Difference between revisions of "Glycoside Hydrolase Family 35"

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Author: ^^^Anna Kulminskaya^^^
Responsible Curator: ^^^Anna Kulminskaya^^^

Glycoside Hydrolase Family GH35
Clan	GH-A
Mechanism	retaining
Active site residues	known
CAZy DB link
http://www.cazy.org/GH35.html

Substrate specificities

The majority of GH35 members are β-galactosidases (EC 3.2.1.23). GH35 enzymes have been isolated from microorganisms such as fungi, bacteria and yeasts, as well as higher organisms such as plants, animals, and human cells. These β-galactosidases catalyse the hydrolysis of terminal non-reducing β-D-galactose residues in, for example, lactose (1,4-O-β-D-galactopyranosyl-D-glucose), oligosaccharides, glycolipids, and glycoproteins. Various GH35 β-galactosidases demonstrate specificity towards β1,3-, β1,6- or β1,4-galactosidic linkages [1, 2, 3], and are often most active under acidic conditions [4, 5, 6, 7]. As with many other CAZy families [8, 9, 10], GH35 members tend to be represented by multi-gene families in plants [3, 11, 12, 13, 14]. Moreover, plant GH35 β-galactosidases have be divided into two classes: members of the first are capable of hydrolyzing pectic β-1,4-galactans, while those of the second can specifically cleave β-1,3- and β1,6-galactosyl linkages of arabinogalactan proteins [15].

In addition to β-galactosidases, GH35 also contains a limited number of archeal exo-β-glucosaminidases (EC 3.2.1.165) [16, 17]. Such enzymes hydrolyze chitosan or chitosan oligosaccharides to remove successive D-glucosamine residues from non-reducing termini.

Kinetics and Mechanism

Beta-galactosidases of GH35 catalyze the hydrolysis of terminal β-galactosyl residues via a double-displacement mechanism, which leads to net retention of the β-anomeric configuration of the released galactose molecule. The stereochemistry of the reaction was first shown by NMR for the human β-galactosidase precursor [4] and has been subsequently confirmed by other investigators for microbial and plant enzymes [1, 6] .

Catalytic Residues

The catalytic residues for family 35 were first predicted on the basis of hydrophobic cluster analysis of proteins of similar protein fold [18]. Experimentally, the glutamic acid residue 268 was first identified as the catalytic nucleophile in human lysosomal β-galactosidase precursor using a slow substrate, 2,4-dinitrophenyl-2-deoxy-2-fluoro- β-D-galactopyranoside, that allowed trapping of a covalent glycosyl-enzyme intermediate. This allowed subsequent peptide mapping to exactly identify the catalytic nucleophile [19]. Subsequently, this approach was repeated for two bacterial β-galactosidases from Xanthomonas manihotis and Bacillus circulans [20]. The general acid/base catalyst was inferred to be Glu200 from structural studies of a Penicillium sp. β-galactosidase [21]. Recent structural studies [22] revealed two different conformations of the general acid/base catalyst in the β-galactosidase of Trichoderma reesei.

Three-dimensional structures

As of February 2011, only three enzymes from GH35 have been structurally characterized. The first 3D-structures of a GH35 enzyme, those of a β-galactosidase from Pencillium sp. (Psp-β-gal) in native (PDB 1tg7) and product-complexed (PDB 1xc6) forms, were reported in 2004 at 1.90 Å and 2.10 Å resolution, respectively [21]. The structure of a β-galactosidase from Bacteriodes thetaiotamicron was subsequently reported by the New York Structural GenomiX Research Consortium in 2008 at 2.15 Å resolution (PDB 3d3a). In 2010, a high (1.2 Å) resolution crystal structure of a Trichoderma reesei (Hypocrea jecorina) β-galactosidase (Tr-β-gal, PDB 3og2) was reported, together with complex structures with galactose, IPTG and PETG at 1.5, 1.75 and 1.4 Å resolutions, respectively (PDB codes 3ogr, 3ogs, and 3ogv, respectively) [22].

GH35 enzymes belong to Clan GH-A, and thus have a (α/β)₈ TIM barrel comprising the catalytic domain. A structural analysis of the galactose-binding active-site was based on the comparison of the crystallographic models of the native Psp-β-gal and Tr-β-gal enzymes and their respective complexes with galactose. A single galactose molecule is bound to the TIM barrel domain of the enzyme in the chair conformation in the β-anomeric configuration. Two glutamic acid residues act as the general acid-base and nucleophilic catalysts; these are presented on strands 4 and 7 of the barrel. Although the crystal structures of Psp-β-gal and Tr-β-gal are similar, interpretation of the structure of Tr-β-gal is somewhat different from that presented earlier for Psp-β-gal: Rojas et al. considered Psp-β-gal to be divided into five domains combining the second and the third domain, although they form separate sub-units in the structure [21]. In contrast, Maksimainen et al. concluded that the Tr-β-gal structure contains a central catalytic α/β-barrel surrounded by a horseshoe consisting of five anti-parallel β-sandwich structures [22].

Additionally, Maksimainen et al. have described conformational changes in two loop regions of the active site of Tr-β-gal, thus implicating a conformational selection mechanism for the enzyme. The acid/base catalyst Glu200 exhibited two different conformations which affect the pK_a value of this residue and thus the catalytic mechanism.

Family Firsts

First stereochemistry determination

Human β-galactosidase precursor by NMR [4]

First catalytic nucleophile identification

Human β-galactosidase precursor by 2-fluorogalactose labeling [19].

First general acid/base residue identification

Penicillium sp. β-galactosidase by structural identification [21].

First 3-D structure

Penicillium sp. β-galactosidase [21].

References

All Medline abstracts: PubMed

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-The majority of GH35 members are β-galactosidases (EC [{{EClink}}3.2.1.23 3.2.1.23]).  GH35 enzymes have been isolated from microorganisms such as fungi, bacteria and yeasts, as well as higher organisms such as plants, animals, and human cells.  These β-galactosidases catalyse the hydrolysis of terminal non-reducing β-D-galactose residues in, for example, lactose (1,4-O-β-D-galactopyranosyl-D-glucose), oligosaccharides, glycolipids, and glycoproteins. Various GH35 β-galactosidases demonstrate specificity towards β1,3-, β1,6- or  β1,4-galactosidic linkages '''(REFS NEEDED)''', and are often most active under acidic conditions '''(REFS NEEDED)'''.  As with many other CAZy families <cite>GeislerLee2006, Henrissat2001, Tuskan2006</cite>, GH35 members tend to be represented by multi-gene families in plants <cite>Ahn2007, Smith2000, Lazan2004, Ross1994, Tanthanuch2008</cite>. Moreover, plant GH35 β-galactosidases have be divided into two classes: members of the first are capable of hydrolyzing pectic β-1,4-galactans, while those of the second can specifically cleave β-1,3- and β1,6-galactosyl linkages of arabinogalactan proteins '''(REFS NEEDED)'''.
+The majority of GH35 members are β-galactosidases (EC [{{EClink}}3.2.1.23 3.2.1.23]).  GH35 enzymes have been isolated from microorganisms such as fungi, bacteria and yeasts, as well as higher organisms such as plants, animals, and human cells.  These β-galactosidases catalyse the hydrolysis of terminal non-reducing β-D-galactose residues in, for example, lactose (1,4-O-β-D-galactopyranosyl-D-glucose), oligosaccharides, glycolipids, and glycoproteins. Various GH35 β-galactosidases demonstrate specificity towards β1,3-, β1,6- or  β1,4-galactosidic linkages <cite>Zinin2002, Gamauf2007, Tanthanuch2008</cite>, and are often most active under acidic conditions <cite>Zhang1994, van Casteren2000, Wang2009</cite>.  As with many other CAZy families <cite>GeislerLee2006, Henrissat2001, Tuskan2006</cite>, GH35 members tend to be represented by multi-gene families in plants <cite>Ahn2007, Smith2000, Lazan2004, Ross1994, Tanthanuch2008</cite>. Moreover, plant GH35 β-galactosidases have be divided into two classes: members of the first are capable of hydrolyzing pectic β-1,4-galactans, while those of the second can specifically cleave β-1,3- and β1,6-galactosyl linkages of arabinogalactan proteins <cite>Kotake2005</cite>.
-In addition to β-galactosidases, GH35 also contains a limited number of archeal exo-β-glucosaminidases (EC [{{EClink}}3.2.1.165 3.2.1.165]) <cite>Tanaka2003 Kawarabayasi1998</cite> '''(NEED ORIGINAL BIOCHEMICAL REF FOR PYROCCOCCUS ENZYME; NOT GENOME PAPER)'''. Such enzymes hydrolyze chitosan or chitosan oligosaccharides to remove successive D-glucosamine residues from non-reducing termini.
+In addition to β-galactosidases, GH35 also contains a limited number of archeal exo-β-glucosaminidases (EC [{{EClink}}3.2.1.165 3.2.1.165]) <cite>Tanaka2003 Liu2006</cite>. Such enzymes hydrolyze chitosan or chitosan oligosaccharides to remove successive D-glucosamine residues from non-reducing termini.
 == Kinetics and Mechanism ==
-Beta-galactosidases of GH35 catalyze the hydrolysis of terminal β-galactosyl residues via a double-displacement mechanism, which leads to net retention of the β-anomeric configuration of the released galactose molecule. The stereochemistry of the reaction was first shown by NMR for the human β-galactosidase precursor <cite>Zhang1994</cite> and has been subsequently confirmed by other investigators for microbial and plant enzymes '''(REFS NEEDED)'''.
+Beta-galactosidases of GH35 catalyze the hydrolysis of terminal β-galactosyl residues via a double-displacement mechanism, which leads to net retention of the β-anomeric configuration of the released galactose molecule. The stereochemistry of the reaction was first shown by NMR for the human β-galactosidase precursor <cite>Zhang1994</cite> and has been subsequently confirmed by other investigators for microbial and plant enzymes <cite>Casteren2000, Zinin2002</cite> .
 == Catalytic Residues ==
-The catalytic residues for family 35 were first predicted on the basis of hydrophobic cluster analysis of proteins of similar protein fold <cite>Henrissat1995</cite>. Experimentally, the glutamic acid residue 268 was first identified as the catalytic nucleophile in human lysosomal β-galactosidase precursor using a slow substrate, 2,4-dinitrophenyl-2-deoxy-2-fluoro- β-D-galactopyranoside, that allowed trapping of a covalent glycosyl-enzyme intermediate. This allowed subsequent peptide mapping to exactly identify the catalytic nucleophile <cite>McCarter</cite>. Subsequently, this approach was repeated for two bacterial β-galactosidases from ''Xanthomonas manihotis'' and ''Bacillus circulans'' <cite>Blanchard2001</cite>. The general acid/base catalyst was inferred to be  Glu200 from structural studies of a ''Penicillium'' sp. β-galactosidase <cite>Rojas2004</cite>. Recent structural studies <cite>Maksimainen2010</cite> revealed two different conformations of the general acid/base catalyst in the β-galactosidase of ''Trichoderma reesei''.
+The catalytic residues for family 35 were first predicted on the basis of hydrophobic cluster analysis of proteins of similar protein fold <cite>Henrissat1995</cite>. Experimentally, the glutamic acid residue 268 was first identified as the catalytic nucleophile in human lysosomal β-galactosidase precursor using a slow substrate, 2,4-dinitrophenyl-2-deoxy-2-fluoro- β-D-galactopyranoside, that allowed trapping of a covalent glycosyl-enzyme intermediate. This allowed subsequent peptide mapping to exactly identify the catalytic nucleophile <cite>McCarter1997</cite>. Subsequently, this approach was repeated for two bacterial β-galactosidases from ''Xanthomonas manihotis'' and ''Bacillus circulans'' <cite>Blanchard2001</cite>. The general acid/base catalyst was inferred to be  Glu200 from structural studies of a ''Penicillium'' sp. β-galactosidase <cite>Rojas2004</cite>. Recent structural studies <cite>Maksimainen2010</cite> revealed two different conformations of the general acid/base catalyst in the β-galactosidase of ''Trichoderma reesei''.
 == Three-dimensional structures ==
@@ Line 67: / Line 67: @@
 #Tanthanuch2008 pmid=18664295
 #Tanka2003 pmid=12923090
-#Kawarabayasi1998 pmid=9679203
+#Liu2006 pmid=16912928
 #Zhang1994 pmid=7998946
 #Henrissat1995 pmid=7624375
@@ Line 77: / Line 77: @@
 #Henrissat2001 pmid=11554480
 #Tuskan2006 pmid=16973872
+#Gamauf2007 pmid=17381511
+#Zinin2002 pmid=11909597
+#van Casteren2000 pmid=11086688
+#Wang2009 pmid=19453169
+#Kotake2005 pmid=15980190
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH035]]