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.
5y6t
From Proteopedia
(Difference between revisions)
| (2 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of endo-1,4-beta-mannanase from Eisenia fetida== | |
| + | <StructureSection load='5y6t' size='340' side='right'caption='[[5y6t]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[5y6t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Eisenia_fetida Eisenia fetida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y6T 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]] 1.7Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</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=5y6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6t OCA], [https://pdbe.org/5y6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y6t RCSB], [https://www.ebi.ac.uk/pdbsum/5y6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6t ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/A0A3B6UEQ6_EISFE A0A3B6UEQ6_EISFE] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The endo-1,4-beta-mannanases (Ef-Man) gene from Eisenia fetida was determined to consist of 1131bp and encode a 377 amino acid protein. The amino acid sequence showed similarity with the endo-1,4-beta-mannanases of Daphnia pulex (62%), Cryptopygus antarcticus (64%), Crassostrea gigas (61%), Mytilus edulis (60%), and Aplysia kurodai (58%). The gene encoding mature Ef-Man was expressed in Pichia pastoris (GS115 strain). Based on SDS-PAGE analysis, the molecular mass of the purified recombinant Ef-Man (rEf-Man) was estimated to be 39kDa. All catalytically important residues of endo-1,4-beta-mannanases in the glycoside hydrolase (GH) family 5 were conserved in Ef-Man. The optimal temperature for rEf-Man was identified as 60 degrees C. HPLC and HPAEC analyses suggest that Ef-Man requires at least six subsites for efficient hydrolysis and is capable of performing transglycosylation reactions. The overall structure of rEf-Man is similar to those of GH5 family proteins, and tertiary structures around the active site are conserved among endo-1,4-beta-mannanase families. X-ray crystallographic analysis supports the hydrolysis and transglycosylation reaction mechanism determined by HPLC and HPAEC analyses. | ||
| - | + | Gene cloning, expression, and X-ray crystallographic analysis of a beta-mannanase from Eisenia fetida.,Ueda M, Hirano Y, Fukuhara H, Naka Y, Nakazawa M, Sakamoto T, Ogata Y, Tamada T Enzyme Microb Technol. 2018 Oct;117:15-22. doi: 10.1016/j.enzmictec.2018.05.014. , Epub 2018 May 25. PMID:30037547<ref>PMID:30037547</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 5y6t" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: | + | <references/> |
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Eisenia fetida]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Hirano Y]] | ||
| + | [[Category: Tamada T]] | ||
| + | [[Category: Ueda M]] | ||
Current revision
Crystal structure of endo-1,4-beta-mannanase from Eisenia fetida
| |||||||||||
