CAZypedia needs your help!
We have many unassigned pages in need of Authors and Responsible Curators. See a page that's out-of-date and just needs a touch-up? - You are also welcome to become a CAZypedian. Here's how.
Scientists at all career stages, including students, are welcome to contribute.
Learn more about CAZypedia's misson here and in this article.
Totally new to the CAZy classification? Read this first.

Difference between revisions of "Glycoside Hydrolase Family 55"

From CAZypedia
Jump to navigation Jump to search
Line 39: Line 39:
 
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 (PDB ID [{{PDBlink}}3eqo 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.
 
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 (PDB ID [{{PDBlink}}3eqo 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]]-&beta;-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>Jeffcoat1987</CITE>.
+
In classical studies of a [[exo]]-&beta;-1,3-glucanase from ''Sporotrichum dimorphosporum'' (formerly known as ''Basidiomycete'' QM-806), Jeffcoat and Kirkwood reported that chemical modification of histidine residues in the catalytic site of the enzyme caused irreversible loss of activity, suggesting a crucial role of a histidine residue <CITE>Jeffcoat1987</CITE>.
  
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
The first solved 3-D structure was Lam55A from ''P. chrysosporium'' <cite>Ishida2009</cite>. In this structure, two tandem &beta;-helix domains are positioned side-by-side to form a rib cage-like structure. The active site is located between the two &beta;-helix domains.  
+
The first solved 3-D structure was Lam55A from ''P. chrysosporium'' <cite>Ishida2009</cite>. In this structure, two tandem &beta;-helix domains are positioned side-by-side to form a rib cage-like structure. The active site is located between the two &beta;-helix domains. A duplicated motif had been found in the primary sequence of EXG1 from ''Cochliobolus carbonum'' <cite>Nikolskaya1998</cite>, predicting the presence of two structurally similar domains in this family.
  
 
== Family Firsts ==
 
== Family Firsts ==
 
;First sterochemistry determination: Probably ExgS from ''A. saitoi'' by H-NMR analysis <CITE>Kasahara1992</CITE>. See [[#Kinetics and Mechanism|kinetics and mechanism]].
 
;First sterochemistry determination: Probably ExgS from ''A. saitoi'' by H-NMR analysis <CITE>Kasahara1992</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>delaCruz1995</cite>; EXG1 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5017 ''Cochliobolus carbonum''], partial gene coning and gene knockout ([http://www.uniprot.org/uniprot/P53626 Uniprot P49426]) <cite>Schaeffer1994</cite>.
+
;First gene cloning: BGN13.1 from ''T. harzianum'' ([http://www.uniprot.org/uniprot/P53626 Uniprot P53626]) <cite>delaCruz1995</cite> and EXG1 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5017 ''C. carbonum''] (partial gene coning and gene knockout) ([http://www.uniprot.org/uniprot/P49426 Uniprot P49426]) <cite>Schaeffer1994</cite>.
  
 
;First [[general acid]] residue identification:
 
;First [[general acid]] residue identification:
Line 53: Line 53:
 
;First [[general base]] residue identification:
 
;First [[general base]] residue identification:
  
;First 3-D structure: Lam55A from ''P. chrysosporium'' by X-ray crystallography <cite>Ishida2009</cite>. A duplicated motif had been found in the primary sequence of EXG1 from ''C. carbonum'' <cite>Nikolskaya1998</cite>.
+
;First 3-D structure: Lam55A from ''P. chrysosporium'' by X-ray crystallography <cite>Ishida2009</cite>.
  
 
== References ==
 
== References ==

Revision as of 19:40, 5 September 2011

Approve icon-50px.png

This page has been approved by the Responsible Curator as essentially complete. CAZypedia is a living document, so further improvement of this page is still possible. If you would like to suggest an addition or correction, please contact the page's Responsible Curator directly by e-mail.


Glycoside Hydrolase Family 55
Clan none
Mechanism inverting
Active site residues not known
CAZy DB link
http://www.cazy.org/GH55.html

Substrate specificities

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 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 [1, 2].

Bgn13.1 from Hypocrea lixii (formerly known as Trichoderma harzianum) [3] and LamAI from Trichoderma viride [4] were characterised as endo-acting enzymes (EC 3.2.1.39).

Kinetics and Mechanism

Family 55 enzymes are inverting enzymes, as shown by 1NMR analysis on ExgS from Aspergillus phoenicis (formerly known as Aspergillus saitoi) [5]. Release of α-glucose was subsequently confirmed by polarimetric analysis on family 55 enzymes from Acremonium persicinum [1]. These results are consistent with many classical reports on gentiobiose-producing exo-β-1,3-glucanases from fungi [6, 7], although the genes for these enzymes have not yet been described.

Catalytic Residues

The crystal structure of exo-β-1,3-glucanase Lam55A from Phanerochaete chrysospoirum K-3 complexed with gluconolactone (PDB ID 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 residues in the catalytic site of the enzyme caused irreversible loss of activity, suggesting a crucial role of a histidine residue [8].

Three-dimensional structures

The first solved 3-D structure was Lam55A from P. chrysosporium [9]. 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. A duplicated motif had been found in the primary sequence of EXG1 from Cochliobolus carbonum [10], predicting the presence of two structurally similar domains in this family.

Family Firsts

First sterochemistry determination
Probably ExgS from A. saitoi by H-NMR analysis [5]. See kinetics and mechanism.
First gene cloning
BGN13.1 from T. harzianum (Uniprot P53626) [3] and EXG1 from C. carbonum (partial gene coning and gene knockout) (Uniprot P49426) [11].
First general acid residue identification
First general base residue identification
First 3-D structure
Lam55A from P. chrysosporium by X-ray crystallography [9].

References

  1. Pitson SM, Seviour RJ, McDougall BM, Woodward JR, and Stone BA. (1995). Purification and characterization of three extracellular (1-->3)-beta-D-glucan glucohydrolases from the filamentous fungus Acremonium persicinum. Biochem J. 1995;308 ( Pt 3)(Pt 3):733-41. DOI:10.1042/bj3080733 | PubMed ID:8948426 [Pitson1995]
  2. Bara MT, Lima AL, and Ulhoa CJ. (2003). Purification and characterization of an exo-beta-1,3-glucanase produced by Trichoderma asperellum. FEMS Microbiol Lett. 2003;219(1):81-5. DOI:10.1016/S0378-1097(02)01191-6 | PubMed ID:12594027 [Bara2003]
  3. de la Cruz J, Pintor-Toro JA, Benítez T, Llobell A, and Romero LC. (1995). A novel endo-beta-1,3-glucanase, BGN13.1, involved in the mycoparasitism of Trichoderma harzianum. J Bacteriol. 1995;177(23):6937-45. DOI:10.1128/jb.177.23.6937-6945.1995 | PubMed ID:7592488 [delaCruz1995]
  4. Nobe R, Sakakibara Y, Fukuda N, Yoshida N, Ogawa K, and Suiko M. (2003). Purification and characterization of laminaran hydrolases from Trichoderma viride. Biosci Biotechnol Biochem. 2003;67(6):1349-57. DOI:10.1271/bbb.67.1349 | PubMed ID:12843664 [Nobe2003]
  5. 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).DOI:10.1016/0922-338X(92)90118-E

    [Kasahara1992]
  6. Nelson TE (1970). The hydrolytic mechanism of an exo-beta-(1--3)-D-glucanase. J Biol Chem. 1970;245(4):869-72. | Google Books | Open Library PubMed ID:5416668 [Nelson1970]
  7. 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).JOI:JST.Journalarchive/bbb1961/41.493

    [Nagasaki1977]
  8. Jeffcoat R and Kirkwood S. (1987). Implication of histidine at the active site of exo-beta-(1-3)-D-glucanase from Basidiomycete sp. QM 806. J Biol Chem. 1987;262(3):1088-91. | Google Books | Open Library PubMed ID:3100526 [Jeffcoat1987]
  9. Ishida T, Fushinobu S, Kawai R, Kitaoka M, Igarashi K, and Samejima M. (2009). Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J Biol Chem. 2009;284(15):10100-9. DOI:10.1074/jbc.M808122200 | PubMed ID:19193645 [Ishida2009]
  10. Nikolskaya AN, Pitkin JW, Schaeffer HJ, Ahn JH, and Walton JD. (1998). EXG1p, a novel exo-beta1,3-glucanase from the fungus Cochliobolus carbonum, contains a repeated motif present in other proteins that interact with polysaccharides. Biochim Biophys Acta. 1998;1425(3):632-6. DOI:10.1016/s0304-4165(98)00117-2 | PubMed ID:9838227 [Nikolskaya1998]
  11. Schaeffer HJ, Leykam J, and Walton JD. (1994). Cloning and targeted gene disruption of EXG1, encoding exo-beta 1, 3-glucanase, in the phytopathogenic fungus Cochliobolus carbonum. Appl Environ Microbiol. 1994;60(2):594-8. DOI:10.1128/aem.60.2.594-598.1994 | PubMed ID:8135518 [Schaeffer1994]

All Medline abstracts: PubMed