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| | <StructureSection load='5t2k' size='340' side='right'caption='[[5t2k]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='5t2k' size='340' side='right'caption='[[5t2k]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5t2k]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_stearothermophilus_10 Bacillus stearothermophilus 10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T2K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5T2K FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5t2k]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus_10 Geobacillus stearothermophilus 10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T2K FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=76R:[3,3,3,3-(3,8,13,17-TETRAMETHYLPORPHYRIN-2,7,12,18-TETRAYL-KAPPA~4~N~21~,N~22~,N~23~,N~24~)TETRA(PROPANOATO)(2-)]MANGANESE'>76R</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]] 1.8Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GT50_08830 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272567 Bacillus stearothermophilus 10])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=76R:[3,3,3,3-(3,8,13,17-TETRAMETHYLPORPHYRIN-2,7,12,18-TETRAYL-KAPPA~4~N~21~,N~22~,N~23~,N~24~)TETRA(PROPANOATO)(2-)]MANGANESE'>76R</scene></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=5t2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t2k OCA], [http://pdbe.org/5t2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t2k RCSB], [http://www.ebi.ac.uk/pdbsum/5t2k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t2k 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=5t2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t2k OCA], [https://pdbe.org/5t2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t2k RCSB], [https://www.ebi.ac.uk/pdbsum/5t2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t2k ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0A0K2H9D8_GEOSE A0A0K2H9D8_GEOSE]] May function as heme-dependent peroxidase.[HAMAP-Rule:MF_01442][SAAS:SAAS00370076] | + | [https://www.uniprot.org/uniprot/CHDC_GEOS3 CHDC_GEOS3] Involved in coproporphyrin-dependent heme b biosynthesis (PubMed:27936663). Catalyzes the decarboxylation of Fe-coproporphyrin III (coproheme) to heme b (protoheme IX), the last step of the pathway (PubMed:27936663). The reaction occurs in a stepwise manner with a three-propionate harderoheme intermediate (PubMed:27936663).<ref>PMID:27936663</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus stearothermophilus 10]] | + | [[Category: Geobacillus stearothermophilus 10]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Celis, A I]] | + | [[Category: Celis AI]] |
| - | [[Category: Dubois, J L]] | + | [[Category: Dubois JL]] |
| - | [[Category: Gauss, G H]] | + | [[Category: Gauss GH]] |
| - | [[Category: Peters, J W]] | + | [[Category: Peters JW]] |
| - | [[Category: Coproporphyrin iii]]
| + | |
| - | [[Category: Decarboxylation]]
| + | |
| - | [[Category: Hemq]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
CHDC_GEOS3 Involved in coproporphyrin-dependent heme b biosynthesis (PubMed:27936663). Catalyzes the decarboxylation of Fe-coproporphyrin III (coproheme) to heme b (protoheme IX), the last step of the pathway (PubMed:27936663). The reaction occurs in a stepwise manner with a three-propionate harderoheme intermediate (PubMed:27936663).[1]
Publication Abstract from PubMed
Coproheme decarboxylase catalyzes two sequential oxidative decarboxylations with H2O2 as the oxidant, coproheme III as substrate and cofactor, and heme b as the product. Each reaction breaks a C-C bond and results in net loss of hydride, via steps that are not clear. Solution and solid-state structural characterization of the protein in complex with a substrate analog revealed a highly unconventional H2O2-activating distal environment with the reactive propionic acids (2 and 4) on the opposite side of the porphyrin plane. This suggested that, in contrast to direct C-H bond cleavage catalyzed by a high-valent iron intermediate, the coproheme oxidations must occur through mediating amino acid residues. A tyrosine that hydrogen bonds to propionate 2 in a position analogous to the substrate in ascorbate peroxidase is essential for both decarboxylations, while a lysine that salt bridges to propionate 4 is required solely for the second. A mechanism is proposed in which propionate 2 relays an oxidizing equivalent from a coproheme compound I intermediate to the reactive deprotonated tyro-sine, forming Tyrblacksquare, square, filled. This residue then abstracts a net hydrogen atom (Hblacksquare, square, filled) from propionate 2, followed by migration of the unpaired propionyl electron to the coproheme iron to yield the ferric harderoheme and CO2 products. A similar pathway is proposed for decarboxylation of propionate 4, but with a lysine residue as an essential proton shuttle. The proposed reaction suggests an extended relay of heme-mediated e-/H+ transfers and a novel route for the conversion of carboxylic acids to alkenes.
A Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ).,Celis AI, Gauss GH, Streit BR, Shisler K, Moraski GC, Rodgers KR, Lukat-Rodgers GS, Peters JW, DuBois JL J Am Chem Soc. 2016 Dec 12. PMID:27936663[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Celis AI, Gauss GH, Streit BR, Shisler K, Moraski GC, Rodgers KR, Lukat-Rodgers GS, Peters JW, DuBois JL. A Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ). J Am Chem Soc. 2016 Dec 12. PMID:27936663 doi:http://dx.doi.org/10.1021/jacs.6b11324
- ↑ Celis AI, Gauss GH, Streit BR, Shisler K, Moraski GC, Rodgers KR, Lukat-Rodgers GS, Peters JW, DuBois JL. A Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ). J Am Chem Soc. 2016 Dec 12. PMID:27936663 doi:http://dx.doi.org/10.1021/jacs.6b11324
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