8i4d
From Proteopedia
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8i4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8i4d OCA], [https://pdbe.org/8i4d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8i4d RCSB], [https://www.ebi.ac.uk/pdbsum/8i4d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8i4d ProSAT]</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=8i4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8i4d OCA], [https://pdbe.org/8i4d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8i4d RCSB], [https://www.ebi.ac.uk/pdbsum/8i4d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8i4d ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| - | == | + | <div style="background-color:#fffaf0;"> |
| - | + | == Publication Abstract from PubMed == | |
| + | Gum arabic (GA) is widely used as an emulsion stabilizer and edible coating and consists of a complex carbohydrate moiety with a rhamnosyl-glucuronate group capping the non-reducing ends. Enzymes that can specifically cleave the glycosidic chains of GA and modify their properties are valuable for structural analysis and industrial application. Cryogenic X-ray crystal structure of GA-specific L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum (FoRham1), belonging to the polysaccharide lyase (PL) family 42, has been previously reported. To determine the specific reaction mechanism based on its hydrogen-containing enzyme structure, we performed joint X-ray/neutron crystallography of FoRham1. Large crystals were grown in the presence of L-rhamnose (a reaction product), and neutron and X-ray diffraction datasets were collected at room temperature at 1.80 and 1.25 A resolutions, respectively. The active site contained L-rhamnose and acetate, the latter being a partial analog of glucuronate. Incomplete H/D exchange between Arg166 and acetate suggested that a strong salt-bridge interaction was maintained. Doubly deuterated His105 and deuterated Tyr150 supported the interaction between Arg166 and the acetate. The unique hydrogen-rich environment functions as a charge neutralizer for glucuronate and stabilizes the oxyanion intermediate. The NE2 atom of His85 was deprotonated and formed a hydrogen bond with the deuterated O1 hydroxy of L-rhamnose, indicating the function of His85 as the base/acid catalyst for bond cleavage via beta-elimination. Asp83 functions as a pivot between the two catalytic histidine residues by bridging them. This His-His-Asp structural motif is conserved in the PL 24, 25, and 42 families. | ||
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| + | Charge neutralization and beta-elimination cleavage mechanism of family 42 L-rhamnose-alpha-1,4-D-glucuronate lyase revealed using neutron crystallography.,Yano N, Kondo T, Kusaka K, Arakawa T, Sakamoto T, Fushinobu S J Biol Chem. 2024 Mar;300(3):105774. doi: 10.1016/j.jbc.2024.105774. Epub 2024 , Feb 19. PMID:38382672<ref>PMID:38382672</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 8i4d" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
X-ray structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex at 100K
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Categories: Fusarium oxysporum | Large Structures | Arakawa T | Fushinobu S | Kondo T | Kusaka K | Sakamoto T | Yamada T | Yano N
