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141 a.a.
Key reference
DOI no: 10.1073/pnas.212516199 Proc Natl Acad Sci U S A 99:14077-14082 (2002) PubMed id: 12391332
Promiscuity in ligand-binding: The three-dimensional structure of a Piromyces carbohydrate-binding module, CBM29-2, in complex with cello- and mannohexaose. S.J.Charnock, D.N.Bolam, D.Nurizzo, L.Szabó, V.A.McKie, H.J.Gilbert, G.J.Davies. ABSTRACT
Carbohydrate-protein recognition is central to many biological processes. Enzymes that act on polysaccharide substrates frequently contain noncatalytic domains, "carbohydrate-binding modules" (CBMs), that target the enzyme to the appropriate substrate. CBMs that recognize specific plant structural polysaccharides are often able to accommodate both the variable backbone and the side-chain decorations of heterogeneous ligands. "CBM29" modules, derived from a noncatalytic component of the Piromyces equi cellulase/hemicellulase complex, provide an example of this selective yet flexible recognition. They discriminate strongly against some polysaccharides while remaining relatively promiscuous toward both beta-1,4-linked manno- and cello-oligosaccharides. This feature may reflect preferential, but flexible, targeting toward glucomannans in the plant cell wall. The three-dimensional structure of CBM29-2 and its complexes with cello- and mannohexaose reveal a beta-jelly-roll topology, with an extended binding groove on the concave surface. The orientation of the aromatic residues complements the conformation of the target sugar polymer while accommodation of both manno- and gluco-configured oligo- and polysaccharides is conferred by virtue of the plasticity of the direct interactions from their axial and equatorial 2-hydroxyls, respectively. Such flexible ligand recognition targets the anaerobic fungal complex to a range of different components in the plant cell wall and thus plays a pivotal role in the highly efficient degradation of this composite structure by the microbial eukaryote.
Selected figure(s)
Figure 2.
Fig 2. Three-dimensional structure of the cellohexaose complex of CBM29. (a) Topological protein cartoon, color-ramped from N to C terminus, with the ligand in "ball-and-stick" representation and the cobalt ion as a sphere, prepared by using MOLSCRIPT/BOBSCRIPT (29, 30). (b) "Hydrophobic surface" figure generated with the SURFGEN algorithm (available at www.biop.ox.ac.uk). Hydrophobic interaction surfaces are color-ramped from red (most hydrophobic) through white to blue (least hydrophobic).Figure 4.
Fig 4. Schematic representation of the direct (nonsolvent mediated) interactions between CBM29 and ligand cellohexaose (a) and mannohexaose (b). The statistical disorder of the glucosyl moiety in subsite 2 is shown in blue, and hydrogen bonds only observed in the mannohexaose complex (subsites 5 and 2) are shown in red.Figures were selected by an automated process.
Literature references that cite this PDB file's key reference
PubMed id Reference
18422658 A.Viegas, N.F.Brás, N.M.Cerqueira, P.A.Fernandes, J.A.Prates, C.M.Fontes, M.Bruix, M.J.Romão, A.L.Carvalho, M.J.Ramos, A.L.Macedo, and E.J.Cabrita (2008).
Molecular determinants of ligand specificity in family 11 carbohydrate binding modules: an NMR, X-ray crystallography and computational chemistry approach.FEBS J, 275, 2524-2535.
17985396 C.Junkes, A.Wessolowski, S.Farnaud, R.W.Evans, L.Good, M.Bienert, and M.Dathe (2008).
The interaction of arginine- and tryptophan-rich cyclic hexapeptides with Escherichia coli membranes.J Pept Sci, 14, 535-543.
18979035 R.K.Raju, A.Ramraj, M.A.Vincent, I.H.Hillier, and N.A.Burton (2008).
Carbohydrate-protein recognition probed by density functional theory and ab initio calculations including dispersive interactions.Phys Chem Chem Phys, 10, 6500-6508.
17622484 O.O.Obembe, E.Jacobsen, J.Timmers, H.Gilbert, A.W.Blake, J.P.Knox, R.G.Visser, and J.P.Vincken (2007).
Promiscuous, non-catalytic, tandem carbohydrate-binding modules modulate the cell-wall structure and development of transgenic tobacco (Nicotiana tabacum) plants.J Plant Res, 120, 605-617.
16521140 C.S.Rye, A.Matte, M.Cygler, and S.G.Withers (2006).
An atypical approach identifies TYR234 as the key base catalyst in chondroitin AC lyase.Chembiochem, 7, 631-637.
16858396 T.Nogi, N.Yasui, M.Hattori, K.Iwasaki, and J.Takagi (2006).
Structure of a signaling-competent reelin fragment revealed by X-ray crystallography and electron tomography.EMBO J, 25, 3675-3683.
PDB code: 2ddu
16607570 V.Spiwok, P.Lipovová, T.Skálová, E.Vondrácková, J.Dohnálek, J.Hasek, and B.Králová (2005).
Modelling of carbohydrate-aromatic interactions: ab initio energetics and force field performance.J Comput Aided Mol Des, 19, 887-901.
15272157 A.W.Schüttelkopf, and D.M.van Aalten (2004).
PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.Acta Crystallogr D Biol Crystallogr, 60, 1355-1363.
14623971 A.L.Carvalho, F.M.Dias, J.A.Prates, T.Nagy, H.J.Gilbert, G.J.Davies, L.M.Ferreira, M.J.Romão, and C.M.Fontes (2003).
Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex.Proc Natl Acad Sci U S A, 100, 13809-13814.
PDB code: 1ohz
14638418 D.O.Krause, S.E.Denman, R.I.Mackie, M.Morrison, A.L.Rae, G.T.Attwood, and C.S.McSweeney (2003).
Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics.FEMS Microbiol Rev, 27, 663-693. The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.
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