7eih: Difference between revisions

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<StructureSection load='7eih' size='340' side='right'caption='[[7eih]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='7eih' size='340' side='right'caption='[[7eih]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7eih]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EIH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EIH FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EIH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EIH FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7eih FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eih OCA], [https://pdbe.org/7eih PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eih RCSB], [https://www.ebi.ac.uk/pdbsum/7eih PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eih 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=7eih FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eih OCA], [https://pdbe.org/7eih PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eih RCSB], [https://www.ebi.ac.uk/pdbsum/7eih PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eih ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A large number of protein sequences are registered in public databases such as PubMed. Functionally uncharacterized enzymes are included in these databases, some of which likely have potential for industrial applications. However, assignment of the enzymes remained difficult tasks for now. In this study, we assigned a total of 28 original sequences to uncharacterized enzymes in the FAD-dependent oxidase family expressed in some species of bacteria including Chryseobacterium, Flavobacterium, and Pedobactor. Progenitor sequence of the assigned 28 sequences was generated by ancestral sequence reconstruction, and the generated sequence exhibited L-lysine oxidase activity; thus, we named the enzyme AncLLysO. Crystal structures of ligand-free and ligand-bound forms of AncLLysO were determined, indicating that the enzyme recognizes L-Lys by hydrogen bond formation with R76 and E383. The binding of L-Lys to AncLLysO induced dynamic structural change at a plug loop formed by residues 251 to 254. Biochemical assays of AncLLysO variants revealed the functional importance of these substrate recognition residues and the plug loop. R76A and E383D variants were also observed to lose their activity, and the kcat/Km value of G251P and Y253A mutations were approximately 800- to 1800-fold lower than that of AncLLysO, despite the indirect interaction of the substrates with the mutated residues. Taken together, our data demonstrate that combinational approaches to sequence classification from database and ancestral sequence reconstruction may be effective not only to find new enzymes using databases of unknown sequences but also to elucidate their functions.
Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining.,Sugiura S, Nakano S, Niwa M, Hasebe F, Matsui D, Ito S J Biol Chem. 2021 Sep;297(3):101043. doi: 10.1016/j.jbc.2021.101043. Epub 2021, Aug 4. PMID:34358565<ref>PMID:34358565</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7eih" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Synthetic construct sequences]]
[[Category: Hasebe F]]
[[Category: Hasebe, F]]
[[Category: Ito S]]
[[Category: Ito, S]]
[[Category: Nakano S]]
[[Category: Nakano, S]]
[[Category: Niwa M]]
[[Category: Niwa, M]]
[[Category: Sugiura S]]
[[Category: Sugiura, S]]
[[Category: L-lys oxidase]]
[[Category: Oxidoreductase]]

Latest revision as of 19:33, 29 May 2024

Ancestral L-Lys oxidase (ligand free form)

7eih, resolution 2.20Å

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