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.


4j49

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:49, 3 April 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==PylD holoenzyme soaked with L-lysine-Ne-D-ornithine==
==PylD holoenzyme soaked with L-lysine-Ne-D-ornithine==
-
<StructureSection load='4j49' size='340' side='right' caption='[[4j49]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+
<StructureSection load='4j49' size='340' side='right'caption='[[4j49]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4j49]] 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=4J49 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J49 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4j49]] 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=4J49 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J49 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1J1:N~6~-[(2R)-3,4-DIHYDRO-2H-PYRROL-2-YLCARBONYL]-L-LYSINE'>1J1</scene>, <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>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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]] 2.2&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3t7v|3t7v]], [[4ffp|4ffp]], [[4j43|4j43]], [[4j4b|4j4b]], [[4j4h|4j4h]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1J1:N~6~-[(2R)-3,4-DIHYDRO-2H-PYRROL-2-YLCARBONYL]-L-LYSINE'>1J1</scene>, <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>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></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>
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4j49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j49 OCA], [https://pdbe.org/4j49 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j49 RCSB], [https://www.ebi.ac.uk/pdbsum/4j49 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j49 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=4j49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j49 OCA], [http://pdbe.org/4j49 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4j49 RCSB], [http://www.ebi.ac.uk/pdbsum/4j49 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4j49 ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/Q46E80_METBF Q46E80_METBF]
-
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4j49" style="background-color:#fffaf0;"></div>
+
-
== 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: Quitterer, F]]
+
[[Category: Groll M]]
-
[[Category: 22nd amino acid]]
+
[[Category: Quitterer F]]
-
[[Category: Biosynthesis]]
+
-
[[Category: Dehydrogenase]]
+
-
[[Category: L-lysine-ne-3r-methyl-d-ornithine]]
+
-
[[Category: Nad]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Pyrrolysine]]
+
-
[[Category: Rossmann fold]]
+

Current revision

PylD holoenzyme soaked with L-lysine-Ne-D-ornithine

PDB ID 4j49

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/4j49"
Personal tools