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2020-05-15T21:29:34Z

Breeanna Urbanowicz: Breeanna Urbanowicz uploaded a new version of File:FUT1 XXXG NCter (1).jpg

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2020-05-15T21:28:43Z

Breeanna Urbanowicz:

2018-11-16T21:34:28Z

Breeanna Urbanowicz:

User:Breeanna Urbanowicz

2018-11-16T21:30:56Z

Breeanna Urbanowicz:

[[File:2018-P08593-Breeanna Urbanowicz|200px|right]]

Breeanna Urbanowicz received her PhD under Jocelyn Rose at Cornell University. Her work contributed to our understanding plant family [[GH9]] and family [[GH10]] glycoside hydrolases. Following her doctorate degree, she joined Dr. William York’s group in the Complex Carbohydrate Research Center at the University of Georgia for her first postdoc. Currently, she is an Assistant Research Scientist at the Complex Carbohydrate Research Center and her research centers on the biosynthesis and modification of plant cell wall polysaccharides. Recently she has made several contributions to our understanding of enzymes involved in the synthesis and modification of glucuronoxylan.

[[Category:Contributors|Urbanowicz,Breeanna]]

2010-08-16T18:48:41Z

Breeanna Urbanowicz:

{{UnderConstruction}}
* [[Author]]s: ^^^David Wilson^^^ and ^^^Breeanna Urbanowicz^^^
* [[Responsible Curator]]: ^^^David Wilson^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH9'''
|-
|'''Clan'''
|GH-G
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known/known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH9.html
|}
</div>


== Substrate specificities ==
GH Family 9 is an inverting glycohydrolase family that mainly contains cellulases and is the second largest cellulase family. It contains mainly endoglucanases with a few processive endoglucanases. All of the processive endoglucanases contain a family 3c CBM rigidly attached to the C-terminus of the family 9 catalytic domain (cd) <cite>Sakon1997</cite>. This domain is part of the active site and is essential for processivity <cite>Sakon1997</cite>. CBM3c domains bind weakly to cellulose as they lack several of the conserved aromatic residues that are important for cellulose binding in family 3a and family 3b members <cite>Tormo1996</cite>. All known plant cellulases belong to family 9, and most of the other members are eubacterial although there are two archael members and some fungal, earthworm, arthropod, chordate, echinoderma and molusk members. There are two subgroups in family 9, E1 which contains only cellulases from bacteria, including ones from both aerobes and anaeobes, and E2 which includes some bacterial and all nonbacterial cellulases <cite>Tomme1995</cite>. An evolutionary study shows that the eucaryote members contain two monophyletic groups that are amcient; one including all animal members and the other including all plant members <cite>Davison2005</cite>. All known processive endoglucanase genes are in subgroup E1.

== Kinetics and Mechanism ==
The processive endoglucanase,Cel9A from Thermobifda fusca, has high activity on bacterial cellulose and is the only cellulase tested that can degrade crystalline regions in bacterial cellulose by itself although it prefers amorphous regions <cite>Chen2007</cite>. A related cellulase in Clostridium phytofermentans, which is the only family 9 cellulase encoded in its genome, has been shown to be essential for cellulose degradation by this organism. This is the only case where a single cellulase has been shown to be essential for growth on cellulose <cite>Tolonen2009</cite>.

== Catalytic Residues ==
Content is to be added here. There is a conserved Glu residue that functions as the catalytic acid and two conserved Asp residues that bind the catalytic water, with one functioning as the catalytic base and mutation of the other also greatly reduces activity on all substrates <cite>Zhou2004</cite>.

== Three-dimensional structures ==
Content is to be added here. All known family 9 cd structures have an ( a / a ) 6 barrel fold that contains an open active site cleft that contains at least six sugar binding subsites -4 to +2 <cite>Sakon1997 Geurin2002</cite>. In processive endoglucanases the catalytic domain is joined to a family 3c CBM that is aligned with the active site cleft <cite>Sakon1997</cite>.

== Family Firsts ==
;First sterochemistry determination: The steriospecificity of three family 9 cellulases were all determined to be inverting by NMR <cite>Gebler1992</cite>.

;First catalytic nucleophile identification: Asp 58 in ''T. fusca'' Cel9A was shown to be the catalytic nucleophile by site directed mutagenesis and azide rescue <cite>Li2007</cite>.

;First general acid/base residue identification: Glu555 was shown to be the catalytic acid in ''C. thermocellum'' CelD by site directed mutagenesis <cite>Chavaux1962</cite>.

;First 3-D structure: The structure of endocellulase CelD from ''Clostridium thermocellum'' was determined by X-ray crystallography (PDB ID [{{PDBlink}}1clc 1clc]) <cite>Lascombe1995</cite>.

== GH9 Enzymes Found in Plants ==

Early reports described the existence of plant ‘cellulases’ or Egases <cite>Hall1963</cite>. Subsequently, cellulases have been shown to be associated with plant cell wall restructuring during cell expansion, the wall disassembly that accompanies processes such as fruit ripening and abscission( reviewed in <cite>Campillo1999 Rose1999 Molhoj2002</cite>) and cellulose biosynthesis <cite>Nicol1998 Lane2001 Sato2001</cite>. The amino acid sequences of the first plant ‘cellulases’/endo-ß-1,4-glucanases revealed that these enzymes belong to the CAZy family GH9 glycoside hydrolases <cite>Henrissat1991</cite>.

Most plant ‘cellulases’ studied to date are endoglucanases (EC 3.2.1.4) with low or no activity on crystalline cellulose, but with discernible activity on soluble cellulose derivatives, including carboxymethyl cellulose (CMC), phosphoric acid swollen non-crystalline cellulose, and numerous plant polysaccharides including xylan, 1,3-1,4-ß-glucan, xyloglucan, and glucomannan <cite> Master2004 YoshidaKomae2006 Ohmiya2000 Woolley2001 Urbanowicz2007</cite>. The inability of plant “cellulases” to hydrolyze crystaline cellulose is distinct from microbial cellulases, whose modular structure and synergistic action with other enzymes facilitates effective degradation of crystalline cellulose. ''In muro'', the substrates of plant cellulases likely include xyloglucan, xylans, and non-crystalline cellulose, especially amorphous regions of cellulose where the microfibrils may be interwoven with xyloglucan.

In the model plant'' Arabidopsis thaliana'', 25 different GH9 coding regions have been identified. Phylogenic analysis of the deduced amino acid sequences group the proteins into nine classes or three subfamilies <cite>Molhoj2002 Libertini2004 Urbanowicz2007 UrbanowiczBennett2007</cite>. Three distinct types of GH9 proteins are present in plants. Class A proteins are membrane-anchored, Class B proteins are secreted, and Class C proteins are also secreted but contain a family 49 carbohydrate binding module (CBM49) <cite>Urbanowicz2007</cite>. Class A plant EGases have been reported to lack tryptophans corresponding to substrate binding at subsites -4, -3, and -2 in ''T. fusca ''Cel9A <cite>Master2004</cite>. Class C EGases are the only plant EGases to date that contain a tryptophan residue corresponding to the one in subsite -2 in TfCel9A <cite>Urbanowicz2007 Master2004</cite>. This tryptophan has been shown to be important for hydrolysis in TfCel9A, and the enzyme retains less than 10% of its normal activity on polymeric cellulose substrates, and less than 1% of wild type activity on cellohexaose when the Trp is replaced by another amino acid <cite>Li2007 Master2004</cite>.

The Class A EGases are integral type II membrane proteins with a GH9 catalytic core that lack a canonical secretion signal sequence. These enzymes are predicted to have a high degree of N-glycosylation and a long amino-terminal extension with a membrane-spanning domain that anchors the protein to the plasma membrane and/or to intracellular organelles <cite>Molhoj2002 Brummell1997</cite>. Membrane anchored EGases were first described in studies of the ''KORRIGAN'' (''KOR'') genes in<sup> </sup>''Arabidopsis thaliana'', which showed that they encode EGases that are required for normal cellulose synthesis or assembly. Plants with mutant alleles of the ''KOR1'' gene are dwarfed, with decreased cellulose content and crystallinity <cite>Molhoj2002 Szyjanowicz2004 Takahashi2009</cite>. The role of the Class A EGases in plants is not known. However, the KOR proteins have been proposed to cleave sitosterol-b-glucoside primers from the growing cellulose polymer, or may have a role in editing incorrectly formed growing microfibrils <cite>Peng2002</cite>. More recently, it has been shown that during cell expansion, KOR1 is cycled from the plasma membrane through intracellular compartments, comprising both<sup> </sup>the Golgi apparatus and early endosomes; however the role of KOR1 in cellulose biosynthesis remains to be determined <cite>Robert2005</cite>. The catalytic domain of PttCel9A, a Class A GH9 enzyme that is upregulated during secondary cell wall synthesis in ''Populus tremula x tremuloides'', has been biochemically characterized and shown to hydrolyse a narrow range of substrates ''in vitro'' including CMC, phosphoric acid swollen cellulose and cellulose oligosaccharides (DP≥5) <cite>Master2004 Rudsander2008</cite>.

Class B proteins are the most common form of plant Egases and are associated with virtually all stages of plant growth and development. These enzymes have a GH9 catalytic domain and a signal sequence for ER targeting and secretion. Different isoforms are expressed during fruit ripening, in abscission zones, in reproductive organ development, and in expanding cells <cite>Brummel1999 Brummel1997 Kalaitzis1999 Shani1997</cite>. Numerous studies, especially in tomato, have also shown that many class B EGases are under hormonal control <cite>Catala1997 Brummell1997 Bonghi1998</cite>.

Plant Class C GH9 enzymes are the least studied. These proteins are predicted to have a signal sequence followed by a GH9 catalytic domain and a long carboxyl-terminal extension, which contains a CBM49 that has been shown to bind to crystalline cellulose ''in vitro'' <cite>Urbanowicz2007 UrbanowiczBennett2007</cite>. CBMs are necessary for activity on crystalline substrates and may promote hydrolysis by increasing the local enzyme concentration at the substrate surface as well as modifying cellulose microfibril structure (for review see <cite>Boraston2004</cite>). The catalytic domain (CD) SlGH9C1 from tomato is promiscuous and can effectively hydrolyze artificial cellulosic polymers, cellulose oligosaccharides, and several plant cell wall polysaccharides <cite>Urbanowicz2007</cite>. Nevertheless, the activity of the full length, modular enzyme has still not been characterized. A Class C EGase from rice, OsCel9A, has been shown to be post-translationaly modified at the linker region to yield a 51 kDa GH9 CD and a CBM49, and it was suggested that the cleavage is necessary for function <cite>YoshidaImaizumi2006</cite>. The OsCel9A CD also displays a broad substrate range and was able to hydrolyze CMC, phosphoric acid-swollen cellulose, mixed linkage 1,3-1,4-ß-glucan,<sup> </sup>xylan, glucomannan, cellooligosaccharides (DP≥3) and 1,4-ß-xylohexaose <cite>YoshidaKomae2006</cite>. For Information regarding nomenclature of plant GH9 enzymes please see Urbanowicz et al 2007 <cite>UrbanowiczBennett2007</cite>.

== References ==
<biblio>
#Sakon1997 pmid=9334746
#Tormo1996 pmid=8918451
#Tomme1995 pmid=8540419
#Davison2005 pmid=15703240
#Geurin2002 pmid=11884144
#Zhou2004 pmid=15274620
#Li2007 pmid=17369336
#Chen2007 Chen, Arthur J. Stipanovic, William T. Winter, David B. Wilson and Young-Jun Kim. Effect of digestion by pure cellulases on crystallinity and average chain length for bacterial and microcrystalline celluloses. Cellulose 2007: 14: 283-293.
#Tolonen2009 pmid=19775243
#Gebler1992 pmid=1618761
#Lascombe1995 Lascombe, M.B., Souchon, H., Juy, M., Alzari, P.M. Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution. Deposited 1995, unpublished.
#Hall1963 pmid=14097721
#Campillo1999 pmid=10417876
#Rose1999 pmid=10322557
#Molhoj2002 pmid=12514237
#Nicol1998 pmid=9755157
#Lane2001 pmid=11351091
#Sato2001 pmid=11266576
#Henrissat1991 pmid=1747104
#Master2004 pmid=15287736
#YoshidaKomae2006 pmid=17056618
#Ohmiya2000 pmid=11069690
#Woolley2001 pmid=11762160
#Urbanowicz2007 pmid=17322304
#Libertini2004 pmid=15170254
#UrbanowiczBennett2007 pmid=17687051
#Peng2002 pmid=11778054
#Szyjanowicz pmid=14871312
#Robert2005 pmid=16284310
#Takahashi2009 pmid=19398462
#Rudsander2008 pmid=18402467
#Brummell1997 pmid=9037162
#Brummel1999 pmid=10480385
#Kalaitzis1999 pmid=10555309
#Shani1997 pmid=9290636
#Catala1997 pmid=9301092
#Bonghi1998 pmid=1281437
#Boraston2004 pmid=15214846
#YoshidaImaizumi2006 pmid=17056619

</biblio>

[[Category:Glycoside Hydrolase Families|GH009]]

Glycoside Hydrolase Family 9

2010-08-12T21:23:14Z

Breeanna Urbanowicz:

{{UnderConstruction}}
* [[Author]]s: ^^^David Wilson^^^ and ^^^Breeanna Urbanowicz^^^
* [[Responsible Curator]]: ^^^David Wilson^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH9'''
|-
|'''Clan'''
|GH-G
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known/known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH9.html
|}
</div>


== Substrate specificities ==
GH Family 9 is an inverting glycohydrolase family that mainly contains cellulases and is the second largest cellulase family. It contains mainly endoglucanases with a few processive endoglucanases. All of the processive endoglucanases contain a family 3c CBM rigidly attached to the C-terminus of the family 9 catalytic domain (cd) <cite>Sakon1997</cite>. This domain is part of the active site and is essential for processivity <cite>Sakon1997</cite>. CBM3c domains bind weakly to cellulose as they lack several of the conserved aromatic residues that are important for cellulose binding in family 3a and family 3b members <cite>Tormo1996</cite>. All known plant cellulases belong to family 9, and most of the other members are eubacterial although there are two archael members and some fungal, earthworm, arthropod, chordate, echinoderma and molusk members. There are two subgroups in family 9, E1 which contains only cellulases from bacteria, including ones from both aerobes and anaeobes, and E2 which includes some bacterial and all nonbacterial cellulases <cite>Tomme1995</cite>. An evolutionary study shows that the eucaryote members contain two monophyletic groups that are amcient; one including all animal members and the other including all plant members <cite>Davison2005</cite>. All known processive endoglucanase genes are in subgroup E1.

== Kinetics and Mechanism ==
The processive endoglucanase,Cel9A from Thermobifda fusca, has high activity on bacterial cellulose and is the only cellulase tested that can degrade crystalline regions in bacterial cellulose by itself although it prefers amorphous regions <cite>Chen2007</cite>. A related cellulase in Clostridium phytofermentans, which is the only family 9 cellulase encoded in its genome, has been shown to be essential for cellulose degradation by this organism. This is the only case where a single cellulase has been shown to be essential for growth on cellulose <cite>Tolonen2009</cite>.

== Catalytic Residues ==
Content is to be added here. There is a conserved Glu residue that functions as the catalytic acid and two conserved Asp residues that bind the catalytic water, with one functioning as the catalytic base and mutation of the other also greatly reduces activity on all substrates <cite>Zhou2004</cite>.

== Three-dimensional structures ==
Content is to be added here. All known family 9 cd structures have an ( a / a ) 6 barrel fold that contains an open active site cleft that contains at least six sugar binding subsites -4 to +2 <cite>Sakon1997 Geurin2002</cite>. In processive endoglucanases the catalytic domain is joined to a family 3c CBM that is aligned with the active site cleft <cite>Sakon1997</cite>.

== Family Firsts ==
;First sterochemistry determination: The steriospecificity of three family 9 cellulases were all determined to be inverting by NMR <cite>Gebler1992</cite>.

;First catalytic nucleophile identification: Asp 58 in ''T. fusca'' Cel9A was shown to be the catalytic nucleophile by site directed mutagenesis and azide rescue <cite>Li2007</cite>.

;First general acid/base residue identification: Glu555 was shown to be the catalytic acid in ''C. thermocellum'' CelD by site directed mutagenesis <cite>Chavaux1962</cite>.

;First 3-D structure: The structure of endocellulase CelD from ''Clostridium thermocellum'' was determined by X-ray crystallography (PDB ID [{{PDBlink}}1clc 1clc]) <cite>Lascombe1995</cite>.

== GH9 Enzymes Found in Plants ==
12.00 Normal 0 false false false EN-US X-NONE X-NONE 12.00 Normal 0 false false false EN-US X-NONE X-NONE

Early reports described the existence of plant ‘cellulases’ or Egases (e.g. Hall, 1963). Subsequently, cellulases have been shown to be associated with plant cell wall restructuring during cell expansion, the wall disassembly that accompanies processes such as fruit ripening and abscission (reviewed in del Campillo, 1999; Rose and Bennett, 1999; '''Mølhøj et al., 2002''') and cellulose biosynthesis (Nicol et al., 1998; Lane et al., 2001; Sato et al., 2001). The amino acid sequences of the first plant ‘cellulases’/endo-b-1,4-glucanases revealed that these enzymes belong to the CAZy family GH9 glycoside hydrolases (Henrissat 1991). Plant GH9 enzymes are expected to affect cell wall strength and extendibility.

Most plant ‘cellulases’ studied to date are endoglucanases (EC 3.2.1.4) with low or no activity on crystalline cellulose, but with discernible activity on soluble cellulose derivatives, including carboxymethyl cellulose (CMC), phosphoric acid swollen non-crystalline cellulose, and numerous plant polysaccharides including xylan, 1,3-1,4-b-glucan, xyloglucan, and glucomannan (Master et al., 2004; Yoshida and Komae 2006; Hayashi et al., 1984; Ohmiya et al., 2000; Woolley et al., 2001; Urbanowicz et al., 2007). The inability of plant “cellulases” to hydrolyze crystaline cellulose is distinct from microbial cellulases, whose modular structure and synergistic action with other enzymes facilitates effective degradation of crystalline cellulose. ''In muro'', the substrates of microbial cellulases likely include xyloglucan, glucomannans, and non-crystalline cellulose, especially amorphous regions of cellulose where the microfibrils may be interwoven with xyloglucan.

In the model plant'' Arabidopsis thaliana'', 25 different GH9 coding regions have been identified. Phylogenic analysis of the deduced amino acid sequences group the proteins into nine classes or three subfamilies ('''Mølhøj''' et al., 2002; Libertini et al., 2004; Urbanowicz et al., 2007a). Three distinct types of GH9 proteins are present in plants. Class A proteins are membrane-anchored, Class B proteins are secreted, and Class C proteins are also secreted but contain a family 49 carbohydrate binding module (CBM49) (Urbanowicz et al., 2007a). Class A plant EGases have been reported to lack tryptophans corresponding to substrate binding at subsites -4, -3, and -2 in ''T. fusca ''Cel9A (Master et al., 2004). Class C EGases are the only plant EGases to date, that contain a tryptophan residue corresponding to the one in subsite -2 in TfCel9A (Urbanowicz et al., 2007b). This tryptophan has been shown to be important for hydrolysis in TfCel9A. The enzyme retains less than 10% of its normal activity on polymeric cellulose substrates, and less than 1% of wild type activity on cellohexaose when the Trp is replaced by another amino acid (Li et al., 2007a; Master et al 2004).

The Class A EGases are integral type II membrane proteins with a GH9 catalytic core that lack a canonical secretion signal sequence. These enzymes are predicted to have a high degree of N-glycosylation and a long amino-terminal extension with a membrane-spanning domain that anchors the protein to the plasma membrane and/or to intracellular organelles ('''Mølhøj''' et al., 2002; Brummell et al., 1997). Membrane anchored EGases were first described in studies of the ''KORRIGAN'' (''KOR'') genes in<sup> </sup>''Arabidopsis thaliana'', which showed that they encode EGases that are required for normal cellulose synthesis or assembly. Plants with mutant alleles of the ''KOR1'' gene are cellulose-deficient and dwarfed ('''Mølhøj''' et al., 2002; Szyjanowicz et al 2004). The role of the Class A EGases is not known. However, the KOR proteins have been proposed to cleave sitosterol-b-glucoside primers from the growing cellulose polymer, or may have a role in editing incorrectly formed growing microfibrils (Peng et al. 2002). Recently, it has been shown that during cell expansion KOR1 is cycled from the plasma membrane through intracellular compartments, comprising both<sup> </sup>the Golgi apparatus and early endosomes; however the role of KOR1 in cellulose biosynthesis remains to be determined (Robert et al., 2005). The catalytic domain of PttCel9A, a Class A GH9 enzyme that is upregulated during secondary cell wall synthesis in ''Populus tremula x tremuloides'', has been biochemically characterized and shown to hydrolyse a narrow range of substrates ''in vitro'' including CMC, phosphoric acid swollen cellulose and cellulose oligosaccharides (DP≥5).

Class B proteins are the most common form of plant Egases and are associated with virtually all stages of plant growth and development. These enzymes have a GH9 catalytic domain and a signal sequence for ER targeting and secretion. Different isoforms are expressed during fruit ripening, in abscission zones, in reproductive organ development, and in expanding cells (Brummel et al., 1999; Brummel et al., 1997; Kalaitzis et al., 1999; Shani et al., 1997). Numerous studies, especially in tomato, have also shown that many class B EGases are under hormonal control (Catalá''' '''et al., 1997; Brummell et al., 1997; Bonghi et al., 1998).

Plant Class C EGases are the least studied. These proteins have a signal sequence followed by a GH9 catalytic domain and a long carboxyl-terminal extension, which contains a CBM49 that has been shown to bind to crystalline cellulose ''in vitro'' (Urbanowicz et al., 2007a; Urbanowicz et al., 2007b). CBMs are necessary for activity on crystalline substrates and may promote hydrolysis by increasing the local enzyme concentration at the substrate surface as well as modifying cellulose microfibril structure (for review see Boraston et al., 2004). The catalytic domain (CD) SlGH9C1 is promiscuous and can effectively hydrolyze artificial cellulosic polymers, cellulose oligosaccharides, and several plant cell wall polysaccharides (Urbanowicz et al., 2007b). Nevertheless, the activity of the full length, modular enzyme has still not been characterized. A Class C EGase from rice, OsCel9A, has been shown to be post-translationaly modified at the linker region to yield a 51 kDa GH9 CD and a CBM49, and it was suggested that the cleavage is necessary for function (Yoshida et al., 2006a). The OsCel9A CD also displays a broad substrate range and was able to hydrolyze CMC, phosphoric acid-swollen cellulose, mixed linkage 1,3-1,4-ß-glucan,<sup> </sup>xylan, glucomannan, cellooligosaccharides (DP≥3) and 1,4-ß-xylohexaose (Yoshida et al., 2006b).

== References ==
<biblio>
#Sakon1997 pmid=9334746
#Tormo1996 pmid=8918451
#Tomme1995 pmid=8540419
#Davison2005 pmid=15703240
#Geurin2002 pmid=11884144
#Zhou2004 pmid=15274620
#Li2007 pmid=17369336
#Chen2007 Chen, Arthur J. Stipanovic, William T. Winter, David B. Wilson and Young-Jun Kim. Effect of digestion by pure cellulases on crystallinity and average chain length for bacterial and microcrystalline celluloses. Cellulose 2007: 14: 283-293.
#Tolonen2009 pmid=19775243
#Gebler1992 pmid=1618761
#Lascombe1995 Lascombe, M.B., Souchon, H., Juy, M., Alzari, P.M. Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution. Deposited 1995, unpublished.
</biblio>

[[Category:Glycoside Hydrolase Families|GH009]]