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.


3t7v

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:04, 1 March 2024) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal structure of methylornithine synthase (PylB)==
==Crystal structure of methylornithine synthase (PylB)==
-
<StructureSection load='3t7v' size='340' side='right' caption='[[3t7v]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+
<StructureSection load='3t7v' size='340' side='right'caption='[[3t7v]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3t7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanosarcina_barkeri Methanosarcina barkeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T7V FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3t7v]] 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=3T7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T7V FirstGlance]. <br>
-
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MD0:5-AMINO-D-ISOLEUCINE'>MD0</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene><br>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1r30|1r30]], [[3ciw|3ciw]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MD0:5-AMINO-D-ISOLEUCINE'>MD0</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Mbar_A0838 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2208 Methanosarcina barkeri])</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=3t7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t7v OCA], [https://pdbe.org/3t7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t7v RCSB], [https://www.ebi.ac.uk/pdbsum/3t7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t7v ProSAT]</span></td></tr>
-
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biotin_synthase Biotin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.8.1.6 2.8.1.6] </span></td></tr>
+
</table>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3t7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t7v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t7v RCSB], [http://www.ebi.ac.uk/pdbsum/3t7v PDBsum]</span></td></tr>
+
== Function ==
-
<table>
+
[https://www.uniprot.org/uniprot/PYLB_METBF PYLB_METBF] Catalyzes the isomerization of L-lysine to (2R,3R)-3-methylornithine via a radical-based mechanism, a step in the biosynthesis pathway of pyrrolysine.<ref>PMID:21455182</ref> <ref>PMID:22095926</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Made by the barrel load: The biosynthetic pathway of the recently discovered 22nd amino acid, pyrrolysine, starts with an isomerization of lysine to methylornithine, catalyzed by PylB. The X-ray crystal structure of PylB is determined and shows it has a TIM barrel fold. The sealed central cavity contains a [4Fe-4S] cluster, S-adenosylmethionine (SAM), and methylornithine, whose 2R,3R configuration could be confirmed. The data suggest a fragmentation-recombination mechanism via a glycyl radical intermediate.
+
-
 
+
-
Crystal Structure of Methylornithine Synthase (PylB): Insights into the Pyrrolysine Biosynthesis.,Quitterer F, List A, Eisenreich W, Bacher A, Groll M Angew Chem Int Ed Engl. 2011 Nov 16. doi: 10.1002/anie.201106765. PMID:22095926<ref>PMID:22095926</ref>
+
-
 
+
-
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Biotin synthase]]
+
[[Category: Large Structures]]
-
[[Category: Methanosarcina barkeri]]
+
[[Category: Methanosarcina barkeri str. Fusaro]]
-
[[Category: Bacher, A.]]
+
[[Category: Bacher A]]
-
[[Category: Eisenreich, W.]]
+
[[Category: Eisenreich W]]
-
[[Category: Groll, M.]]
+
[[Category: Groll M]]
-
[[Category: List, A.]]
+
[[Category: List A]]
-
[[Category: Quitterer, F.]]
+
[[Category: Quitterer F]]
-
[[Category: 3-methylornithine]]
+
-
[[Category: Lysine]]
+
-
[[Category: Mutase]]
+
-
[[Category: Sam]]
+
-
[[Category: Tim-barrel fold]]
+
-
[[Category: Transferase]]
+

Current revision

Crystal structure of methylornithine synthase (PylB)

PDB ID 3t7v

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools