4j4b: Difference between revisions
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The | ==PylD in complex with L-lysine-Ne-D-ornithine and NADH== | ||
<StructureSection load='4j4b' size='340' side='right'caption='[[4j4b]], [[Resolution|resolution]] 1.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4j4b]] is a 2 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=4J4B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J4B 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]] 1.9Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TF:N~6~-D-ORNITHYL-L-LYSINE'>0TF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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=4j4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j4b OCA], [https://pdbe.org/4j4b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j4b RCSB], [https://www.ebi.ac.uk/pdbsum/4j4b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j4b ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The final step in the biosynthesis of the 22nd genetically encoded amino acid, pyrrolysine, is catalyzed by PylD, a structurally and mechanistically unique dehydrogenase. This catalyzed reaction includes an induced-fit mechanism achieved by major structural rearrangements of the N-terminal helix upon substrate binding. Different steps of the reaction trajectory are visualized by complex structures of PylD with substrate and product. | |||
Structure and Reaction Mechanism of Pyrrolysine Synthase (PylD).,Quitterer F, Beck P, Bacher A, Groll M Angew Chem Int Ed Engl. 2013 May 29. doi: 10.1002/anie.201301164. PMID:23720358<ref>PMID:23720358</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4j4b" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Methanosarcina barkeri str. Fusaro]] | |||
[[Category: Bacher A]] | |||
[[Category: Beck P]] | |||
[[Category: Groll M]] | |||
[[Category: Quitterer F]] | |||
Latest revision as of 06:37, 17 October 2024
PylD in complex with L-lysine-Ne-D-ornithine and NADH
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