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| | ==Crystal structure of branching enzyme from Cyanothece sp. ATCC 51142== | | ==Crystal structure of branching enzyme from Cyanothece sp. ATCC 51142== |
| - | <StructureSection load='5gqu' size='340' side='right' caption='[[5gqu]], [[Resolution|resolution]] 1.85Å' scene=''> | + | <StructureSection load='5gqu' size='340' side='right'caption='[[5gqu]], [[Resolution|resolution]] 1.85Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5gqu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GQU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GQU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5gqu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Crocosphaera_subtropica_ATCC_51142 Crocosphaera subtropica ATCC 51142]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GQU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GQU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5gqv|5gqv]], [[5gqw|5gqw]], [[5gqx|5gqx]], [[5gqy|5gqy]], [[5gqz|5gqz]], [[5gr0|5gr0]], [[5gr1|5gr1]], [[5gr2|5gr2]], [[5gr3|5gr3]], [[5gr4|5gr4]], [[5gr5|5gr5]], [[5gr6|5gr6]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,4-alpha-glucan_branching_enzyme 1,4-alpha-glucan branching enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.18 2.4.1.18] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5gqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gqu OCA], [https://pdbe.org/5gqu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gqu RCSB], [https://www.ebi.ac.uk/pdbsum/5gqu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gqu ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5gqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gqu OCA], [http://pdbe.org/5gqu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gqu RCSB], [http://www.ebi.ac.uk/pdbsum/5gqu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gqu ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/B1WPM8_CYAA5 B1WPM8_CYAA5]] Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position.[HAMAP-Rule:MF_00685] | + | [https://www.uniprot.org/uniprot/B1WPM8_CROS5 B1WPM8_CROS5] Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position.[HAMAP-Rule:MF_00685] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| - | Several cyanobacterial species, including Cyanothece sp. ATCC 51142, remarkably have four isoforms of alpha-glucan branching enzymes (BEs). Based on their primary structures, they are classified into glycoside hydrolase (GH) family 13 (BE1, BE2 and BE3) or family 57 (GH57 BE). In the present study, GH13-type BEs from Cyanothece sp. ATCC 51142 (BE1, BE2 and BE3) have been overexpressed in Escherichia coli and biochemically characterized. The recombinant BE1 was crystallized by the hanging-drop vapour-diffusion method. Crystals of BE1 were obtained at 293 K in the presence of 0.2 M Mg(2+), 7-10%(w/v) ethanol, 0.1 M HEPES-NaOH pH 7.2-7.9. The crystals belonged to the tetragonal space group P41212, with unit-cell parameters a = b = 133.75, c = 185.90 A, and diffracted to beyond 1.85 A resolution. Matthews coefficient calculations suggested that the crystals of BE1 contained two molecules in the asymmetric unit.
| + | Branching enzyme (BE) catalyzes the formation of alpha-1,6-glucosidic linkages in amylopectin and glycogen. The reaction products are variable, depending on the organism sources, and the mechanistic basis for these different outcomes is unclear. Although most cyanobacteria have only one BE isoform belonging to glycoside hydrolase family 13, Cyanothece sp. ATCC 51142 has three isoforms (BE1, BE2, and BE3) with distinct enzymatic properties, suggesting that investigations of these enzymes might provide unique insights into this system. Here, we report the crystal structure of ligand-free wild-type BE1 (residues 5-759 of 1-773) at 1.85 A resolution. The enzyme consists of four domains, including domain N, carbohydrate-binding module family 48 (CBM48), domain A containing the catalytic site, and domain C. The central domain A displays a (beta/alpha)8-barrel fold, whereas the other domains adopt beta-sandwich folds. Domain N was found in a new location at the back of the protein, forming hydrogen bonds and hydrophobic interactions with CBM48 and domain A. Site-directed mutational analysis identified a mutant (W610N) that bound maltoheptaose with sufficient affinity to enable structure determination at 2.30 A resolution. In this structure, maltoheptaose was bound in the active site cleft, allowing us to assign subsites -7 to -1. Moreover, seven oligosaccharide-binding sites were identified on the protein surface, and we postulated that two of these in domain A served as the entrance and exit of the donor/acceptor glucan chains, respectively. Based on these structures, we propose a substrate binding model explaining the mechanism of glycosylation/deglycosylation reactions catalyzed by BE. |
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| - | Crystallization and crystallographic analysis of branching enzymes from Cyanothece sp. ATCC 51142.,Hayashi M, Suzuki R, Colleoni C, Ball SG, Fujita N, Suzuki E Acta Crystallogr F Struct Biol Commun. 2015 Aug;71(Pt 8):1109-13. doi:, 10.1107/S2053230X1501198X. Epub 2015 Jul 29. PMID:26249708<ref>PMID:26249708</ref>
| + | Bound Substrate in the Structure of Cyanobacterial Branching Enzyme Supports a New Mechanistic Model.,Hayashi M, Suzuki R, Colleoni C, Ball SG, Fujita N, Suzuki E J Biol Chem. 2017 Mar 31;292(13):5465-5475. doi: 10.1074/jbc.M116.755629. Epub, 2017 Feb 13. PMID:28193843<ref>PMID:28193843</ref> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 1,4-alpha-glucan branching enzyme]] | + | [[Category: Crocosphaera subtropica ATCC 51142]] |
| - | [[Category: Suzuki, E]] | + | [[Category: Large Structures]] |
| - | [[Category: Suzuki, R]] | + | [[Category: Suzuki E]] |
| - | [[Category: Branching enzyme]] | + | [[Category: Suzuki R]] |
| - | [[Category: Cyanobacteria]]
| + | |
| - | [[Category: Glycoside hydrolase family 13]]
| + | |
| - | [[Category: Starch]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
B1WPM8_CROS5 Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position.[HAMAP-Rule:MF_00685]
Publication Abstract from PubMed
Branching enzyme (BE) catalyzes the formation of alpha-1,6-glucosidic linkages in amylopectin and glycogen. The reaction products are variable, depending on the organism sources, and the mechanistic basis for these different outcomes is unclear. Although most cyanobacteria have only one BE isoform belonging to glycoside hydrolase family 13, Cyanothece sp. ATCC 51142 has three isoforms (BE1, BE2, and BE3) with distinct enzymatic properties, suggesting that investigations of these enzymes might provide unique insights into this system. Here, we report the crystal structure of ligand-free wild-type BE1 (residues 5-759 of 1-773) at 1.85 A resolution. The enzyme consists of four domains, including domain N, carbohydrate-binding module family 48 (CBM48), domain A containing the catalytic site, and domain C. The central domain A displays a (beta/alpha)8-barrel fold, whereas the other domains adopt beta-sandwich folds. Domain N was found in a new location at the back of the protein, forming hydrogen bonds and hydrophobic interactions with CBM48 and domain A. Site-directed mutational analysis identified a mutant (W610N) that bound maltoheptaose with sufficient affinity to enable structure determination at 2.30 A resolution. In this structure, maltoheptaose was bound in the active site cleft, allowing us to assign subsites -7 to -1. Moreover, seven oligosaccharide-binding sites were identified on the protein surface, and we postulated that two of these in domain A served as the entrance and exit of the donor/acceptor glucan chains, respectively. Based on these structures, we propose a substrate binding model explaining the mechanism of glycosylation/deglycosylation reactions catalyzed by BE.
Bound Substrate in the Structure of Cyanobacterial Branching Enzyme Supports a New Mechanistic Model.,Hayashi M, Suzuki R, Colleoni C, Ball SG, Fujita N, Suzuki E J Biol Chem. 2017 Mar 31;292(13):5465-5475. doi: 10.1074/jbc.M116.755629. Epub, 2017 Feb 13. PMID:28193843[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Hayashi M, Suzuki R, Colleoni C, Ball SG, Fujita N, Suzuki E. Bound Substrate in the Structure of Cyanobacterial Branching Enzyme Supports a New Mechanistic Model. J Biol Chem. 2017 Mar 31;292(13):5465-5475. doi: 10.1074/jbc.M116.755629. Epub, 2017 Feb 13. PMID:28193843 doi:http://dx.doi.org/10.1074/jbc.M116.755629
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