5KLF

Structure of CBM_E1, a novel carbohydrate-binding module found by sugar cane soil metagenome, complexed with cellopentaose and gadolinium ion

Summary for 5KLF

• Entry DOI: 10.2210/pdb5klf/pdb
• Related: 5KLC 5KLE
• Related PRD ID: PRD_900016
• Descriptor: Carbohydrate binding module E1, beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose, GADOLINIUM ATOM, ... (4 entities in total)
• Functional Keywords: carbohydrate-binding protein, metagenomics, cellulose, biofuels, sugar binding protein
• Biological source: uncultured bacterium
• Total number of polymer chains: 1
• Total formula weight: 12727.68

Authors

Liberato, M.V.,Campos, B.M.,Zeri, A.C.M.,Squina, F.M. (deposition date: 2016-06-24, release date: 2016-09-21, Last modification date: 2020-07-29)

Primary citation

Campos, B.M.,Liberato, M.V.,Alvarez, T.M.,Zanphorlin, L.M.,Ematsu, G.C.,Barud, H.,Polikarpov, I.,Ruller, R.,Gilbert, H.J.,Zeri, A.C.,Squina, F.M.
A Novel Carbohydrate-binding Module from Sugar Cane Soil Metagenome Featuring Unique Structural and Carbohydrate Affinity Properties.
J.Biol.Chem., 291:23734-23743, 2016

PubMed Abstract: Carbohydrate-binding modules (CBMs) are appended to glycoside hydrolases and can contribute to the degradation of complex recalcitrant substrates such as the plant cell wall. For application in bioethanol production, novel enzymes with high catalytic activity against recalcitrant lignocellulosic material are being explored and developed. In this work, we report the functional and structural study of CBM_E1, which was discovered through a metagenomics approach and is the founding member of a novel CBM family, CBM81. CBM_E1, which is linked to an endoglucanase, displayed affinity for mixed linked β1,3-β1,4-glucans, xyloglucan, Avicel, and cellooligosaccharides. The crystal structure of CBM_E1 in complex with cellopentaose displayed a canonical β-sandwich fold comprising two β-sheets. The planar ligand binding site, observed in a parallel orientation with the β-strands, is a typical feature of type A CBMs, although the expected affinity for bacterial crystalline cellulose was not detected. Conversely, the binding to soluble glucans was enthalpically driven, which is typical of type B modules. These unique properties of CBM_E1 are at the interface between type A and type B CBMs.

PubMed: 27621314
DOI: 10.1074/jbc.M116.744383

Experimental method

X-RAY DIFFRACTION (1.801 Å)