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6d9f

From Proteopedia

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Current revision (14:33, 13 March 2024) (edit) (undo)
 
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<StructureSection load='6d9f' size='340' side='right'caption='[[6d9f]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
<StructureSection load='6d9f' size='340' side='right'caption='[[6d9f]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6d9f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Kitsk Kitsk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D9F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6D9F FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6d9f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Kitasatospora_setae_KM-6054 Kitasatospora setae KM-6054]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D9F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D9F FirstGlance]. <br>
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</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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.03&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">vlmB, KSE_09070 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=452652 KITSK])</td></tr>
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<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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6d9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d9f OCA], [http://pdbe.org/6d9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d9f RCSB], [http://www.ebi.ac.uk/pdbsum/6d9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d9f ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6d9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d9f OCA], [https://pdbe.org/6d9f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d9f RCSB], [https://www.ebi.ac.uk/pdbsum/6d9f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d9f ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/E4N6B3_KITSK E4N6B3_KITSK]
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To complement established rational and evolutionary protein design approaches, significant efforts are being made to utilize computational modeling and the diversity of naturally occurring protein sequences. Here, we combine structural biology, genomic mining, and computational modeling to identify structural features critical to aldehyde deformylating oxygenases (ADOs), an enzyme family that has significant implications in synthetic biology and chemoenzymatic synthesis. Through these efforts, we discovered latent ADO-like function across the ferritin-like superfamily in various species of Bacteria and Archaea. We created a machine learning model that uses protein structural features to discriminate ADO-like activity. Computational enzyme design tools were then utilized to introduce ADO-like activity into the small subunit of Escherichia coli class I ribonucleotide reductase. The integrated approach of genomic mining, structural biology, molecular modeling, and machine learning has the potential to be utilized for rapid discovery and modulation of functions across enzyme families.
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Discovery, Design, and Structural Characterization of Alkane-Producing Enzymes across the Ferritin-like Superfamily.,Mak WS, Wang X, Arenas R, Cui Y, Bertolani S, Deng WQ, Tagkopoulos I, Wilson DK, Siegel JB Biochemistry. 2020 Oct 13;59(40):3834-3843. doi: 10.1021/acs.biochem.0c00665., Epub 2020 Sep 23. PMID:32935984<ref>PMID:32935984</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6d9f" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Kitsk]]
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[[Category: Kitasatospora setae KM-6054]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Arenas, R]]
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[[Category: Arenas R]]
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[[Category: Mak, W S]]
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[[Category: Mak WS]]
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[[Category: Siegel, J B]]
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[[Category: Siegel JB]]
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[[Category: Wilson, D K]]
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[[Category: Wilson DK]]
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[[Category: Ferritin-like]]
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[[Category: Lyase]]
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Current revision

Protein 60 with aldehyde deformylating oxidase activity from Kitasatospora setae

PDB ID 6d9f

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