This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


4ffr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:47, 3 April 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==SeMet-labeled PylC (remote)==
==SeMet-labeled PylC (remote)==
-
<StructureSection load='4ffr' size='340' side='right' caption='[[4ffr]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+
<StructureSection load='4ffr' size='340' side='right'caption='[[4ffr]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4ffr]] 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=4FFR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FFR FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4ffr]] 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=4FFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FFR FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 1.8&#8491;</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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2yzg|2yzg]], [[3ouz|3ouz]], [[4ffl|4ffl]], [[4ffm|4ffm]], [[4ffn|4ffn]], [[4ffo|4ffo]], [[4ffp|4ffp]]</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=4ffr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ffr OCA], [https://pdbe.org/4ffr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ffr RCSB], [https://www.ebi.ac.uk/pdbsum/4ffr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ffr ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ffr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ffr OCA], [http://pdbe.org/4ffr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ffr RCSB], [http://www.ebi.ac.uk/pdbsum/4ffr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ffr 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 4ffr" 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]]
+

Current revision

SeMet-labeled PylC (remote)

PDB ID 4ffr

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4ffr"
Personal tools