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Difference between revisions of "Glycoside Hydrolase Family 112"

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* [[Author]]: [[User:Motomitsu Kitaoka|Motomitsu Kitaoka]]
 
* [[Author]]: [[User:Motomitsu Kitaoka|Motomitsu Kitaoka]]
* [[Responsible Curator]]:  [[User:ShinyaFushinobu|Shinya Fushinobu]]
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* [[Responsible Curator]]:  [[User:Shinya Fushinobu|Shinya Fushinobu]]
 
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|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 
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| colspan="2" |http://www.cazy.org/fam/GH112.html
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| colspan="2" |{{CAZyDBlink}}GH112.html
 
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</div>
 
</div>
  
 
== Substrate specificities ==
 
== Substrate specificities ==
This family contains beta-galactoside phosphorolyzing enzymes, &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase (EC [http://us.expasy.org/cgi-bin/nicezyme.pl?2.4.1.211 2.4.1.211]) <cite>REF1</cite>  and &beta;-1,4-D-galactosyl-L-rhamnose phosphorylase (EC 2.4.1.-) <cite>REF2</cite>. The former enzymes are subcategorized into galacto-''N''-biose phosphorylase, (GNBP) <cite>REF3</cite>, lacto-''N''-biose I phosphorylase (LNBP) <cite>REF4</cite>, and galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) <cite>REF1,REF4,REF5</cite> based on the substrate preference on galacto-''N''-biose (GNB, Gal-&beta;1,3-GalNAc) and lacto-''N''-biose I (LNB, Gal-&beta;1,3-GlcNAc) <cite>REF4</cite>.
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This family of [[glycoside hydrolases]] contains [[phosphorylases]]; beta-galactoside phosphorylase, &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase (EC [{{EClink}}2.4.1.211 2.4.1.211]) <cite>DerensyDron1999</cite>  and &beta;-1,4-D-galactosyl-L-rhamnose phosphorylase (EC 2.4.1.-) <cite>Nakajima2009</cite>. The former enzymes are subcategorized into galacto-''N''-biose phosphorylase, (GNBP) <cite>NakajimaAMB2008</cite>, lacto-''N''-biose I phosphorylase (LNBP) <cite>NakajimaAEM2008</cite>, and galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) <cite>DerensyDron1999 NakajimaAEM2008 Kitaoka2005</cite> based on the substrate preference on galacto-''N''-biose (GNB, Gal-&beta;1,3-GalNAc) and lacto-''N''-biose I (LNB, Gal-&beta;1,3-GlcNAc) <cite>NakajimaAEM2008</cite>.
  
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==
Phosphorolysis by GH112 enzymes proceeds with inversion of anomeric configuration, as first shown by Derensy-Dron et al. <cite>REF1</cite> on &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium bifidum'', i.e. LNB + Pi &harr; &alpha;-galactose 1-phosphate + GlcNAc. Considering the topology of the active site structure, the reaction mechanism for inverting phosphorylase is proposed to be similar to that for inverting GH. With the aid of general acid residue, the enzymatic phosphorolysis begins with direct nucleophilic attack by phosphate on the anomeric C-1 carbon, instead of the water molecule activated by a general base residue in inverting GH reaction.
+
Phosphorolysis by GH112 enzymes proceeds with inversion of anomeric configuration, as first shown by Derensy-Dron et al. <cite>DerensyDron1999</cite> on &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium bifidum'', i.e. LNB + Pi &harr; &alpha;-galactose 1-phosphate + GlcNAc. Considering the topology of the active site structure, the reaction mechanism for [[inverting]] phosphorylase is proposed to be similar to that for [[inverting]] glycoside hydrolases. With the aid of general acid residue, the enzymatic phosphorolysis occurs through direct nucleophilic attack by phosphate on the anomeric C-1 carbon, instead of the water molecule activated by a general base residue in the [[Glycoside Hydrolases#Inverting glycoside hydrolases | inverting glycoside hydrolase]] reaction.
  
 
== Catalytic Residues ==
 
== Catalytic Residues ==
The catalytic proton donar residue was firstly estimated by mutational analysis on &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>REF6</cite>. Catalytic nucleophile is phosphate.
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The [[general acid]] residue was firstly estimated by mutational analysis on &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>Nishimoto2007</cite>.
  
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
The first solved 3-D structure was &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>REF7</cite>. The catalytic domain consists of a partially broken TIM barrel fold that is structurally similar to a &beta;-galactosidase of [[Glycoside Hydrolase Family 42]], supporting the classification of these phosphorolytic enzymes as one of the GH families. A large conformational change in TIM barrel scaffold was observerd with substrate-binding.
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[[Image:GLNBPmov.gif|'''Figure 1:''' Movement of the catalytic TIM barrel domain induced by substrate binding. <span style="color:#0000ff"> The TIM barrel domain is in blue</span>, <span style="color:#00cc00"> an IG-like domain is in green </span>, <span style="color:#999900"> an &alpha;/&beta; domain is in yellow </span> and <span style="color:#ff0000"> a C-terminal domain is in red </span>.|frame|right]]
 +
The first solved 3-D structure was &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' (PDB [{{PDBlink}}2zuv 2ZUV] in complex with GlcNAc, ethylene glycol, and nitrate) <cite>Hidaka2009</cite>. The catalytic domain consists of a partially broken TIM barrel fold that is structurally similar to a &beta;-galactosidase of [[Glycoside Hydrolase Family 42]], supporting the classification of these phosphorolytic enzymes as one of the GH families. A large conformational change in TIM barrel scaffold was observerd with substrate-binding ('''Figure 1''').
  
 
== Family Firsts ==
 
== Family Firsts ==
;First sterochemistry determination: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium bifidum'' <cite>REF1</cite>.
+
;First sterochemistry determination: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium bifidum'' <cite>DerensyDron1999</cite>.
;First cloned: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>REF5</cite>.
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;First sequence identification: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>Kitaoka2005</cite>.
;First catalytic nucleophile identification: phosphate
+
;First [[general acid]] residue identification: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>Nishimoto2007</cite>.
;First general acid/base residue identification: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>REF6</cite>.
+
;First 3-D structure: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>Hidaka2009</cite>.
;First 3-D structure: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>REF7</cite>.
 
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
#REF1 pmid=9889079
+
#DerensyDron1999 pmid=9889079
#REF2 pmid=19491100
+
#Nakajima2009 pmid=19491100
#REF3 pmid=18183385
+
#NakajimaAMB2008 pmid=18183385
#REF4 pmid=18723650  
+
#NakajimaAEM2008 pmid=18723650  
#REF5 pmid=15933016
+
#Kitaoka2005 pmid=15933016
#REF6 pmid=17587697
+
#Nishimoto2007 pmid=17587697
#REF7 pmid=19124470
+
#Hidaka2009 pmid=19124470
 
 
 
</biblio>
 
</biblio>
  
 
[[Category:Glycoside Hydrolase Families|GH112]]
 
[[Category:Glycoside Hydrolase Families|GH112]]

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Glycoside Hydrolase Family 112
Clan none
Mechanism inverting
Active site residues known
CAZy DB link
http://www.cazy.org/GH112.html

Substrate specificities

This family of glycoside hydrolases contains phosphorylases; beta-galactoside phosphorylase, β-1,3-D-galactosyl-D-hexososamine phosphorylase (EC 2.4.1.211) [1] and β-1,4-D-galactosyl-L-rhamnose phosphorylase (EC 2.4.1.-) [2]. The former enzymes are subcategorized into galacto-N-biose phosphorylase, (GNBP) [3], lacto-N-biose I phosphorylase (LNBP) [4], and galacto-N-biose/lacto-N-biose I phosphorylase (GLNBP) [1, 4, 5] based on the substrate preference on galacto-N-biose (GNB, Gal-β1,3-GalNAc) and lacto-N-biose I (LNB, Gal-β1,3-GlcNAc) [4].

Kinetics and Mechanism

Phosphorolysis by GH112 enzymes proceeds with inversion of anomeric configuration, as first shown by Derensy-Dron et al. [1] on β-1,3-D-galactosyl-D-hexososamine phosphorylase from Bifidobacterium bifidum, i.e. LNB + Pi ↔ α-galactose 1-phosphate + GlcNAc. Considering the topology of the active site structure, the reaction mechanism for inverting phosphorylase is proposed to be similar to that for inverting glycoside hydrolases. With the aid of general acid residue, the enzymatic phosphorolysis occurs through direct nucleophilic attack by phosphate on the anomeric C-1 carbon, instead of the water molecule activated by a general base residue in the inverting glycoside hydrolase reaction.

Catalytic Residues

The general acid residue was firstly estimated by mutational analysis on β-1,3-D-galactosyl-D-hexososamine phosphorylase from Bifidobacterium longum [6].

Three-dimensional structures

Figure 1: Movement of the catalytic TIM barrel domain induced by substrate binding. The TIM barrel domain is in blue, an IG-like domain is in green , an α/β domain is in yellow and a C-terminal domain is in red .

The first solved 3-D structure was β-1,3-D-galactosyl-D-hexososamine phosphorylase from Bifidobacterium longum (PDB 2ZUV in complex with GlcNAc, ethylene glycol, and nitrate) [7]. The catalytic domain consists of a partially broken TIM barrel fold that is structurally similar to a β-galactosidase of Glycoside Hydrolase Family 42, supporting the classification of these phosphorolytic enzymes as one of the GH families. A large conformational change in TIM barrel scaffold was observerd with substrate-binding (Figure 1).

Family Firsts

First sterochemistry determination
β-1,3-D-galactosyl-D-hexososamine phosphorylase from Bifidobacterium bifidum [1].
First sequence identification
β-1,3-D-galactosyl-D-hexososamine phosphorylase from Bifidobacterium longum [5].
First general acid residue identification
β-1,3-D-galactosyl-D-hexososamine phosphorylase from Bifidobacterium longum [6].
First 3-D structure
β-1,3-D-galactosyl-D-hexososamine phosphorylase from Bifidobacterium longum [7].

References

  1. Derensy-Dron D, Krzewinski F, Brassart C, and Bouquelet S. (1999). Beta-1,3-galactosyl-N-acetylhexosamine phosphorylase from Bifidobacterium bifidum DSM 20082: characterization, partial purification and relation to mucin degradation. Biotechnol Appl Biochem. 1999;29 ( Pt 1):3-10. | Google Books | Open Library PubMed ID:9889079 [DerensyDron1999]
  2. Nakajima M, Nishimoto M, and Kitaoka M. (2009). Characterization of three beta-galactoside phosphorylases from Clostridium phytofermentans: discovery of d-galactosyl-beta1->4-l-rhamnose phosphorylase. J Biol Chem. 2009;284(29):19220-7. DOI:10.1074/jbc.M109.007666 | PubMed ID:19491100 [Nakajima2009]
  3. Nakajima M, Nihira T, Nishimoto M, and Kitaoka M. (2008). Identification of galacto-N-biose phosphorylase from Clostridium perfringens ATCC13124. Appl Microbiol Biotechnol. 2008;78(3):465-71. DOI:10.1007/s00253-007-1319-8 | PubMed ID:18183385 [NakajimaAMB2008]
  4. Nakajima M and Kitaoka M. (2008). Identification of lacto-N-Biose I phosphorylase from Vibrio vulnificus CMCP6. Appl Environ Microbiol. 2008;74(20):6333-7. DOI:10.1128/AEM.02846-07 | PubMed ID:18723650 [NakajimaAEM2008]
  5. Kitaoka M, Tian J, and Nishimoto M. (2005). Novel putative galactose operon involving lacto-N-biose phosphorylase in Bifidobacterium longum. Appl Environ Microbiol. 2005;71(6):3158-62. DOI:10.1128/AEM.71.6.3158-3162.2005 | PubMed ID:15933016 [Kitaoka2005]
  6. Nishimoto M and Kitaoka M. (2007). Identification of the putative proton donor residue of lacto-N-biose phosphorylase (EC 2.4.1.211). Biosci Biotechnol Biochem. 2007;71(6):1587-91. DOI:10.1271/bbb.70064 | PubMed ID:17587697 [Nishimoto2007]
  7. Hidaka M, Nishimoto M, Kitaoka M, Wakagi T, Shoun H, and Fushinobu S. (2009). The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: a large deformation of a TIM barrel scaffold. J Biol Chem. 2009;284(11):7273-83. DOI:10.1074/jbc.M808525200 | PubMed ID:19124470 [Hidaka2009]

All Medline abstracts: PubMed