8pvm
From Proteopedia
(Difference between revisions)
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<table><tr><td colspan='2'>[[8pvm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PVM FirstGlance]. <br> | <table><tr><td colspan='2'>[[8pvm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PVM FirstGlance]. <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]] 1.38Å</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]] 1.38Å</td></tr> | ||
| - | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=402:DICARBONYL[BIS(CYANIDE-KAPPAC)]-MU-(IMINODIMETHANETHIOLATATO-1KAPPAS 2KAPPAS)-MU-(OXOMETHYLIDENE)DIIRON(2+)'>402</scene>, <scene name='pdbligand=74C: | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=402:DICARBONYL[BIS(CYANIDE-KAPPAC)]-MU-(IMINODIMETHANETHIOLATATO-1KAPPAS 2KAPPAS)-MU-(OXOMETHYLIDENE)DIIRON(2+)'>402</scene>, <scene name='pdbligand=74C:$l^{3}-carbane'>74C</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FOR:FORMYL+GROUP'>FOR</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=8pvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pvm OCA], [https://pdbe.org/8pvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pvm RCSB], [https://www.ebi.ac.uk/pdbsum/8pvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pvm ProSAT]</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=8pvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pvm OCA], [https://pdbe.org/8pvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pvm RCSB], [https://www.ebi.ac.uk/pdbsum/8pvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pvm ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/PHF1_CLOPA PHF1_CLOPA] | [https://www.uniprot.org/uniprot/PHF1_CLOPA PHF1_CLOPA] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | [FeFe]-hydrogenases are efficient H(2) converting biocatalysts that are inhibited by formaldehyde (HCHO). The molecular mechanism of this inhibition has so far not been experimentally solved. Here, we obtained high-resolution crystal structures of the HCHO-treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum, showing HCHO reacts with the secondary amine base of the catalytic cofactor and the cysteine C299 of the proton transfer pathway which both are very important for catalytic turnover. Kinetic assays via protein film electrochemistry show the CpI variant C299D is significantly less inhibited by HCHO, corroborating the structural results. By combining our data from protein crystallography, site-directed mutagenesis and protein film electrochemistry, a reaction mechanism involving the cofactor's amine base, the thiol group of C299 and HCHO can be deduced. In addition to the specific case of [FeFe]-hydrogenases, our study provides additional insights into the reactions between HCHO and protein molecules. | ||
| + | |||
| + | Insights into the Molecular Mechanism of Formaldehyde Inhibition of [FeFe]-Hydrogenases.,Duan J, Veliju A, Lampret O, Liu L, Yadav S, Apfel UP, Armstrong FA, Hemschemeier A, Hofmann E J Am Chem Soc. 2023 Dec 6;145(48):26068-26074. doi: 10.1021/jacs.3c07800. Epub , 2023 Nov 20. PMID:37983562<ref>PMID:37983562</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 8pvm" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
formaldehyde-inhibited [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299D
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