2009-11-12T12:53:12Z

Takuya Ishida:

{{CuratorApproved}}
* [[Author]]s: [[User:Takuya_Ishida|Takuya Ishida]] and ^^^Kiyohiko Igarashi^^^
* [[Responsible Curator]]: ^^^User:ShinyaFushinobu|Shinya Fushinobu^^^
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<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family 55'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH55.html
|}
</div>

== Substrate specificities ==
[[Glycoside Hydrolases|Glycoside Hydrolase]] family 55 consists exclusively of β-1,3-glucanases, including both [[exo]]- and [[endo]]-enzymes. All biochemically characterized members of this family are of fungal origin, although there are no yeast homologues. Several homologous genes have been identified in bacterial genomes, but none of the corresponding gene products have been characterized.

The enzymes belonging to this family are generally called "laminarinases," because they hydrolyze laminarin from brown algae (β-1,3-glucan having single β-1,6-glucoside side chains: β-1,3/1,6-glucan). However, the physiological substrate for the enzymes might be fungal cell wall, whose major component is also β-1,3/1,6-glucan.

The majority of the members in this family are [[exo]]-glucan-1,3-β-glucosidases (EC[http://us.expasy.org/cgi-bin/nicezyme.pl?3.2.1.58 3.2.1.58]), which cleave the terminal β-1,3-glycosidic linkage at the non-reducing end of β-1,3-glucans or β-1,3/1,6-glucans. Many produce gentiobiose (β-D-glucopyranosyl-1,6-D-glucose) in addition to glucose during the degradation of β-1,3/1,6-glucan <CITE>REF2 REF3</CITE>.

Bgn13.1 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5544 ''Hypocrea lixii''] (formerly known as ''Trichoderma harzianum'') <CITE>REF4</CITE> and LamAI from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5547 ''Trichoderma viride''] <CITE>REF5</CITE> were characterised as [[endo]]-acting enzymes (EC[http://us.expasy.org/cgi-bin/nicezyme.pl?3.2.1.39 3.2.1.39]).

== Kinetics and Mechanism ==
Family 55 enzymes are [[inverting]] enzymes, as shown by <sup>1</sup>NMR analysis on ExgS from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5063 ''Aspergillus phoenicis''] (formerly known as ''Aspergillus saitoi'') <CITE>REF6</CITE>. Release of α-glucose was subsequently confirmed by polarimetric analysis on family 55 enzymes from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5051 ''Acremonium persicinum''] <CITE>REF2</CITE>. These results are consistent with many classical reports on gentiobiose-producing exo-β-1,3-glucanases from fungi <CITE>REF7 REF8</CITE>, although the genes for these enzymes have not yet been described.

== Catalytic Residues ==
The crystal structure of [[exo]]-β-1,3-glucanase Lam55A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5306 ''Phanerochaete chrysospoirum''] K-3 complexed with gluconolactone ([http://www.rcsb.org/pdb/explore/explore.do?structureId=3EQO PDB 3eqo]) suggests that Glu633 is the [[general acid]]. A candidate nucleophilic water was found near the C-1 atom of gluconolactone, but no acidic residue corresponding to the [[general base]] was identified in the vicinity of the water molecule.

In classical studies of a [[exo]]-β-1,3-glucanase from ''Sporotrichum dimorphosporum'' (formerly known as ''Basidiomycete'' QM-806), Jeffcoat and Kirkwood reported that chemical modification of histidine in the catalytic site of the enzyme caused irreversible loss of activity, suggesting a crucial role of the histidine residues <CITE>REF9</CITE>.

== Three-dimensional structures ==
The first solved 3-D structure was Lam55A from ''P. chrysosporium'' <cite>REF1</cite>. In this structure, two tandem β-helix domains are positioned side-by-side to form a rib cage-like structure. The active site is located between the two β-helix domains.

== Family Firsts ==
;First sterochemistry determination: Probably ExgS from ''A. saitoi'' by H-NMR analysis <CITE>REF6</CITE>. See [[#Kinetics and Mechanism|kinetics and mechanism]].

;First gene cloning: BGN13.1 from ''T. harzianum'' ([http://www.uniprot.org/uniprot/P53626 Uniprot P53626]) <cite>REF4</cite>.

;First [[general acid]] residue identification:

;First [[general base]] residue identification:

;First 3-D structure: Lam55A from ''P. chrysosporium'' by X-ray crystallography <cite>REF1</cite>.

== References ==
<biblio>
#REF1 pmid=19193645
#REF2 pmid=8948426
#REF3 pmid=12594027
#REF4 pmid=7592488
#REF5 pmid=12843664
#REF6 Kasahara S, Nakajima T, Miyamoto C, Wada K, Furuichi Y, and Ichishima E. Characterization and mode of action of exo-1,3-β-D-glucanase from ''Aspergillus saitoi''. J Ferment Bioeng 74 (4), 238-240 (1992).[http://dx.doi.org/10.1016/0922-338X(92)90118-E DOI:10.1016/0922-338X(92)90118-E]
#REF7 pmid=5416668
#REF8 Nagasaki N, Saito K, and Yarnamoto S. Purification and characterization of an exo-β-l,3-glucanase from a fungi imperfecti. Agric Biol Cbem 41, 493-502 (1977).[http://joi.jlc.jst.go.jp/JST.Journalarchive/bbb1961/41.493 JOI:JST.Journalarchive/bbb1961/41.493]
#REF9 pmid=3100526
</biblio>

[[Category:Glycoside Hydrolase Families|GH055]]

User:Takuya Ishida

2009-11-02T10:40:02Z

Takuya Ishida: Created page with 'I am a PhD student in the Laboratory of Forest Chemistry at Department of Biomaterials Sciences, [http://www.a.u-tokyo.ac.jp/english/index.html Graduate School of Agricultural an…'

I am a PhD student in the Laboratory of Forest Chemistry at Department of Biomaterials Sciences, [http://www.a.u-tokyo.ac.jp/english/index.html Graduate School of Agricultural and Life Sciences], [http://www.u-tokyo.ac.jp/index_e.html The University of Tokyo]. Under the supervision of Professor Masahiro Samejima and Associate Professor Kiyohiko Igarashi, I'm now working on GH-55 and GH-74 enzymes from wood rotting fungi ''Phanerochaete chrysosporium''.