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==Structure of coproheme decarboxylase from Corynebacterium dipththeriae W183Y mutant in complex with coproheme== | ==Structure of coproheme decarboxylase from Corynebacterium dipththeriae W183Y mutant in complex with coproheme== | ||
<StructureSection load='7q4f' size='340' side='right'caption='[[7q4f]]' scene=''> | <StructureSection load='7q4f' size='340' side='right'caption='[[7q4f]], [[Resolution|resolution]] 2.15Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Q4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Q4F FirstGlance]. <br> | <table><tr><td colspan='2'>[[7q4f]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Q4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Q4F FirstGlance]. <br> | ||
</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=7q4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q4f OCA], [https://pdbe.org/7q4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q4f RCSB], [https://www.ebi.ac.uk/pdbsum/7q4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q4f ProSAT]</span></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]] 2.15Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FEC:1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC+ACID+FERROUS+COMPLEX'>FEC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=7q4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q4f OCA], [https://pdbe.org/7q4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q4f RCSB], [https://www.ebi.ac.uk/pdbsum/7q4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q4f ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q6NGV6_CORDI Q6NGV6_CORDI] Involved in coproporphyrin-dependent heme b biosynthesis. Catalyzes the decarboxylation of Fe-coproporphyrin III (coproheme) to heme b (protoheme IX), the last step of the pathway. The reaction occurs in a stepwise manner with a three-propionate intermediate.[HAMAP-Rule:MF_02244] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The oxidative decarboxylation of coproheme to form heme b by coproheme decarboxylase is a stereospecific two-step reaction. In the first step, the propionate at position two (p2) is cleaved off the pyrrole ring A to form a vinyl group at this position. Subsequently, the propionate at position four (p4) on pyrrole ring B is cleaved off and heme b is formed. In this study, we attempted to engineer coproheme decarboxylase from Corynebacterium diphtheriae to alter the stereospecificity of this reaction. By introducing a tyrosine residue in proximity to the propionate at position 4, we were able to create a new radical center in the active site. However, the artificial Tyr183(*) radical could not be shown to catalyze any decarboxylation. | |||
Initial Steps to Engineer Coproheme Decarboxylase to Obtain Stereospecific Monovinyl, Monopropionyl Deuterohemes.,Michlits H, Valente N, Mlynek G, Hofbauer S Front Bioeng Biotechnol. 2022 Jan 24;9:807678. doi: 10.3389/fbioe.2021.807678., eCollection 2021. PMID:35141216<ref>PMID:35141216</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7q4f" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Corynebacterium diphtheriae]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Hofbauer S]] | [[Category: Hofbauer S]] | ||
Latest revision as of 16:13, 1 February 2024
Structure of coproheme decarboxylase from Corynebacterium dipththeriae W183Y mutant in complex with coprohemeStructure of coproheme decarboxylase from Corynebacterium dipththeriae W183Y mutant in complex with coproheme
Structural highlights
FunctionQ6NGV6_CORDI Involved in coproporphyrin-dependent heme b biosynthesis. Catalyzes the decarboxylation of Fe-coproporphyrin III (coproheme) to heme b (protoheme IX), the last step of the pathway. The reaction occurs in a stepwise manner with a three-propionate intermediate.[HAMAP-Rule:MF_02244] Publication Abstract from PubMedThe oxidative decarboxylation of coproheme to form heme b by coproheme decarboxylase is a stereospecific two-step reaction. In the first step, the propionate at position two (p2) is cleaved off the pyrrole ring A to form a vinyl group at this position. Subsequently, the propionate at position four (p4) on pyrrole ring B is cleaved off and heme b is formed. In this study, we attempted to engineer coproheme decarboxylase from Corynebacterium diphtheriae to alter the stereospecificity of this reaction. By introducing a tyrosine residue in proximity to the propionate at position 4, we were able to create a new radical center in the active site. However, the artificial Tyr183(*) radical could not be shown to catalyze any decarboxylation. Initial Steps to Engineer Coproheme Decarboxylase to Obtain Stereospecific Monovinyl, Monopropionyl Deuterohemes.,Michlits H, Valente N, Mlynek G, Hofbauer S Front Bioeng Biotechnol. 2022 Jan 24;9:807678. doi: 10.3389/fbioe.2021.807678., eCollection 2021. PMID:35141216[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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