Towards the molecular understanding of glycogen elongation by amylosucrase. Cécile Albenne, Lars K Skov, Vinh Tran, Michael Gajhede, Pierre Monsan, Magali Remaud Simeon, Gwenaëlle André-Leroux To cite this version: Cécile Albenne, Lars K Skov, Vinh Tran, Michael Gajhede, Pierre Monsan, et al.. Towards the molecular understanding of glycogen elongation by amylosucrase.. Proteins - Structure, Function and Bioinformatics, Wiley, 2007, 66 (1), pp.118-26. 10.1002/prot.21083. hal-02663870 HAL Id: hal-02663870 https://hal.inrae.fr/hal-02663870 Submitted on 31 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - ShareAlike| 4.0 International License PROTEINS: Structure, Function, and Bioinformatics 66:118–126 (2007) Towards the Molecular Understanding of Glycogen Elongation by Amylosucrase Ce´cile Albenne,1 Lars K. Skov,2 Vinh Tran,3 Michael Gajhede,2 Pierre Monsan,4 Magali Remaud-Sime´on,4* and Gwe´nae¨lle Andre´-Leroux5 1Laboratoire Surfaces Cellulaires et Signalisation chez les Ve´ge´taux, UMR 5546 CNRS-Universite´ Paul Sabatier-Toulouse III, 24 Chemin de Borde Rouge, BP42617, 31326 Castanet-Tolosan, France 2Biostructural Research, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken2, DK-2100 Copenhagen, Denmark 3Unite´ Biotechnologie, Biocatalyse, Biore´gulation (U3B) UMR-CNRS 6204, Universite´ de Sciences et Techniques de Nantes, 2, rue de la Houssinie`re, 44322 Nantes, France 4Laboratoire de Biotechnologie–Bioproce´de´s, UMR CNRS 5504, UMR INRA 792, INSA DGBA, 135, avenue de Rangueil, 31077 Toulouse Cedex 04, France 5INRA, Institut Pasteur, Unite´ de Biochimie Structurale, 25, rue du Dr Roux, 75724 Paris Cedex 15, France ABSTRACT Amylosucrase from Neisseria poly- polymer from sucrose with concomitant release of fructose.1 saccharea (AS) is a transglucosidase from the glyco- This reaction starts by sucrose hydrolysis. The glucose side-hydrolase family 13 that catalyzes the synthe- formed is in turn used as an acceptor that is then succes- sis of an amylose-like polymer from sucrose, with- sively elongated to produce a series of maltooligosacchar- out any primer. Its affinity towards glycogen is ides that are soluble until their size and concentration particularly noteworthy since glycogen is the best cause their precipitation.4,5 In contrast, when glycogen is D-glucosyl unit acceptor and the most efficient acti- added into the medium at a concentration higher than vator (98-fold kcat increase) known for this enzyme. 0.5 g/L, neither glucose nor oligosaccharide formation is ob- Glycogen–enzyme interactions were modeled start- served.6 The glucosyl units of sucrose are transferred exclu- ing from the crystallographic AS: maltoheptaose sively onto some glycogen branches until a critical size complex, where two key oligosaccharide binding causing polymer insolubilization. For example, the modi- sites, OB1 and OB2, were identified. Two maltohep- fied glycogen formed from 146 mM sucrose and 1 g/L glyco- taose molecules were connected by an a-1,6 branch gen displays some branches with a degree of polymeriza- by molecular modeling to mimic a glycogen branch- tion (DP) of 75.6 Moreover, a strong increase of the sucrose ing. Among the various docking positions obtained, consumption rate is observed in the presence of glycogen.6 four models were chosen based on geometry and This activation is dependant on both sucrose and glycogen energy criteria. Robotics calculations enabled us to concentrations. For example, using 106 mM sucrose, and describe a back and forth motion of a hairpin loop 30 g/L glycogen, a 98-fold increase of sucrose consumption of the AS specific B0-domain, a movement that as- rate is obtained.6 Other a-1,4 glucans can also be modified sists the elongation of glycogen branches. Modeling via glucosylation by AS,7 but they were shown, so far, to be data combined with site-directed mutagenesis ex- less efficient activators. This strongly suggests that the in periments revealed that the OB2 surface site pro- vivo function of AS could be glycogen elongation. vides an anchoring platform at the enzyme surface From a structural point of view, AS consists of five to capture the polymer and direct the branches domains, named N, A, B, B0,andC8 (Fig. 1). Domains A, B, towards the OB1 acceptor site for elongation. On and C are common to family 13 enzymes, with the charac- the basis of the data obtained, a semiprocessive teristic (b/a)8-barrel catalytic A-domain, whereas the heli- glycogen elongation mechanism can be proposed. cal N-terminal domain and the B0-domain, corresponding Proteins 2007;66:118–126. VC 2006 Wiley-Liss, Inc. to an extended loop 7 of the barrel, are specific to AS. The 3D-structures of AS in complex with sucrose9 or maltohep- Key words: molecular modeling; robotics; docking; taose10 enabled us to localize the active site as well as transglucosylation; site-directed muta- genesis; enzymatic mechanism The Supplementary Material referred to in this article can be found at http://www.interscience.wiley.com/jpages/0887-3585/suppmat INTRODUCTION *Correspondence to: Magali Remaud-Sime´on, Laboratoire de Bio- Amylosucrase (E.C. 2.4.1.4) from Neisseria polysaccharea technologie–Bioproce´de´s, UMR CNRS 5504, UMR INRA 792, INSA DGBA, 135, avenue de Rangueil, 31077 Toulouse Cedex 04, France. (AS) is a bacterial transglucosidase from glycoside hydro- E-mail: [email protected] lase family 13, also named the a-amylase family.1–3 AS is Received 20 June 2005; Revised 14 April 2006; Accepted 27 April closely related to other transferases of this family such as 2006 CGTase or amylomaltase; however, it is the only polymer- Published online 16 October 2006 in Wiley InterScience (www. ase. AS catalyzes the synthesis of an insoluble amylose-like interscience.wiley.com). DOI: 10.1002/prot.21083 VC 2006 WILEY-LISS, INC. GLYCOGEN ELONGATION BY AMYLOSUCRASE 119 bined to robotics calculations and site-directed mutagenesis experiments, provided fruitful information on the AS speci- ficity towards glycogen and enabled us to propose an ad- vanced dynamic mechanism of glycogen elongation. MATERIALS AND METHODS Molecular Modeling The molecular modeling was carried out on Silicon Graphics computers with the Accelrys packages (Accelrys, San Diego, CA). Molecular displays and energy minimiza- tions were performed with InsightII, Biopolymer, and Dis- cover modules. For all calculations, the CFF91 force-field with the steepest descent minimization was selected. Fig. 1. Overall structure of AS with a sucrose molecule occupying Glycogen Docking the active site and three maltooligosaccharides bound in the oligosac- 0 Definition of the starting coordinates charides binding sites OB1 to OB3. The B -domain hairpin loop Gly 433–Gly449 is shown in dark grey. X-ray data of the complex between AS (inactive mutant E328Q) and maltoheptaose (G7) fragments bound at the 10 three additional oligosaccharide binding sites (OB1–OB3) OB1 and OB2 binding sites were used as starting coordi- (Fig. 1). The active site, consisting of À1andþ1 subsites9 nates for the modeling of glycogen docking (1MW0.pdb). (according to the nomenclature defined by Davies and To spare cpu time, the protein was reduced to the residues 11 b?a Henrissat ), is situated at the bottom of a narrow pocket involved in the complex, which included all loops b a delimited by a salt bridge. The first oligosaccharide bind- belonging to the ( / )8-barrel and residues from the neigh- b ing site OB1 spans over the active site and five additional boring C-terminal ends of strands and N-terminal ends 10 a acceptor subsites (þ2toþ6). The two other sites OB2 of helices. This procedure led to an enzyme of 309 resi- and OB3, located at the enzyme surface, are expected to dues out of the 628 where the following segments have provide additional binding sites for acceptor molecules.10 been included in the computations: 102–112, 131–163, The catalytic active site residues are the nucleophile 182–278, 284–304, 328–332, 348–358, 387–464, 484–536. Asp286, the general acid/base catalyst Glu328, and Asp393 However, the term ‘‘enzyme’’ will be used for this trun- that assists catalysis.8,12 The catalysis proceeds via a dou- cated protein in the following text. The 14 glucosyl resi- ble-displacement mechanism involving the formation of a dues of the two maltoheptaose molecules docked in OB1 covalent glucosyl-enzyme intermediate13–15 that has re- and OB2 were kept in their crystallographic positions with cently been characterized by X-ray crystallography.16 the exception of the three residues involved in the branch The AS-specific B0-domain (residues 395–460) is expected construction (Fig. 2): to be involved in the polymerase activity, notably via con- formational movements. Indeed, we have recently shown the two loosely defined glucosyl moieties bound at OB1 þ þ by fluorimetry experiments that the addition of sucrose or subsites 5 and 6 (reducing end); glycogen induces enzyme conformational changes, sup- the glucosyl unit