Movatterモバイル変換

[0]ホーム
URL:

Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
Thehttps:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

NIH NLM Logo
Log inShow account info
Access keysNCBI HomepageMyNCBI HomepageMain ContentMain Navigation
pubmed logo
Advanced Clipboard
User Guide

Full text links

Silverchair Information Systems full text link Silverchair Information Systems Free PMC article
Full text links

Actions

Share

Review
.2004 Sep 15;382(Pt 3):769-81.
doi: 10.1042/BJ20040892.

Carbohydrate-binding modules: fine-tuning polysaccharide recognition

Affiliations
Review

Carbohydrate-binding modules: fine-tuning polysaccharide recognition

Alisdair B Boraston et al. Biochem J..

Abstract

The enzymic degradation of insoluble polysaccharides is one of the most important reactions on earth. Despite this, glycoside hydrolases attack such polysaccharides relatively inefficiently as their target glycosidic bonds are often inaccessible to the active site of the appropriate enzymes. In order to overcome these problems, many of the glycoside hydrolases that utilize insoluble substrates are modular, comprising catalytic modules appended to one or more non-catalytic CBMs (carbohydrate-binding modules). CBMs promote the association of the enzyme with the substrate. In view of the central role that CBMs play in the enzymic hydrolysis of plant structural and storage polysaccharides, the ligand specificity displayed by these protein modules and the mechanism by which they recognize their target carbohydrates have received considerable attention since their discovery almost 20 years ago. In the last few years, CBM research has harnessed structural, functional and bioinformatic approaches to elucidate the molecular determinants that drive CBM-carbohydrate recognition. The present review summarizes the impact structural biology has had on our understanding of the mechanisms by which CBMs bind to their target ligands.

PubMed Disclaimer

Figures

Figure 1
Figure 1. The big picture: CBMs, shown as ribbon structures, grouped as fold families and functional types
Dotted boxes surround examples of CBMs belonging to the functional Types A, B, and C. Brackets with numbers indicate examples of CBMs belonging to fold families 1–7. CBMs shown are as follows: (a) family 17 CBM,CcCBM17, fromClostridium cellulovorans in complex with cellotetraose (PDB code 1J84 [60]); (b) family 4 CBM,TmCBM4-2, fromT. maritima in complex with laminariohexaose (PDB code 1GUI [68]); (c) family 15 CBM,CjCBM15, fromCellvibrio japonicus in complex with xylopentaose (PDB code 1GNY [67]); (d) family 3 CBM,CtCBM3, fromClostridium thermocellum (PDB code 1NBC [52]); (e) family 2 CBM,CfCBM2, fromCellulomonas fimi (PDB code 1EXG [81]); (f) family 9 CBM,TmCBM9-2, fromT. maritima in complex with cellobiose (PDB code 1I82 [33]); (g) family 32 CBM,MvCBM32, fromMicromonospora viridifaciens in complex with galactose (PDB code 1EUU [65]); (h) family 5 CBM,EcCBM5, fromErwinia chrysanthemi (PDB code 1AIW [82]); (i) family 13 CBM,SlCBM13, fromS. lividans in complex with xylopentaose (PDB code 1MC9 [48]); (j) family 1 CBM,TrCBM1, fromTrichoderma reesi (PDB code 1CBH [83]); (k) family 10 CBM,CjCBM10, fromCellvibrio japonicus (PDB code 1E8R [84]); (l) family 18 CBM fromUrtica dioca in complex with chitotriose (PDB code 1EN2 [85]); (m) family 14 CBM, tachychitin, fromTachypleus tridentatus (PDB code 1DQC [86]). Bound ligands are shown as ‘liquorice’ representations, while bound metal ions are shown as a blue spheres.
Figure 2
Figure 2. Schematic diagram showing the location of binding sites in the β-sandwich Type B CBMs
This Figure was produced by overlapping the C-α carbons for all of the β-sandwich Type B CBMs for which ligand bound complexes were available. Only the ribbon structure of the family 4 CBM from the N-terminus of Cel9B fromCellulomonas fimi is shown as a representative β-sandwich Type B CBM. Oligosaccharide ligands are shown in ‘liquorice’ representation and coloured as follows: cyan, cellotetraose fromCcCBM17 (PDB code 1J84 [60]); blue, laminariohexaose fromTmCBM4-2 (PDB code 1GUI [68]); pink, cellopentaose fromCfCBM4-2 (PDB code 1GU3 [68]); marine/aqua, xylotriose fromCsCBM6-3 (PDB code 1NAE [61]); orange, cellohexaose fromPeCBM29-2 (PDB code 1GWM [69]); green, mannopentaose fromTmCBM27 (PDB code 1OF4 [73]); purple, xylopentaose fromCjCBM15 (PDB code 1GNY [67]).
Figure 3
Figure 3. Solvent-accessible surface representations of two CBMs showing the depth of binding grooves in Type B CBMs
(A) Example of a cellopentaose molecule occupying a deep binding groove inCfCBM4-2 (PDB code 1GU3 [68]). (B) Example of a cellotetraose molecule occupying a shallow binding groove inCcCBM17 (PDB code 1J84 [60]). The surfaces created by the aromatic amino acid side chains involved in binding are shown in magenta.
Figure 4
Figure 4. The three types of binding-site ‘platforms’ formed by aromatic amino acid residues
(A) The ‘planar’ platform in the family 10 Type A CBM,CjCBM10. (B) The ‘twisted’ platform of the Type B family 29 CBM,PeCBM29-2. (C) The ‘sandwich’ platform of the Type B family 4 CBM,CfCBM4-2. The C-α backbone is shown as grey cylinders, the aromatic amino acid side chains forming the binding sites are shown in grey ‘liquorice’ representations, and the bound oligosaccharides are shown in blue ‘liquorice’ representation.
Figure 5
Figure 5. Binding-site topography and oligosaccharide recognition
Surface representations of the NMR structures of wild-typeCfCBM2b-1 (A) and the same protein with an Arg262→Gly mutation (B). The arrow indicates the tryptophan residue that changes conformation due to the mutation. The binding site ofCfCBM4-1 extend in a straight path across the face of one of the β-sheets of this CBM creating a linear binding site appropriate for binding cello-oligosaccharides (C). InTmCBM4-2, which has significant sequence identity withCfCBM4-1, two loops are extended (D); one to block an end of the binding site (shown by the arrow labelled 1) and another to accommodate the curvature of the laminarioligosaccharide (shown by the arrow labelled 2). Solvent-accessible surfaces are shown in transparent grey with surfaces created by the aromatic amino acid side chains involved in binding shown in magenta. C-α traces are shown in blue.
Figure 6
Figure 6. The role of calcium in xylan recognition by the family 36 CBM,PpCBM36, fromPa. polymyxa xylanase 43
The calcium atom bound in the binding site ofPpCBM36 is shown as a blue sphere. The amino acid residues involved in co-ordinating the calcium and binding the sugar are shown in grey ‘liquorice’ representation, the bound xylo-oligosaccharide is shown in blue ‘liquorice’ representation and the C-α backbone is represented as grey cylinders.
Figure 7
Figure 7. The accommodation of galactomannan by a family 27 CBM,TmCBM27
The overall structure surrounding the binding site ofTmCBM27 fromT. maritima is shown as a ribbon diagram. The three tryptophan side chains comprising the carbohydrate-binding site are shown in grey ‘liquorice’ representation and are numbered. The ligand, G2M5, a fragment of galactomannan, is shown in ‘liquorice’ representation with mannose residues in blue and galactose residues in yellow. The uppermost galactose residue in the Figure is clearly bent back over the top of the mannose backbone by Trp28, while the other galactose residue extends comfortably away from the mannose backbone.
Figure 8
Figure 8. Multivalent CBMs
The family 13 CBM fromS. lividans xylanase 10A,SlCBM13, is shown in complex with three lactose molecules occupying its three binding sites (A), while the family 6 CBM fromCellvibrio mixtus endoglucanase 5A,CmCBM6, is shown in complex with two cellobiose molecules occupying its two binding sites (B). Both are shown as ribbon diagrams with relevant aromatic amino acid side chains in the binding sites shown in grey ‘liquorice’ representation. The three β-trefoil subdomains ofSlCBM13 are labelled as α, β and γ, and the two binding sites ofCmCBM6 are labelled according to the cleft in which they reside.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Van Tilbeurgh H., Tomme P., Claeyssens M., Bhikhabhai R., Pettersson G. Limited proteolysis of the cellobiohydrolase I from Trichoderma reesei. FEBS Lett. 1986;204:223–227.
    1. Tomme P., Van Tilbeurgh H., Pettersson G., Van Damme J., Vandekerckhove J., Knowles J., Teeri T., Claeyssens M. Studies of the cellulolytic system of Trichoderma reesei QM 9414: analysis of domain function in two cellobiohydrolases by limited proteolysis. Eur. J. Biochem. 1988;170:575–581. - PubMed
    1. Gilkes N. R., Warren R. A. J., Miller R. C., Jr, Kilburn D. G. Precise excision of the cellulose binding domains from two Cellulomonas fimi cellulases by a homologous protease and the effect on catalysis. J. Biol. Chem. 1988;263:10401–10407. - PubMed
    1. Boraston A. B., McLean B. W., Kormos J. M., Alam M., Gilkes N. R., Haynes C. A., Tomme P., Kilburn D. G., Warren R. A. J. Carbohydrate-binding modules: diversity of structure and function. In: Gilbert H. J., Davies G. J., Henrissat B., Svensson B., editors. Recent Advances in Carbohydrate Bioengineering. Cambridge: Royal Society of Chemistry; 1999. pp. 202–211.
    1. Coutinho P. M., Henrissat B. Carbohydrate-active enzymes: an integrated database approach. In: Gilbert H. J., Davies G. J., Henrissat B., Svensson B., editors. Recent Advances in Carbohydrate Bioengineering. Cambridge: Royal Society of Chemistry; 1999. pp. 3–12.

Publication types

MeSH terms

Substances

Related information

LinkOut - more resources

Full text links
Silverchair Information Systems full text link Silverchair Information Systems Free PMC article
Cite
Send To

NCBI Literature Resources

MeSHPMCBookshelfDisclaimer

The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Unauthorized use of these marks is strictly prohibited.

[8]ページ先頭
©2009-2025 Movatter.jp