6c8v: Difference between revisions

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<StructureSection load='6c8v' size='340' side='right'caption='[[6c8v]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
<StructureSection load='6c8v' size='340' side='right'caption='[[6c8v]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6c8v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_extorquens"_bassalik_1913 "bacillus extorquens" bassalik 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C8V FirstGlance]. <br>
<table><tr><td colspan='2'>[[6c8v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylorubrum_extorquens Methylorubrum extorquens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C8V FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 3.2&#8491;</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=6c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c8v OCA], [http://pdbe.org/6c8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c8v RCSB], [http://www.ebi.ac.uk/pdbsum/6c8v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c8v ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</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'>[https://proteopedia.org/fgij/fg.htm?mol=6c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c8v OCA], [https://pdbe.org/6c8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c8v RCSB], [https://www.ebi.ac.uk/pdbsum/6c8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c8v ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/PQQE_METEA PQQE_METEA]
The Radical SAM (RS) enzyme PqqE catalyzes the first step in the biosynthesis of the bacterial cofactor pyrroloquinoline quinone, forming a new carbon-carbon bond between two side chains within the ribosomally synthesized peptide substrate PqqA. In addition to the active site RS 4Fe-4S cluster, PqqE is predicted to have two auxiliary Fe-S clusters, like the other members of the SPASM domain family. Here we identify these sites and examine their structure using a combination of X-ray crystallography and Mossbauer and electron paramagnetic resonance (EPR) spectroscopies. X-ray crystallography allows us to identify the ligands to each of the two auxiliary clusters at the C-terminal region of the protein. The auxiliary cluster nearest the RS site (AuxI) is in the form of a 2Fe-2S cluster ligated by four cysteines, an Fe-S center not seen previously in other SPASM domain proteins; this assignment is further supported by Mossbauer and EPR spectroscopies. The second, more remote cluster (AuxII) is a 4Fe-4S center that is ligated by three cysteine residues and one aspartate residue. In addition, we examined the roles these ligands play in catalysis by the RS and AuxII clusters using site-directed mutagenesis coupled with EPR spectroscopy. Lastly, we discuss the possible functional consequences that these unique AuxI and AuxII clusters may have in catalysis for PqqE and how these may extend to additional RS enzymes catalyzing the post-translational modification of ribosomally encoded peptides.
 
X-ray and EPR Characterization of the Auxiliary Fe-S Clusters in the Radical SAM Enzyme PqqE.,Barr I, Stich TA, Gizzi AS, Grove TL, Bonanno JB, Latham JA, Chung T, Wilmot CM, Britt RD, Almo SC, Klinman JP Biochemistry. 2018 Feb 6. doi: 10.1021/acs.biochem.7b01097. PMID:29405700<ref>PMID:29405700</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6c8v" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus extorquens bassalik 1913]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Almo, S C]]
[[Category: Methylorubrum extorquens]]
[[Category: Bonanno, J B]]
[[Category: Almo SC]]
[[Category: Gizzi, A S]]
[[Category: Bonanno JB]]
[[Category: Grove, T L]]
[[Category: Gizzi AS]]
[[Category: Oxidoreductase]]
[[Category: Grove TL]]
[[Category: Peptide modifying enzyme]]

Revision as of 14:27, 13 March 2024

X-ray structure of PqqE from Methylobacterium extorquens

6c8v, resolution 3.20Å

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