View source for 7yqs


==Neutron structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex==
<StructureSection load='7yqs' size='340' side='right'caption='[[7yqs]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7yqs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YQS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YQS FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Neutron Diffraction , X-ray diffraction, [[Resolution|Resolution]] 1.25&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=7yqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yqs OCA], [https://pdbe.org/7yqs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yqs RCSB], [https://www.ebi.ac.uk/pdbsum/7yqs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yqs ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A0A8D5PZ14_FUSOX A0A8D5PZ14_FUSOX] 
<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.

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>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7yqs" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Fusarium oxysporum]]
[[Category: Large Structures]]
[[Category: Arakawa T]]
[[Category: Fushinobu S]]
[[Category: Kondo T]]
[[Category: Kusaka K]]
[[Category: Sakamoto T]]
[[Category: Yamada T]]
[[Category: Yano N]]