4ffp
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4ffp]] is a 1 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=4FFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FFP FirstGlance]. <br> | <table><tr><td colspan='2'>[[4ffp]] is a 1 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=4FFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FFP FirstGlance]. <br> | ||
| - | </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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2Å</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4ffp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ffp OCA], [https://pdbe.org/4ffp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ffp RCSB], [https://www.ebi.ac.uk/pdbsum/4ffp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ffp 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=4ffp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ffp OCA], [https://pdbe.org/4ffp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ffp RCSB], [https://www.ebi.ac.uk/pdbsum/4ffp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ffp ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/PYLC_METBF PYLC_METBF] Is required for the biosynthesis of pyrrolysine (By similarity). Catalyzes the ATP-dependent ligation between (3R)-3-methyl-D-ornithine and L-lysine, leading to (3R)-3-methyl-D-ornithyl-N6-L-lysine (Probable).[UniProtKB:Q8TUC0]<ref>PMID:22985965</ref> | [https://www.uniprot.org/uniprot/PYLC_METBF PYLC_METBF] Is required for the biosynthesis of pyrrolysine (By similarity). Catalyzes the ATP-dependent ligation between (3R)-3-methyl-D-ornithine and L-lysine, leading to (3R)-3-methyl-D-ornithyl-N6-L-lysine (Probable).[UniProtKB:Q8TUC0]<ref>PMID:22985965</ref> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | The second step in the biosynthesis of the 22nd genetically encoded amino acid pyrrolysine (Pyl) is catalyzed by PylC that forms the pseudopeptide L-lysine-N(epsilon)-3R-methyl-D-ornithine. Here, we present six crystal structures of the monomeric active ligase in complex with substrates, reaction intermediates, and products including ATP, the non-hydrolyzable ATP analogue 5'-adenylyl-beta-gamma-imidodiphosphate, ADP, D-ornithine (D-Orn), L-lysine (Lys), phosphorylated D-Orn, L-lysine-N(epsilon)-D-ornithine, inorganic phosphate, carbonate, and Mg(2+). The overall structure of PylC reveals similarities to the superfamily of ATP-grasp enzymes; however, there exist unique structural and functional features for a topological control of successive substrate entry and product release. Furthermore, the presented high-resolution structures provide detailed insights into the reaction mechanism of isopeptide bond formation starting with phosphorylation of D-Orn by transfer of a phosphate moiety from activated ATP. The binding of Lys to the enzyme complex is then followed by an S(N)2 reaction resulting in L-lysine-N(epsilon)-D-ornithine and inorganic phosphate. Surprisingly, PylC harbors two adenine nucleotides bound at the active site, what has not been observed in any ATP-grasp protein analyzed to date. Whereas one ATP molecule is involved in catalysis, the second adenine nucleotide functions as a selective anchor for the C- and N-terminus of the Lys substrate and is responsible for protein stability as shown by mutagenesis. | ||
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| - | Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.,Quitterer F, List A, Beck P, Bacher A, Groll M J Mol Biol. 2012 Dec 14;424(5):270-82. doi: 10.1016/j.jmb.2012.09.007. Epub 2012 , Sep 14. PMID:22985965<ref>PMID:22985965</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4ffp" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Current revision
PylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with L-lysine and D-ornithine)
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