This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
5y6u
From Proteopedia
(Difference between revisions)
| Line 3: | Line 3: | ||
<StructureSection load='5y6u' size='340' side='right'caption='[[5y6u]], [[Resolution|resolution]] 1.50Å' scene=''> | <StructureSection load='5y6u' size='340' side='right'caption='[[5y6u]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5y6u]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6U OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[5y6u]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacnb Bacnb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y6U FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene></td></tr> | ||
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qd9|1qd9]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qd9|1qd9]]</div></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yabJ, BSNT_00084 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=645657 BACNB])</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=5y6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6u OCA], [https://pdbe.org/5y6u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y6u RCSB], [https://www.ebi.ac.uk/pdbsum/5y6u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6u ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Bacillus subtilis YabJ protein belongs to the highly conserved YjgF/YER057c/UK114 family, which has a homotrimeric quaternary structure. The dominant allele of yabJ gene that is caused by a single amino acid mutation of Ser103Phe enables poly-gamma-glutamic acid (gammaPGA) production of B. subtilis under conditions where the cell-density signal transduction was disturbed by the loss of DegQ function. X-ray crystallography of recombinant proteins revealed that unlike the homotrimeric wild-type YabJ, the mutant YabJ(Ser103Phe) had a homotetrameric quaternary structure, and the structural change appeared to be triggered by an inversion of the fifth beta-strand. The YabJ homotetramer has a hole that is highly accessible, penetrating through the tetramer, and 2 surface concaves as potential ligand-binding sites. Western blot analyses revealed that the conformational change was also induced in vivo by the Ser103Phe mutation. | ||
| + | |||
| + | Tetramer formation of Bacillus subtilis YabJ protein that belongs to YjgF/YER057c/UK114 family.,Fujimoto Z, Hong LTT, Kishine N, Suzuki N, Kimura K Biosci Biotechnol Biochem. 2021 Feb 18;85(2):297-306. doi: 10.1093/bbb/zbaa037. PMID:33590041<ref>PMID:33590041</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 5y6u" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Bacnb]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Fujimoto, Z]] | [[Category: Fujimoto, Z]] | ||
Revision as of 14:52, 3 March 2021
Crystal structure of wild-type YabJ protein from Bacillus subtilis (natto).
| |||||||||||
