6fxq
From Proteopedia
(Difference between revisions)
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<StructureSection load='6fxq' size='340' side='right'caption='[[6fxq]], [[Resolution|resolution]] 1.69Å' scene=''> | <StructureSection load='6fxq' size='340' side='right'caption='[[6fxq]], [[Resolution|resolution]] 1.69Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6fxq]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FXQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FXQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6fxq]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Lismo Lismo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FXQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FXQ FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FEC:1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC+ACID+FERROUS+COMPLEX'>FEC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=VOV:harderoheme+(III)'>VOV</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FEC:1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC+ACID+FERROUS+COMPLEX'>FEC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=VOV:harderoheme+(III)'>VOV</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lmo2113 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=169963 LISMO])</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=6fxq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fxq OCA], [http://pdbe.org/6fxq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fxq RCSB], [http://www.ebi.ac.uk/pdbsum/6fxq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fxq ProSAT]</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=6fxq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fxq OCA], [http://pdbe.org/6fxq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fxq RCSB], [http://www.ebi.ac.uk/pdbsum/6fxq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fxq ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[http://www.uniprot.org/uniprot/Y2113_LISMO Y2113_LISMO]] May function as heme-dependent peroxidase. | [[http://www.uniprot.org/uniprot/Y2113_LISMO Y2113_LISMO]] May function as heme-dependent peroxidase. | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Coproheme decarboxylase (ChdC) catalyzes the last step in the heme biosynthesis pathway of monoderm bacteria with coproheme acting both as redox cofactor and substrate. Hydrogen peroxide mediates the stepwise decarboxylation of propionates 2 and 4 of coproheme. Here we present the crystal structures of coproheme-loaded ChdC from Listeria monocytogenes (LmChdC) and the three-propionate intermediate, for which the propionate at position 2 (p2) has been converted to a vinyl group and is rotated by 90 degrees compared to the coproheme complex structure. Single, double, and triple mutants of LmChdC, in which H-bonding interactions to propionates 2, 4, 6, and 7 were eliminated, allowed us to obtain the assignment of the coproheme propionates by resonance Raman spectroscopy and to follow the H2O2-mediated conversion of coproheme to heme b. Substitution of H2O2 by chlorite allowed us to monitor compound I formation in the inactive Y147H variant which lacks the catalytically essential Y147. This residue was demonstrated to be oxidized during turnover by using the spin-trap 2-methyl-2-nitrosopropane. Based on these findings and the data derived from molecular dynamics simulations of cofactor structures in distinct poses, we propose a reaction mechanism for the stepwise decarboxylation of coproheme that includes a 90 degrees rotation of the intermediate three-propionate redox cofactor. | ||
| + | |||
| + | Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Heme b.,Milazzo L, Gabler T, Puhringer D, Jandova Z, Maresch D, Michlits H, Pfanzagl V, Djinovic-Carugo K, Oostenbrink C, Furtmuller PG, Obinger C, Smulevich G, Hofbauer S ACS Catal. 2019 Aug 2;9(8):6766-6782. doi: 10.1021/acscatal.9b00963. Epub 2019, Jun 18. PMID:31423350<ref>PMID:31423350</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6fxq" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Lismo]] | ||
[[Category: Hofbauer, S]] | [[Category: Hofbauer, S]] | ||
[[Category: Mlynek, G]] | [[Category: Mlynek, G]] | ||
Current revision
Structure of coproheme decarboxylase from Listeria monocytogenes during turnover
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