Difference between revisions of "Glycoside Hydrolase Family 35"

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

Substrate specificities

The majority of glycoside hydrolases of GH35 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 β-1,3-, β-1,6- or β-1,4-galactosidic linkages [1, 2, 3], and are often most active under acidic conditions [4, 5, 6]. As with many other CAZy families [7, 8, 9], GH35 members tend to be represented by multi-gene families in plants [3, 10, 11, 12, 13]. 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 β-1,6-galactosyl linkages of arabinogalactan proteins [14].

In addition to β-galactosidases, GH35 also contains a limited number of archeal exo-β-glucosaminidases (EC 3.2.1.165) [15, 16]. 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 classical Koshland retaining 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, 5] .

Catalytic Residues

The catalytic residues for family 35 were first predicted on the basis of hydrophobic cluster analysis of proteins of similar protein fold [17]. 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, which allowed trapping of a covalent glycosyl-enzyme intermediate and subsequent peptide mapping [18]. This approach was repeated for two bacterial β-galactosidases from Xanthomonas manihotis and Bacillus circulans [19]. The general acid/base residue was inferred to be Glu200 from structural studies of a Penicillium sp. β-galactosidase [20]. Recent structural studies (vide infra) revealed two different conformations of the general acid/base residue in the β-galactosidase of Trichoderma reesei [21].

Three-dimensional structures

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 [20]. The structure of a β-galactosidase from Bacteriodes thetaiotamicron (Btm-β-gal) was subsequently reported by the New York Structural GenomiX Research Consortium in 2008 at 2.15 Å resolution (PDB 3d3a). In 2010, an atomic (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) [21].

GH35 enzymes belong to Clan GH-A, and thus have an (α/β)₈ (TIM) barrel as the catalytic domain, in which two glutamic acid residues act as the general acid-base and nucleophilic catalysts. These residues are located in strands 4 and 7 of the barrel.

The comparison of the native structures of Psp-β-gal, Tr-β-gal and Btmβ-gal reveals two things (Figure 1): Firstly, Btm-β-gal consists of three distinct domains, whereas Psp-β-gal and Tr-β-gal consist of five and six domains, respectively. The second and third domains of Btm-β-gal are quite similar with the fourth and fifth domains of Psp-β-gal, and with the fifth and sixth domains of Tr-β-gal. Secondly, major structural differences between Psp-β-gal and Tr-β-gal are in the conformations of the loop regions. Although the crystal structures of Psp-β-gal and Tr-β-gal are similar, the 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 composed of five distinct structural domains. The overall structure is built around the first, TIM barrel, domain. Domain 2 is an all β-sheet domain containing an immunoglobulin-like subdomain, Domain 3 is based on a Greek-key β-sandwich, and Domains 4 and 5 are jelly rolls [20]. In contrast, Maksimainen et al. concluded the domain 2 includes two different domains and thus the Tr-β-gal and Psp-β-gal structures both form six similar domains [21].

The superimposition of the active sites of the GH35 β-galactosidases shows a remarkable similarity. In addition to the catalytic residues, the active sites of the GH35 β-galactosidases contain many identical residues (Figure 1B). Based on the galactose-bound crystallographic models of Psp-β-gal and Tr-β-gal, a single galactose molecule is bound to the active site of the GH35 enzyme in the chair conformation in the β-anomeric configuration.

Additionally, Maksimainen et al. have described conformational changes in two loop regions of the active site of Tr-β-gal, that implicates a conformational selection mechanism for the enzyme (Figure 2). Unlike the induced fit theory, which assumes that the initial interaction between a protein and its binding partner induces a conformational change in the protein through a stepwise process, the conformational selection theory is based on the assumption that the unbound protein exists as an ensemble of conformations in dynamic equilibrium. Interaction between a weakly populated, higher-energy conformation and a binding partner causes the equilibrium to move in favor of the selected conformation [22, 23]. This can be seen in the structures of Tr-β-gal: the open and closed conformation are both favorable in the native structure and the closed conformation becomes more favorable in the complex structures. Furthermore, The acid/base catalyst Glu200 has two different conformations in the IPTG and PETG complex structures that clearly affects the pK_a value of this residue and thus the catalytic mechanism of the enzyme [21].

Structure images

Figure 1. Comparison of the native structures of GH35 β-galactosidases. A. Global structures, B. Active sites. Psp-β-gal (PDB code 1tg7), Tr-β-gal (PDB code 3og2) and Btm-β-gal (PDB code 3d3a) are colored in green, brown and blue, respectively.

Figure 2. Illustration of the conformational selection mechanism observed in Tr-β-gal [21].

Family Firsts

First stereochemistry determination

Retaining stereochemical outcome for human β-galactosidase precursor by NMR [4]

First catalytic nucleophile identification

Human β-galactosidase precursor by 2-fluorogalactose labeling [18].

First general acid/base residue identification

Penicillium sp. β-galactosidase by structural identification [20].

First 3-D structure

Penicillium sp. β-galactosidase [20].

References

All Medline abstracts: PubMed

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-{{UnderConstruction}}
+{{CuratorApproved}}
-* [[Author]]: ^^^Anna Kulminskaya^^^, ^^^Mirko Maksimainen^^^, Juha Rouvinen
+* [[Author]]s: [[User:Anna Kulminskaya|Anna Kulminskaya]], [[User:Mirko Maksimainen|Mirko Maksimainen]], [[User:Juha Rouvinen|Juha Rouvinen]]
-* [[Responsible Curator]]:  ^^^Anna Kulminskaya^^^
+* [[Responsible Curator]]:  [[User:Anna Kulminskaya|Anna Kulminskaya]]
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@@ 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 <cite>Zinin2002, Gamauf2007, Tanthanuch2008</cite>, and are often most active under acidic conditions <cite>Zhang1994, vanCasteren2000, 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>.
+The majority of [[glycoside hydrolases]] of GH35 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 β-1,3-, β-1,6- or  β-1,4-galactosidic linkages <cite>Zinin2002, Gamauf2007, Tanthanuch2008</cite>, and are often most active under acidic conditions <cite>Zhang1994, vanCasteren2000, 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 β-1,6-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 Liu2006</cite>. 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 <cite>vanCasteren2000, Zinin2002</cite> .
+Beta-galactosidases of GH35 catalyze the hydrolysis of terminal β-galactosyl residues via a [[classical Koshland retaining 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>vanCasteren2000, 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>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''.
+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, which allowed trapping of a covalent glycosyl-enzyme intermediate and subsequent peptide mapping <cite>McCarter1997</cite>. This approach was repeated for two bacterial β-galactosidases from ''Xanthomonas manihotis'' and ''Bacillus circulans'' <cite>Blanchard2001</cite>. The [[general acid/base]] residue was inferred to be Glu200 from structural studies of a ''Penicillium'' sp. β-galactosidase <cite>Rojas2004</cite>. Recent structural studies (''vide infra'') revealed two different conformations of the [[general acid/base]] residue in the β-galactosidase of ''Trichoderma reesei'' <cite> Maksimainen2010</cite>.
 == 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 [{{PDBlink}}1tg7 1tg7]) and product-complexed (PDB [{{PDBlink}}1xc6 1xc6]) forms, were reported in 2004 at 1.90 Å and 2.10 Å resolution, respectively <cite>Rojas2004</cite>.  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 [{{PDBlink}}3d3a 3d3a]). In 2010, a high (1.2 Å) resolution crystal structure of a ''Trichoderma reesei'' (''Hypocrea jecorina'') β-galactosidase (Tr-β-gal, PDB [{{PDBlink}}3og2 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 [{{PDBlink}}3ogr 3ogr], [{{PDBlink}}3ogs 3ogs], and [{{PDBlink}}3ogv 3ogv], respectively) <cite>Maksimainen2010</cite>.
+The first 3D-structures of a GH35 enzyme, those of a β-galactosidase from ''Pencillium'' sp. (Psp-β-gal) in native (PDB [{{PDBlink}}1tg7 1tg7]) and product-complexed (PDB [{{PDBlink}}1xc6 1xc6]) forms, were reported in 2004 at 1.90 Å and 2.10 Å resolution, respectively <cite>Rojas2004</cite>.  The structure of a β-galactosidase from ''Bacteriodes thetaiotamicron'' (Btm-β-gal) was subsequently reported by the New York Structural GenomiX Research Consortium in 2008 at 2.15 Å resolution (PDB [{{PDBlink}}3d3a 3d3a]). In 2010, an atomic (1.2 Å) resolution crystal structure of a ''Trichoderma reesei'' (''Hypocrea jecorina'') β-galactosidase (Tr-β-gal, PDB [{{PDBlink}}3og2 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 [{{PDBlink}}3ogr 3ogr], [{{PDBlink}}3ogs 3ogs], and [{{PDBlink}}3ogv 3ogv], respectively) <cite>Maksimainen2010</cite>.
-GH35 enzymes belong to Clan GH-A, and thus have a (α/β)<sub>8</sub> 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 composed of five distinct structural domains. The overall structure is built around the first, TIM barrel, domain. Domain 2 us an all β-sheet domain containing an immunoglobulin-like subdomain, domain 3 is based on a Greek-key β-sandwich and domains 4 and 5 are jelly rolls <cite>Rojas2004</cite>. In contrast, Maksimainen et al. concluded that the Tr-β-gal and Psp-β-gal structures both form six similar domains and <cite>Maksimainen2010</cite>. The most of the structural differences between them are in the conformations of the loop regions.
+GH35 enzymes belong to Clan GH-A, and thus have an (α/β)<sub>8</sub> (TIM) barrel as the catalytic domain, in which two glutamic acid residues act as the general acid-base and nucleophilic catalysts. These residues are located in strands 4 and 7 of the barrel.
-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 p''K''<sub>a</sub> value of this residue and thus the catalytic mechanism.
+The comparison of the native structures of Psp-β-gal, Tr-β-gal and Btmβ-gal reveals two things ('''Figure 1'''): Firstly, Btm-β-gal consists of three distinct domains, whereas Psp-β-gal and Tr-β-gal consist of five and six domains, respectively. The second and third domains of Btm-β-gal are quite similar with the fourth and fifth domains of Psp-β-gal, and with the fifth and sixth domains of Tr-β-gal. Secondly, major structural differences between Psp-β-gal and Tr-β-gal are in the conformations of the loop regions. Although the crystal structures of Psp-β-gal and Tr-β-gal are similar, the 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 composed of five distinct structural domains. The overall structure is built around the first, TIM barrel, domain. Domain 2 is an all β-sheet domain containing an immunoglobulin-like subdomain, Domain 3 is based on a Greek-key β-sandwich, and Domains 4 and 5 are jelly rolls <cite>Rojas2004</cite>. In contrast, Maksimainen et al. concluded the domain 2 includes two different domains and thus the Tr-β-gal and Psp-β-gal structures both form six similar domains <cite>Maksimainen2010</cite>.
+The superimposition of the active sites of the GH35 β-galactosidases shows a remarkable similarity. In addition to the catalytic residues, the active sites of the GH35 β-galactosidases contain many identical residues ('''Figure 1B'''). Based on the galactose-bound crystallographic models of Psp-β-gal and Tr-β-gal, a single galactose molecule is bound to the active site of the GH35 enzyme in the chair conformation in the β-anomeric configuration.
+Additionally, Maksimainen et al. have described conformational changes in two loop regions of the active site of Tr-β-gal, that implicates a conformational selection mechanism for the enzyme (Figure 2). Unlike the induced fit theory, which assumes that the initial interaction between a protein and its binding partner induces a conformational change in the protein through a stepwise process, the conformational selection theory is based on the assumption that the unbound protein exists as an ensemble of conformations in dynamic equilibrium. Interaction between a weakly populated, higher-energy conformation and a binding partner causes the equilibrium to move in favor of the selected conformation <cite>Tsai1999, Boehr2008</cite>. This can be seen in the structures of Tr-β-gal: the open and closed conformation are both favorable in the native structure and the closed conformation becomes more favorable in the complex structures. Furthermore, The acid/base catalyst Glu200 has two different conformations in the IPTG and PETG complex structures that clearly affects the p''K''<sub>a</sub> value of this residue and thus the catalytic mechanism of the enzyme <cite>Maksimainen2010</cite>.
 === Structure images ===
-[[File:GH35 comparison.png|thumb|left|1200px|'''Figure 1. A)''' Comparison of the native structures of the GH35 β-galactosidases. Psp-β-gal (PDB code [http://www.rcsb.org/pdb/explore/explore.do?structureId=1TG7 1tg7]), Tr-β-gal (PDB code [http://www.rcsb.org/pdb/search/structidSearch.do?structureId=3OG2 3og2]) and Btm-β-gal (PDB code [http://www.rcsb.org/pdb/explore/explore.do?structureId=3D3A 3d3a]) are colored in green, brown and blue, respectively. '''B)''' Comparison of the active sites of the GH35 β-galactosidases. Psp-β-gal, Tr-β-gal and Btm-β-gal are colored as above-mentioned.]]
+[[Image: GH35 comparison.png|thumb|left|750px|'''Figure 1. Comparison of the native structures of GH35 β-galactosidases.'''  A. Global structures, B. Active sites.  Psp-β-gal (PDB code [{{PDBlink}}1tg7 1tg7]), Tr-β-gal (PDB code [{{PDBlink}}3og2 3og2]) and Btm-β-gal (PDB code [{{PDBlink}}3d3a 3d3a]) are colored in green, brown and blue, respectively.]]
-[[File:Conf selection.png|thumb|left|1200px|'''Figure 2. A)''' Molecular recognition mechanisms in proteins: Induced fit vs. conformational selection. The picture is taken from reference <cite>Boehr2008</cite> '''B)''' The native structure of Tr-β-gal]]
+[[Image: Conformational selection.png|thumb|left|750px| '''Figure 2. Illustration of the conformational selection mechanism observed in Tr-β-gal <cite>Maksimainen2010</cite>.''']]
 <br style="clear: both" />
@@ Line 56: / Line 60: @@
 == Family Firsts ==
 ;First stereochemistry determination:
-Human β-galactosidase precursor by NMR <cite>Zhang1994</cite>
+[[Retaining]] stereochemical outcome for human β-galactosidase precursor by NMR <cite>Zhang1994</cite>
-;First catalytic nucleophile identification:
+;First [[catalytic nucleophile]] identification:
 Human β-galactosidase precursor by 2-fluorogalactose labeling <cite>McCarter1997</cite>.
-;First general acid/base residue identification:
+;First [[general acid/base]] residue identification:
 ''Penicillium sp.'' β-galactosidase by structural identification <cite>Rojas2004</cite>.
@@ Line 81: / Line 85: @@
 #Rojas2004 pmid=15491613
 #Blanchard2001 pmid=11423106
-#Maksimainen2010 Maksimainen M, Hakulinen N, Kallio JM, Timoharju T, Turunen O, Rouvinen J. ''Crystal structures of Trichoderma reesei beta-galactosidase reveal conformational changes in the active site.'' J Struct Biol. 2010, ''in press.'' //''Note: Due to a problem with PubMed data, this reference is not automatically formatted.  Please see these links out:'' [http://dx.doi.org/10.1016/j.jsb.2010.11.024 DOI:10.1016/j.jsb.2010.11.024] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21130883  PMID:21130883]
+#Maksimainen2010 pmid=21130883
 #GeislerLee2006 pmid=16415215
 #Henrissat2001 pmid=11554480
@@ Line 90: / Line 94: @@
 #Wang2009 pmid=19453169
 #Kotake2005 pmid=15980190
-#Boehr2008 Boehr DD, Wright PE "How do proteins interact?" Science 2008, 320 1429-1430.
+#Boehr2008 Boehr DD, Wright PE ''How do proteins interact?'' Science 2008, 320 1429-1430.
+#Tsai1999  pmid=10468538
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH035]]