4q3c

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==PylD cocrystallized with L-Lysine-Ne-L-lysine and NAD+==
==PylD cocrystallized with L-Lysine-Ne-L-lysine and NAD+==
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<StructureSection load='4q3c' size='340' side='right' caption='[[4q3c]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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<StructureSection load='4q3c' size='340' side='right'caption='[[4q3c]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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[[4q3c]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q3C OCA]. <br>
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<table><tr><td colspan='2'>[[4q3c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_barkeri_str._Fusaro Methanosarcina barkeri str. Fusaro]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q3C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q3C FirstGlance]. <br>
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<b>[[Ligand|Ligands:]]</b> <scene name='pdbligand=2YG:N~6~-L-LYSYL-L-LYSINE'>2YG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene><br>
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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]] 2.1&#8491;</td></tr>
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<b>[[Related_structure|Related:]]</b> [[3t7v|3t7v]], [[4ffp|4ffp]], [[4q39|4q39]], [[4q3e|4q3e]], [[4q3a|4q3a]], [[4q3b|4q3b]], [[4q3d|4q3d]]<br>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2YG:N~6~-L-LYSYL-L-LYSINE'>2YG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
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<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
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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=4q3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q3c OCA], [https://pdbe.org/4q3c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q3c RCSB], [https://www.ebi.ac.uk/pdbsum/4q3c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q3c ProSAT]</span></td></tr>
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<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4q3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q3c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q3c RCSB], [http://www.ebi.ac.uk/pdbsum/4q3c PDBsum]</span><br>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PYLD_METBF PYLD_METBF] Catalyzes the ultimate step of the pyrrolysine biosynthesis pathway by converting the isopeptide (3R)-3-methyl-D-ornithyl-N(6)-L-lysine to the 22nd proteinogenic amino acid (PubMed:24916332). Is able to use surrogate substrates such as (3R)-D-ornithyl-N(6)-L-lysine in vitro (PubMed:23720358, PubMed:24916332).<ref>PMID:23720358</ref> <ref>PMID:24916332</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The dehydrogenase PylD catalyzes the ultimate step of the pyrrolysine pathway by converting the isopeptide L-lysine-Nepsilon-3R-methyl-D-ornithine to the 22nd proteinogenic amino acid. In this study, we demonstrate how PylD can be harnessed to oxidize various isopeptides to novel amino acids by combining chemical synthesis with enzyme kinetics and X-ray crystallography. The data enable a detailed description of the PylD reaction trajectory for the biosynthesis of pyrroline and tetrahydropyridine rings as constituents of pyrrolysine analogues.
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The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD).,Quitterer F, Beck P, Bacher A, Groll M Angew Chem Int Ed Engl. 2014 Jun 10. doi: 10.1002/anie.201402595. PMID:24916332<ref>PMID:24916332</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 4q3c" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacher, A.]]
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[[Category: Large Structures]]
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[[Category: Beck, P.]]
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[[Category: Methanosarcina barkeri str. Fusaro]]
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[[Category: Groll, M.]]
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[[Category: Bacher A]]
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[[Category: Quitterer, F.]]
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[[Category: Beck P]]
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[[Category: Dehydrogenase]]
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[[Category: Groll M]]
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[[Category: Oxidoreductase]]
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[[Category: Quitterer F]]
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[[Category: Pyrrolysine]]
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[[Category: Rossmann fold]]
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Current revision

PylD cocrystallized with L-Lysine-Ne-L-lysine and NAD+

PDB ID 4q3c

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