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| | <StructureSection load='5zt7' size='340' side='right'caption='[[5zt7]], [[Resolution|resolution]] 2.94Å' scene=''> | | <StructureSection load='5zt7' size='340' side='right'caption='[[5zt7]], [[Resolution|resolution]] 2.94Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5zt7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZT7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZT7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5zt7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZT7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZT7 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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]] 2.94Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sirB, ylnE, BSU15620 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sirohydrochlorin_ferrochelatase Sirohydrochlorin ferrochelatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.99.1.4 4.99.1.4] </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=5zt7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zt7 OCA], [https://pdbe.org/5zt7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zt7 RCSB], [https://www.ebi.ac.uk/pdbsum/5zt7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zt7 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=5zt7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zt7 OCA], [http://pdbe.org/5zt7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zt7 RCSB], [http://www.ebi.ac.uk/pdbsum/5zt7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zt7 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SIRB_BACSU SIRB_BACSU]] Chelates iron to the siroheme precursor. | + | [https://www.uniprot.org/uniprot/SIRB_BACSU SIRB_BACSU] Chelates iron to the siroheme precursor. |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | The crystal structure of Bacillus subtilis SirB, which catalyses the insertion of Fe2+ into the substrate sirohydrochlorin (SHC) in siroheme biosynthesis, is reported herein as the last of the structures of class II chelatases. The structure of SirB with Co2+ showed that the active site of SirB is located at the N-terminal domain with metal-binding amino acid residues His10, Glu43, and His76, which was also predicted for CbiX, but is distinct from the C-terminal active sites of CbiK and HemH. The biosynthetic model reactions using SirB, Co2+ and uroporphyrin I or protoporphyrin IX as a SHC analogue revealed that SirB showed chelatase activity for uroporphyrin I, but not for protoporphyrin IX. Simulations of tetrapyrroles docking to SirB provided an insight into its tetrapyrrole substrate recognition: SHC and uroporphyrin I were suitably bound beside the Co2+ ion-binding site at the active site cavity; protoporphyrin IX was also docked to the active site but its orientation was different from those of the other two tetrapyrroles. Summarizing the present data, it was proposed that the key structural features for substrate recognition of SirB could be the hydrophobic area at the active site as well as the substituents of the tetrapyrroles.
| + | |
| - | | + | |
| - | Structure of sirohydrochlorin ferrochelatase SirB: the last of the structures of the class II chelatase family.,Fujishiro T, Shimada Y, Nakamura R, Ooi M Dalton Trans. 2019 Feb 19. doi: 10.1039/c8dt04727h. PMID:30778451<ref>PMID:30778451</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 5zt7" style="background-color:#fffaf0;"></div>
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| | | | |
| | ==See Also== | | ==See Also== |
| | *[[Ferrochelatase 3D structures|Ferrochelatase 3D structures]] | | *[[Ferrochelatase 3D structures|Ferrochelatase 3D structures]] |
| - | == References == | |
| - | <references/> | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacsu]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Sirohydrochlorin ferrochelatase]]
| + | [[Category: Fujishiro T]] |
| - | [[Category: Fujishiro, T]] | + | |
| - | [[Category: Biosynthetic protein]]
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| - | [[Category: Chelatase]]
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