &alpha;-mannose 1-phosphate is generated.
+
GH130 phosphorylases phosphorolyze &beta;-mannosidic linkage at the non-reducing end of substrates with net inversion of anomeric configuration affording &alpha;-mannose-1-phosphate. Senoura et al. <cite>Senoura2011</cite> demonstrated that 4-''O''-&beta;-D-mannosyl-D-glucose phosphorylase from ''Bacteroides fragilis'' (BfMGP) produces &alpha;-mannose 1-phosphate and glucose from 4-''O''-&beta;-D-mannosyl-D-glucose and inorganic phosphate. A unique proton relay mechanism for GH130 enzymes was proposed on the basis of the three-dimensional strucuture of BfMGP <cite>Nakae2013</cite>. In contrast to other inverting glycoside phosphorylases, where a general acid catalyst is proposed to directly protonate the glycosidic oxygen, the catalytic Asp of GH130 enzymes (Asp131 in BfMGP) donates a proton to O3 of mannosyl group bound to subsite -1, and a proton is transferred intramolecularly to the glycosidic oxygen from 3OH group. Inorganic phosphate attacks C1 of the mannosyl residue at the non-reducing end of substrate and &alpha;-mannose 1-phosphate is generated.
  
 
== Catalytic Residues ==
 
== Catalytic Residues ==
Ladevèze et al. <cite>Ladeveze2013</cite> compared 369 protein sequences of GH130 members and selected Asp104, Glu273, and Asp304 of UhgbMP as putative catalytic amino acid residues. Substitution of these acidic amino acid residues resulted in large reduction of enzyme activity. Especially, the D104N mutation comletely abolished the activity. Consistent with this result, three dimensional structure analysis demonstrated that only Asp131 of BfMGP, corresponding to Asp104 of UhgbMP, is situated near the scicile glycosidic oxigen <cite>Nakae2013</cite>. However, this Asp appeared to be too distant from the the scicile glycosidic oxigen for a direct protonation. Thus the proton relay mechanism described above has been posturated.
+
Ladevèze et al. <cite>Ladeveze2013</cite> compared 369 protein sequences of GH130 members and selected Asp104, Glu273, and Asp304 of UhgbMP as putative catalytic amino acid residues. Mutation of these acidic amino acid residues resulted in large reduction of enzyme activity. Especially, the D104N mutation completely abolished the catalytic activity. Consistent with this result, three dimensional structure analysis demonstrated that only Asp131 of BfMGP, corresponding to Asp104 of UhgbMP, is situated near the glycosidic oxygen <cite>Nakae2013</cite>. However, this Asp appeared to be too distant from the the glycosidic oxygen for direct protonation, and the proton relay mechanism described above was therefore proposed.
 
   
 
   
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
Three-dimensinal structure of BfMGP has been first reported as a characterized enzyme <cite>Nakae2013</cite>. The structures of BfMGP in complex with phosphate; 4-''O''-&beta;-D-mannosyl-D-glucose and phosphate; mannose, glucose, and phosphate; and &alpha;-mannose 1-phosphate were determined. The structure of catalytic domain of BfMGP is a five-bladed &beta;-propeller fold. BfMGP forms a homohexamer. It has long &alpha;-helices at the N- and C-termini, and these structure are predicted to be responsible for the quaternary structure formation.
+
Three-dimensional structures of several GH130 phosphorylases have been reported. The structure of ''Bacteroides fragilis'' BfMGP has been reported in complex with phosphate; 4-''O''-&beta;-D-mannosyl-D-glucose and phosphate; mannose, glucose, and phosphate; and &alpha;-mannose 1-phosphate <cite>Nakae2013</cite>. BfMGP forms a homohexamer, and each monomer has a five-bladed &beta;-propeller fold. It has long &alpha;-helices at the N- and C-termini, and these structure are predicted to be responsible for the quaternary structure formation.
  
 
== Family Firsts ==
 
== Family Firsts ==
Line 52: Line 52:
 
: Thermoanaerobacter sp. X-514 &beta;-1,2-mannnobiose phosphorylase <cite>Chiku2014</cite>   
 
: Thermoanaerobacter sp. X-514 &beta;-1,2-mannnobiose phosphorylase <cite>Chiku2014</cite>   
  
;First 3-D structure: BfMGP <cite>Nakae2013</cite>
+
;First 3-D structure: ''Bacteroides fragis'' BfMGP <cite>Nakae2013</cite>
  
 
== References ==
 
== References ==

Revision as of 17:52, 24 March 2015

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Glycoside Hydrolase Family GH130
Clan none
Mechanism inverting
Active site residues known
CAZy DB link
http://www.cazy.org/GH130.html


Substrate specificities

Family GH130 contains phosphorylases that catalyze the phosphorolysis of β-mannosidic linkages at the non-reducing end of substrates. 4-O-β-D-Mannosyl-D-glucose phosphorylase (EC 2.4.1.281), β-1,4-mannooligosaccharide phosphorylase (EC 2.4.1.319), 1,4-β-mannosyl-N-acetylglucosamine phosphorylase (EC 2.4.1.320), 1,2-β-oligomannan phosphorylase, and β-1,2-mannnobiose phosphorylase are members of this family. A GH130 mannoside phosphorylase, unknown human gut bacterium mannoside phosphorylase (UhgbMP), discovered by functional metagenomics of the human gut microbiota, phosphorolyzes 4-O-β-D-mannosyl-N,N'-diacetylchitobiose, and exhibits higher synthetic activity when using N,N'-diacetylchitobiose as an acceptor substrate compared to N-acetyl-D-glucosamine [1].

Kinetics and Mechanism

GH130 phosphorylases phosphorolyze β-mannosidic linkage at the non-reducing end of substrates with net inversion of anomeric configuration affording α-mannose-1-phosphate. Senoura et al. [2] demonstrated that 4-O-β-D-mannosyl-D-glucose phosphorylase from Bacteroides fragilis (BfMGP) produces α-mannose 1-phosphate and glucose from 4-O-β-D-mannosyl-D-glucose and inorganic phosphate. A unique proton relay mechanism for GH130 enzymes was proposed on the basis of the three-dimensional strucuture of BfMGP [3]. In contrast to other inverting glycoside phosphorylases, where a general acid catalyst is proposed to directly protonate the glycosidic oxygen, the catalytic Asp of GH130 enzymes (Asp131 in BfMGP) donates a proton to O3 of mannosyl group bound to subsite -1, and a proton is transferred intramolecularly to the glycosidic oxygen from 3OH group. Inorganic phosphate attacks C1 of the mannosyl residue at the non-reducing end of substrate and α-mannose 1-phosphate is generated.

Catalytic Residues

Ladevèze et al. [1] compared 369 protein sequences of GH130 members and selected Asp104, Glu273, and Asp304 of UhgbMP as putative catalytic amino acid residues. Mutation of these acidic amino acid residues resulted in large reduction of enzyme activity. Especially, the D104N mutation completely abolished the catalytic activity. Consistent with this result, three dimensional structure analysis demonstrated that only Asp131 of BfMGP, corresponding to Asp104 of UhgbMP, is situated near the glycosidic oxygen [3]. However, this Asp appeared to be too distant from the the glycosidic oxygen for direct protonation, and the proton relay mechanism described above was therefore proposed.

Three-dimensional structures

Three-dimensional structures of several GH130 phosphorylases have been reported. The structure of Bacteroides fragilis BfMGP has been reported in complex with phosphate; 4-O-β-D-mannosyl-D-glucose and phosphate; mannose, glucose, and phosphate; and α-mannose 1-phosphate [3]. BfMGP forms a homohexamer, and each monomer has a five-bladed β-propeller fold. It has long α-helices at the N- and C-termini, and these structure are predicted to be responsible for the quaternary structure formation.

Family Firsts

First stereochemistry determination
BfMGP [2]
First general acid residue identification
BfMGP [3]
First sequence identification
BfMGP [2]
Ruminococcus albus β-1,4-mannooligosaccharide phosphorylase [4]
Bacteroides thetaiotaomicron 4-O-β-D-Mannosyl-D-glucose phosphorylase [5]
Thermoanaerobacter sp. X-514 1,2-β-oligomannan phosphorylase [6]
Thermoanaerobacter sp. X-514 β-1,2-mannnobiose phosphorylase [6]
First 3-D structure
Bacteroides fragis BfMGP [3]

References

  1. Ladevèze S, Tarquis L, Cecchini DA, Bercovici J, André I, Topham CM, Morel S, Laville E, Monsan P, Lombard V, Henrissat B, and Potocki-Véronèse G. (2013) Role of glycoside phosphorylases in mannose foraging by human gut bacteria. J Biol Chem. 288, 32370-32383. DOI:10.1074/jbc.M113.483628 | PubMed ID:24043624 | HubMed [Ladeveze2013]
  2. Senoura T, Ito S, Taguchi H, Higa M, Hamada S, Matsui H, Ozawa T, Jin S, Watanabe J, Wasaki J, and Ito S. (2011) New microbial mannan catabolic pathway that involves a novel mannosylglucose phosphorylase. Biochem Biophys Res Commun. 408, 701-6. DOI:10.1016/j.bbrc.2011.04.095 | PubMed ID:21539815 | HubMed [Senoura2011]
  3. Nakae S, Ito S, Higa M, Senoura T, Wasaki J, Hijikata A, Shionyu M, Ito S, and Shirai T. (2013) Structure of novel enzyme in mannan biodegradation process 4-O-β-D-mannosyl-D-glucose phosphorylase MGP. J Mol Biol. 425, 4468-78. DOI:10.1016/j.jmb.2013.08.002 | PubMed ID:23954514 | HubMed [Nakae2013]
  4. Kawahara R, Saburi W, Odaka R, Taguchi H, Ito S, Mori H, and Matsui H. (2012) Metabolic mechanism of mannan in a ruminal bacterium, Ruminococcus albus, involving two mannoside phosphorylases and cellobiose 2-epimerase: discovery of a new carbohydrate phosphorylase, β-1,4-mannooligosaccharide phosphorylase. J Biol Chem. 287, 42389-99. DOI:10.1074/jbc.M112.390336 | PubMed ID:23093406 | HubMed [Kawahara2012]
  5. Nihira T, Suzuki E, Kitaoka M, Nishimoto M, Ohtsubo K, and Nakai H. (2013) Discovery of β-1,4-D-mannosyl-N-acetyl-D-glucosamine phosphorylase involved in the metabolism of N-glycans. J Biol Chem. 288, 27366-27374. DOI:10.1074/jbc.M113.469080 | PubMed ID:23943617 | HubMed [Nihira2013]
  6. Chiku K, Nihira T, Suzuki E, Nishimoto M, Kitaoka M, Ohtsubo K, and Nakai H. (2014) Discovery of two β-1,2-mannoside phosphorylases showing different chain-length specificities from Thermoanaerobacter sp. X-514. PLoS One. 9, e114882. DOI:10.1371/journal.pone.0114882 | PubMed ID:25500577 | HubMed [Chiku2014]
All Medline abstracts: PubMed | HubMed