4YEF

beta1 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclododextrin

Summary for 4YEF

• Entry DOI: 10.2210/pdb4yef/pdb
• Related: 4Y0G 4YEE
• Related PRD ID: PRD_900012
• Descriptor: 5'-AMP-activated protein kinase subunit beta-1, Cycloheptakis-(1-4)-(alpha-D-glucopyranose), GLYCEROL, ... (5 entities in total)
• Functional Keywords: carbohydrate binding module, cbm, ampk, amp-activated protein kinase, cyclodextrin, sugar binding protein
• Biological source: Rattus norvegicus (Rat)
• Total number of polymer chains: 7
• Total formula weight: 78201.47

Authors

Mobbs, J.,Gorman, M.A.,Parker, M.W.,Gooley, P.R.,Griffin, M. (deposition date: 2015-02-24, release date: 2015-06-24, Last modification date: 2023-09-27)

Primary citation

Mobbs, J.I.,Koay, A.,Di Paolo, A.,Bieri, M.,Petrie, E.J.,Gorman, M.A.,Doughty, L.,Parker, M.W.,Stapleton, D.I.,Griffin, M.D.,Gooley, P.R.
Determinants of oligosaccharide specificity of the carbohydrate-binding modules of AMP-activated protein kinase.
Biochem.J., 468:245-257, 2015

PubMed Abstract: AMP-activated protein kinase (AMPK) is an αβγ heterotrimer that is important in regulating energy metabolism in all eukaryotes. The β-subunit exists in two isoforms (β1 and β2) and contains a carbohydrate-binding module (CBM) that interacts with glycogen. The two CBM isoforms (β1- and β2-CBM) are near identical in sequence and structure, yet show differences in carbohydrate-binding affinity. β2-CBM binds linear carbohydrates with 4-fold greater affinity than β1-CBM and binds single α1,6-branched carbohydrates up to 30-fold tighter. To understand these affinity differences, especially for branched carbohydrates, we determined the NMR solution structure of β2-CBM in complex with the single α1,6-branched carbohydrate glucosyl-β-cyclodextrin (gBCD) which supported the dynamic nature of the binding site, but resonance broadening prevented defining where the α1,6 branch bound. We therefore solved the X-ray crystal structures of β1- and β2-CBM, in complex with gBCD, to 1.7 and 2.0 Å (1 Å=0.1 nm) respectively. The additional threonine (Thr101) of β2-CBM expands the size of the surrounding loop, creating a pocket that accommodates the α1,6 branch. Hydrogen bonds are formed between the α1,6 branch and the backbone of Trp99 and Lys102 side chain of β2-CBM. In contrast, the α1,6 branch could not be observed in the β1-CBM structure, suggesting that it does not form a specific interaction. The orientation of gBCD bound to β1- and β2-CBM is supported by thermodynamic and kinetic data obtained through isothermal titration calorimetry (ITC) and NMR. These results suggest that AMPK containing the muscle-specific β2-isoform may have greater affinity for partially degraded glycogen.

PubMed: 25774984
DOI: 10.1042/BJ20150270

Experimental method

X-RAY DIFFRACTION (1.72 Å)