5E6Y

Crystal structure of E.Coli branching enzyme in complex with alpha cyclodextrin

Summary for 5E6Y

• Entry DOI: 10.2210/pdb5e6y/pdb
• Related: 1M7X 2R4U 3COP 3CX4 4LPC 4LQ1 5E6Z 5E70
• Related PRD ID: PRD_900015
• Descriptor: 1,4-alpha-glucan branching enzyme GlgB, Cyclohexakis-(1-4)-(alpha-D-glucopyranose), GLYCEROL, ... (4 entities in total)
• Functional Keywords: branching enzyme, cyclodextrin, glycogen, starch, glucan, transferase
• Biological source: Escherichia coli O139:H28 (strain E24377A / ETEC)
• Total number of polymer chains: 4
• Total formula weight: 294488.74

Authors

Feng, L.,Nosrati, M.,Geiger, J.H. (deposition date: 2015-10-11, release date: 2015-12-16, Last modification date: 2023-09-27)

Primary citation

Feng, L.,Fawaz, R.,Hovde, S.,Sheng, F.,Nosrati, M.,Geiger, J.H.
Crystal structures of Escherichia coli branching enzyme in complex with cyclodextrins.
Acta Crystallogr D Struct Biol, 72:641-647, 2016

PubMed Abstract: Branching enzyme (BE) is responsible for the third step in glycogen/starch biosynthesis. It catalyzes the cleavage of α-1,4 glucan linkages and subsequent reattachment to form α-1,6 branch points. These branches are crucial to the final structure of glycogen and starch. The crystal structures of Escherichia coli BE (EcBE) in complex with α-, β- and γ-cyclodextrin were determined in order to better understand substrate binding. Four cyclodextrin-binding sites were identified in EcBE; they were all located on the surface of the enzyme, with none in the vicinity of the active site. While three of the sites were also identified as linear polysaccharide-binding sites, one of the sites is specific for cyclodextrins. In previous work three additional binding sites were identified as exclusively binding linear malto-oligosaccharides. Comparison of the binding sites shed light on this apparent specificity. Binding site IV is located in the carbohydrate-binding module 48 (CBM48) domain of EcBE and superimposes with the cyclodextrin-binding site found in the CBM48 domain of 5'-AMP-activated protein kinase (AMPK). Comparison of these sites shows the similarities and differences in the two binding modes. While some of the binding sites were found to be conserved between branching enzymes of different organisms, some are quite divergent, indicating both similarities and differences between oligosaccharide binding in branching enzymes from various sources.

PubMed: 27139627
DOI: 10.1107/S2059798316003272

Experimental method

X-RAY DIFFRACTION (2.6 Å)