6bxl

From Proteopedia

(Difference between revisions)

Revision as of 08:52, 11 November 2020

Crystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S cluster and SAM

Structural highlights

6bxl is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Activity:	2-(3-amino-3-carboxypropyl)histidine synthase, with EC number 2.5.1.108
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DPH2_PYRHO] Catalyzes the first step of diphthamide biosynthesis, i.e. the transfer of the 3-amino-3-carboxypropyl group from S-adenosyl-L-methionine (SAM) to the C2 position of the imidazole ring of the target histidine residue in translation elongation factor 2 (EF-2).^[1]

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.

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^[2]

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

References

↑ Zhang Y, Zhu X, Torelli AT, Lee M, Dzikovski B, Koralewski RM, Wang E, Freed J, Krebs C, Ealick SE, Lin H. Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme. Nature. 2010 Jun 17;465(7300):891-6. PMID:20559380 doi:10.1038/nature09138
↑ 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. Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis. Science. 2018 Mar 16;359(6381):1247-1250. doi: 10.1126/science.aao6595. PMID:29590073 doi:http://dx.doi.org/10.1126/science.aao6595

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6bxl"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S cluster and SAM==
-<StructureSection load='6bxl' size='340' side='right' caption='[[6bxl]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='6bxl' size='340' side='right'caption='[[6bxl]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6bxl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BXL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6bxl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BXL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6BXL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-(3-amino-3-carboxypropyl)histidine_synthase 2-(3-amino-3-carboxypropyl)histidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.108 2.5.1.108] </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=6bxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bxl OCA], [http://pdbe.org/6bxl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bxl RCSB], [http://www.ebi.ac.uk/pdbsum/6bxl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bxl ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6bxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bxl OCA], [http://pdbe.org/6bxl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bxl RCSB], [http://www.ebi.ac.uk/pdbsum/6bxl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bxl ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Carantoa, J D]]
 [[Category: Dong, M]]

6bxl

From Proteopedia

Revision as of 08:52, 11 November 2020

Crystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S cluster and SAM

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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