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| | ==PylD holoenzyme (SeMet)== | | ==PylD holoenzyme (SeMet)== |
| - | <StructureSection load='4jk3' size='340' side='right' caption='[[4jk3]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='4jk3' size='340' side='right'caption='[[4jk3]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4jk3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Metbf Metbf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JK3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JK3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4jk3]] 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=4JK3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JK3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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></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]] 2.5Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4j43|4j43]], [[4j49|4j49]], [[4j4b|4j4b]], [[4j4h|4j4h]]</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=4jk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jk3 OCA], [https://pdbe.org/4jk3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jk3 RCSB], [https://www.ebi.ac.uk/pdbsum/4jk3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jk3 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Mbar_A0835 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269797 METBF])</td></tr>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4jk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jk3 OCA], [http://pdbe.org/4jk3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jk3 RCSB], [http://www.ebi.ac.uk/pdbsum/4jk3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jk3 ProSAT]</span></td></tr> | + | |
| | </table> | | </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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Metbf]] | + | [[Category: Large Structures]] |
| - | [[Category: Bacher, A]] | + | [[Category: Methanosarcina barkeri str. Fusaro]] |
| - | [[Category: Beck, P]] | + | [[Category: Bacher A]] |
| - | [[Category: Groll, M]] | + | [[Category: Beck P]] |
| - | [[Category: Quitterer, F]] | + | [[Category: Groll M]] |
| - | [[Category: 22nd amino acid]]
| + | [[Category: Quitterer F]] |
| - | [[Category: Biosynthesis]]
| + | |
| - | [[Category: Dehydrogenase]]
| + | |
| - | [[Category: Nad]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Pyrrolysine]]
| + | |
| - | [[Category: Rossmann fold]]
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| Structural highlights
Function
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).[1] [2]
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Quitterer F, Beck P, Bacher A, Groll M. Structure and Reaction Mechanism of Pyrrolysine Synthase (PylD). Angew Chem Int Ed Engl. 2013 May 29. doi: 10.1002/anie.201301164. PMID:23720358 doi:10.1002/anie.201301164
- ↑ Quitterer F, Beck P, Bacher A, Groll M. The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD). Angew Chem Int Ed Engl. 2014 Jun 10. doi: 10.1002/anie.201402595. PMID:24916332 doi:http://dx.doi.org/10.1002/anie.201402595
- ↑ Quitterer F, Beck P, Bacher A, Groll M. Structure and Reaction Mechanism of Pyrrolysine Synthase (PylD). Angew Chem Int Ed Engl. 2013 May 29. doi: 10.1002/anie.201301164. PMID:23720358 doi:10.1002/anie.201301164
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