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==PylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with L-lysine-Ne-D-ornithine)==
==PylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with L-lysine-Ne-D-ornithine)==
<StructureSection load='4ffm' size='340' side='right' caption='[[4ffm]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
<StructureSection load='4ffm' size='340' side='right'caption='[[4ffm]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4ffm]] is a 1 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=4FFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FFM FirstGlance]. <br>
<table><tr><td colspan='2'>[[4ffm]] 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=4FFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FFM FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0TF:N~6~-D-ORNITHYL-L-LYSINE'>0TF</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.91&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2yzg|2yzg]], [[3ouz|3ouz]], [[4ffl|4ffl]], [[4ffn|4ffn]], [[4ffo|4ffo]], [[4ffp|4ffp]], [[4ffr|4ffr]]</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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Mbar_A0837 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269797 METBF])</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=4ffm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ffm OCA], [https://pdbe.org/4ffm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ffm RCSB], [https://www.ebi.ac.uk/pdbsum/4ffm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ffm ProSAT]</span></td></tr>
<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=4ffm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ffm OCA], [http://pdbe.org/4ffm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ffm RCSB], [http://www.ebi.ac.uk/pdbsum/4ffm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ffm ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[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>  
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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4ffm" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__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: List, A]]
[[Category: Groll M]]
[[Category: Quitterer, F]]
[[Category: List A]]
[[Category: Amino acid]]
[[Category: Quitterer F]]
[[Category: Atp-binding]]
[[Category: Atp-grasp fold]]
[[Category: Biosynthesis of pyrrolysine]]
[[Category: Cytosol]]
[[Category: Isopeptide bond formation]]
[[Category: L-lysine and 3r-methyl-d-ornithine]]
[[Category: Ligase]]
[[Category: Ligase-product complex]]

Latest revision as of 11:16, 1 March 2024

PylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with L-lysine-Ne-D-ornithine)

4ffm, resolution 1.91Å

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