8fsd: Difference between revisions

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-'''Unreleased structure'''
-The entry 8fsd is ON HOLD  until 2025-01-09
+==P130R mutant of soybean SHMT8 in complex with PLP-glycine and formylTHF==
+<StructureSection load='8fsd' size='340' side='right'caption='[[8fsd]], [[Resolution|resolution]] 1.49&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8fsd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8FSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8FSD FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.49&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FFO:N-[4-({[(6S)-2-AMINO-5-FORMYL-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC+ACID'>FFO</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</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=8fsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8fsd OCA], [https://pdbe.org/8fsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8fsd RCSB], [https://www.ebi.ac.uk/pdbsum/8fsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8fsd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A0R0IK90_SOYBN A0A0R0IK90_SOYBN] Interconversion of serine and glycine.[RuleBase:RU000585]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Two amino acid variants in soybean serine hydroxymethyltransferase 8 (SHMT8) are associated with resistance to the soybean cyst nematode (SCN), a devastating agricultural pathogen with worldwide economic impacts on soybean production. SHMT8 is a cytoplasmic enzyme that catalyzes the pyridoxal 5-phosphate-dependent conversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methylenetetrahydrofolate. A previous study of the P130R/N358Y double variant of SHMT8, identified in the SCN-resistant soybean cultivar (cv.) Forrest, showed profound impairment of folate binding affinity and reduced THF-dependent enzyme activity, relative to the highly active SHMT8 in cv. Essex, which is susceptible to SCN. Given the importance of SCN-resistance in soybean agriculture, we report here the biochemical and structural characterization of the P130R and N358Y single variants to elucidate their individual effects on soybean SHMT8. We find that both single variants have reduced THF-dependent catalytic activity relative to Essex SHMT8 (10- to 50-fold decrease in k(cat) /K(m) ) but are significantly more active than the P130R/N368Y double variant. The kinetic data also show that the single variants lack THF-substrate inhibition as found in Essex SHMT8, an observation with implications for regulation of the folate cycle. Five crystal structures of the P130R and N358Y variants in complex with various ligands (resolutions from 1.49 to 2.30 A) reveal distinct structural impacts of the mutations and provide new insights into allosterism. Our results support the notion that the P130R/N358Y double variant in Forrest SHMT8 produces unique and unexpected effects on the enzyme, which cannot be easily predicted from the behavior of the individual variants.
-Authors:
+Structural and functional analysis of two SHMT8 variants associated with soybean cyst nematode resistance.,Korasick DA, Owuocha LF, Kandoth PK, Tanner JJ, Mitchum MG, Beamer LJ FEBS J. 2023 Oct 9. doi: 10.1111/febs.16971. PMID:37811683<ref>PMID:37811683</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 8fsd" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Glycine max]]
+[[Category: Large Structures]]
+[[Category: Beamer LJ]]
+[[Category: Korasick DA]]