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.


4m2j

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:55, 20 March 2024) (edit) (undo)
 
(5 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal structure of PLP-dependent cyclase OrfR in complex with Au==
==Crystal structure of PLP-dependent cyclase OrfR in complex with Au==
-
<StructureSection load='4m2j' size='340' side='right' caption='[[4m2j]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
+
<StructureSection load='4m2j' size='340' side='right'caption='[[4m2j]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4m2j]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M2J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M2J FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4m2j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lavendulae_subsp._lavendulae Streptomyces lavendulae subsp. lavendulae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M2J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M2J FirstGlance]. <br>
-
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.95&#8491;</td></tr>
-
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4m23|4m23]], [[4m25|4m25]], [[4m26|4m26]], [[4m27|4m27]], [[4m2c|4m2c]], [[4m2e|4m2e]], [[4m2f|4m2f]], [[4m2g|4m2g]], [[4m2i|4m2i]], [[4m2k|4m2k]], [[4m2m|4m2m]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-
<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=4m2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m2j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4m2j RCSB], [http://www.ebi.ac.uk/pdbsum/4m2j PDBsum]</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=4m2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m2j OCA], [https://pdbe.org/4m2j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m2j RCSB], [https://www.ebi.ac.uk/pdbsum/4m2j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m2j ProSAT]</span></td></tr>
-
<table>
+
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/G9MBV4_STRLA G9MBV4_STRLA]
-
Streptothricin-F (STT-F), one of the early-discovered antibiotics, consists of three components, a beta-lysine homopolymer, an aminosugar D-gulosamine, and an unusual bicyclic streptolidine. The biosynthesis of streptolidine is a long-lasting but unresolved puzzle. Herein, a combination of genetic/biochemical/structural approaches was used to unravel this problem. The STT gene cluster was first sequenced from a Streptomyces variant BCRC 12163, wherein two gene products OrfP and OrfR were characterized in vitro to be a dihydroxylase and a cyclase, respectively. Thirteen high-resolution crystal structures for both enzymes in different reaction intermediate states were snapshotted to help elucidate their catalytic mechanisms. OrfP catalyzes an Fe(II) -dependent double hydroxylation reaction converting L-Arg into (3R,4R)-(OH)2 -L-Arg via (3S)-OH-L-Arg, while OrfR catalyzes an unusual PLP-dependent elimination/addition reaction cyclizing (3R,4R)-(OH)2 -L-Arg to the six-membered (4R)-OH-capreomycidine. The biosynthetic mystery finally comes to light as the latter product was incorporation into STT-F by a feeding experiment.
+
-
 
+
-
Biosynthesis of streptolidine involved two unexpected intermediates produced by a dihydroxylase and a cyclase through unusual mechanisms.,Chang CY, Lyu SY, Liu YC, Hsu NS, Wu CC, Tang CF, Lin KH, Ho JY, Wu CJ, Tsai MD, Li TL Angew Chem Int Ed Engl. 2014 Feb 10;53(7):1943-8. doi: 10.1002/anie.201307989., Epub 2014 Jan 21. PMID:24505011<ref>PMID:24505011</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Chang, C Y.]]
+
[[Category: Large Structures]]
-
[[Category: Li, T L.]]
+
[[Category: Streptomyces lavendulae subsp. lavendulae]]
-
[[Category: Liu, Y C.]]
+
[[Category: Chang CY]]
-
[[Category: Lyu, S Y.]]
+
[[Category: Li TL]]
-
[[Category: Wu, C C.]]
+
[[Category: Liu YC]]
-
[[Category: Cyclase]]
+
[[Category: Lyu SY]]
-
[[Category: Plp binding]]
+
[[Category: Wu CC]]
-
[[Category: Transferase]]
+

Current revision

Crystal structure of PLP-dependent cyclase OrfR in complex with Au

PDB ID 4m2j

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/4m2j"
Personal tools