6bxm: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 6bxm is ~~ON HOLD until Paper~~ Publication

==Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM==

== Structural highlights ==

<table><tr><td colspan='2'>[[6bxm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BXM FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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=6bxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bxm OCA], [http://pdbe.org/6bxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bxm RCSB], [http://www.ebi.ac.uk/pdbsum/6bxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bxm ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Diphthamide biosynthesis involves a carbon-carbon bond-forming reaction catalyzed by a radical S-adenosylmethionine (SAM) enzyme that cleaves a carbon-sulfur (C-S) bond in SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. Using rapid freezing, we have captured an organometallic intermediate with an iron-carbon (Fe-C) bond between ACP and the enzyme's [4Fe-4S] cluster. In the presence of the substrate protein, elongation factor 2, this intermediate converts to an organic radical, formed by addition of the ACP radical to a histidine side chain. Crystal structures of archaeal diphthamide biosynthetic radical SAM enzymes reveal that the carbon of the SAM C-S bond being cleaved is positioned near the unique cluster Fe, able to react with the cluster. Our results explain how selective C-S bond cleavage is achieved in this radical SAM enzyme.

~~Authors: Fenwick, M.K., Torelli, A.T., Zhang, Y~~., Dong, M., Kathiresan, V., ~~Carantoa~~, ~~J.D.~~, Dzikovski, B., Lancaster~~, K.M.~~, Freed, ~~J.H.~~, Hoffman, B.M.~~, Lin, H~~.~~, Ealick, S~~.E.

Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.,Dong M, Kathiresan V, Fenwick MK, Torelli AT, Zhang Y, Caranto JD, Dzikovski B, Sharma A, Lancaster KM, Freed JH, Ealick SE, Hoffman BM, Lin H Science. 2018 Mar 16;359(6381):1247-1250. doi: 10.1126/science.aao6595. PMID:29590073<ref>PMID:29590073</ref>

~~Description: Crystal structure~~ of ~~Candidatus Methanoperedens nitroreducens Dph2 with 4Fe~~-~~4S cluster and SAM~~/~~cleaved SAM~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

~~[[Category: Unreleased Structures]]~~

</div>

~~[[Category: Ealick, S.E]]~~

~~[[Category: Lancaster, K.M]]~~

== References ==

[[Category: Carantoa, J.D]]

__TOC__

</StructureSection>

[[Category: Carantoa, J D]]

[[Category: Dong, M]]

~~[[Category: Zhang, Y]]~~

~~[[Category: Freed, J.H]]~~

[[Category: Dzikovski, B]]

[[Category: Ealick, S E]]

[[Category: Fenwick, M K]]

[[Category: Freed, J H]]

[[Category: Hoffman, B M]]

[[Category: Kathiresan, V]]

[[Category: Lancaster, K M]]

[[Category: Lin, H]]

[[Category: ~~Hoffman~~, ~~B.M~~]]

[[Category: Torelli, A T]]

[[Category: ~~Kathiresan~~, V]]

[[Category: Zhang, Y]]

[[Category: ~~Fenwick, M.K~~]]

[[Category: Biosynthetic protein]]

[[Category: ~~Torelli, A.T~~]]

[[Category: Diphthamide biosynthesis]]

[[Category: Radical sam enzyme]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6bxm is ON HOLD  until Paper Publication
+==Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM==
+<StructureSection load='6bxm' size='340' side='right' caption='[[6bxm]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6bxm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BXM FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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=6bxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bxm OCA], [http://pdbe.org/6bxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bxm RCSB], [http://www.ebi.ac.uk/pdbsum/6bxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bxm ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Diphthamide biosynthesis involves a carbon-carbon bond-forming reaction catalyzed by a radical S-adenosylmethionine (SAM) enzyme that cleaves a carbon-sulfur (C-S) bond in SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. Using rapid freezing, we have captured an organometallic intermediate with an iron-carbon (Fe-C) bond between ACP and the enzyme's [4Fe-4S] cluster. In the presence of the substrate protein, elongation factor 2, this intermediate converts to an organic radical, formed by addition of the ACP radical to a histidine side chain. Crystal structures of archaeal diphthamide biosynthetic radical SAM enzymes reveal that the carbon of the SAM C-S bond being cleaved is positioned near the unique cluster Fe, able to react with the cluster. Our results explain how selective C-S bond cleavage is achieved in this radical SAM enzyme.
-Authors: Fenwick, M.K., Torelli, A.T., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J.H., Hoffman, B.M., Lin, H., Ealick, S.E.
+Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.,Dong M, Kathiresan V, Fenwick MK, Torelli AT, Zhang Y, Caranto JD, Dzikovski B, Sharma A, Lancaster KM, Freed JH, Ealick SE, Hoffman BM, Lin H Science. 2018 Mar 16;359(6381):1247-1250. doi: 10.1126/science.aao6595. PMID:29590073<ref>PMID:29590073</ref>
-Description: Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Ealick, S.E]]
+<div class="pdbe-citations 6bxm" style="background-color:#fffaf0;"></div>
-[[Category: Lancaster, K.M]]
+== References ==
-[[Category: Carantoa, J.D]]
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Carantoa, J D]]
 [[Category: Dong, M]]
-[[Category: Zhang, Y]]
-[[Category: Freed, J.H]]
 [[Category: Dzikovski, B]]
+[[Category: Ealick, S E]]
+[[Category: Fenwick, M K]]
+[[Category: Freed, J H]]
+[[Category: Hoffman, B M]]
+[[Category: Kathiresan, V]]
+[[Category: Lancaster, K M]]
 [[Category: Lin, H]]
-[[Category: Hoffman, B.M]]
+[[Category: Torelli, A T]]
-[[Category: Kathiresan, V]]
+[[Category: Zhang, Y]]
-[[Category: Fenwick, M.K]]
+[[Category: Biosynthetic protein]]
-[[Category: Torelli, A.T]]
+[[Category: Diphthamide biosynthesis]]
+[[Category: Radical sam enzyme]]