6m2g: Difference between revisions

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== Structural highlights ==

<table><tr><td colspan='2'>~~[[6m2g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M2G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M2G FirstGlance]. <br>

<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M2G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M2G 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]] 2.8Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F0X:cobalt-sirohydrochlorin'>F0X</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=6m2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m2g OCA], [https://pdbe.org/6m2g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m2g RCSB], [https://www.ebi.ac.uk/pdbsum/6m2g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m2g ProSAT]</span></td></tr>

</table>

~~== Function ==~~

[https://www.uniprot.org/uniprot/CFBA_METJA CFBA_METJA] Catalyzes the insertion of Co(2+) into sirohydrochlorin as part of the anaerobic pathway to cobalamin biosynthesis. Involved in the biosynthesis of the unique nickel-containing tetrapyrrole coenzyme F430, the prosthetic group of methyl-coenzyme M reductase (MCR), which plays a key role in methanogenesis and anaerobic methane oxidation. Catalyzes the insertion of Ni(2+) into sirohydrochlorin to yield Ni-sirohydrochlorin.

~~<div style="background-color:#fffaf0;">~~

~~== Publication Abstract from PubMed ==~~

The class II chelatase CfbA catalyzes Ni(2+) insertion into sirohydrochlorin (SHC) to yield the product nickel-sirohydrochlorin (Ni-SHC) during coenzyme F430 biosynthesis. CfbA is an important ancestor of all the class II chelatase family of enzymes, including SirB and CbiK/CbiX, functioning not only as a nickel-chelatase, but also as a cobalt-chelatase in vitro. Thus, CfbA is a key enzyme in terms of diversity and evolution of the chelatases catalyzing formation of metal-SHC-type of cofactors. However, the reaction mechanism of CfbA with Ni(2+) and Co(2+) remains elusive. To understand the structural basis of the underlying mechanisms and evolutionary aspects of the class II chelatases, X-ray crystal structures of Methanocaldococcus jannaschii wild-type CfbA with various ligands, including SHC, Ni(2+), Ni-SHC, and Co(2+) were determined. Further, X-ray crystallographic snapshot analysis captured a unique Ni(2+)-SHC-His intermediate complex and Co-SHC-bound CfbA, which resulted from a more rapid chelatase reaction for Co(2+) than Ni(2+). Meanwhile, an in vitro activity assay confirmed the different reaction rates for Ni(2+) and Co(2+) by CfbA. Based on these structural and functional analyses, the following substrate-SHC-assisted Ni(2+) insertion catalytic mechanism was proposed: Ni(2+) insertion to SHC is promoted by the support of an acetate side chain of SHC.

The nickel-sirohydrochlorin formation mechanism of the ancestral class II chelatase CfbA in coenzyme F430 biosynthesis.,Fujishiro T, Ogawa S Chem Sci. 2021 Jan 4;12(6):2172-2180. doi: 10.1039/d0sc05439a. PMID:34163982<ref>PMID:34163982</ref>

~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~

~~</div>~~

~~<div class="pdbe-citations 6m2g" style="background-color:#fffaf0;"></div>~~

~~== References ==~~

~~<references/>~~

__TOC__

</StructureSection>

[[Category: Large Structures]]

~~[[Category: Methanocaldococcus jannaschii DSM 2661]]~~

[[Category: Fujishiro T]]

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@@ Line 3: / Line 3: @@
 <StructureSection load='6m2g' size='340' side='right'caption='[[6m2g]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6m2g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M2G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M2G FirstGlance]. <br>
+<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M2G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M2G 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]] 2.8&#8491;</td></tr>
 <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F0X:cobalt-sirohydrochlorin'>F0X</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=6m2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m2g OCA], [https://pdbe.org/6m2g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m2g RCSB], [https://www.ebi.ac.uk/pdbsum/6m2g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m2g ProSAT]</span></td></tr>
 </table>
-== Function ==
-[https://www.uniprot.org/uniprot/CFBA_METJA CFBA_METJA] Catalyzes the insertion of Co(2+) into sirohydrochlorin as part of the anaerobic pathway to cobalamin biosynthesis. Involved in the biosynthesis of the unique nickel-containing tetrapyrrole coenzyme F430, the prosthetic group of methyl-coenzyme M reductase (MCR), which plays a key role in methanogenesis and anaerobic methane oxidation. Catalyzes the insertion of Ni(2+) into sirohydrochlorin to yield Ni-sirohydrochlorin.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The class II chelatase CfbA catalyzes Ni(2+) insertion into sirohydrochlorin (SHC) to yield the product nickel-sirohydrochlorin (Ni-SHC) during coenzyme F430 biosynthesis. CfbA is an important ancestor of all the class II chelatase family of enzymes, including SirB and CbiK/CbiX, functioning not only as a nickel-chelatase, but also as a cobalt-chelatase in vitro. Thus, CfbA is a key enzyme in terms of diversity and evolution of the chelatases catalyzing formation of metal-SHC-type of cofactors. However, the reaction mechanism of CfbA with Ni(2+) and Co(2+) remains elusive. To understand the structural basis of the underlying mechanisms and evolutionary aspects of the class II chelatases, X-ray crystal structures of Methanocaldococcus jannaschii wild-type CfbA with various ligands, including SHC, Ni(2+), Ni-SHC, and Co(2+) were determined. Further, X-ray crystallographic snapshot analysis captured a unique Ni(2+)-SHC-His intermediate complex and Co-SHC-bound CfbA, which resulted from a more rapid chelatase reaction for Co(2+) than Ni(2+). Meanwhile, an in vitro activity assay confirmed the different reaction rates for Ni(2+) and Co(2+) by CfbA. Based on these structural and functional analyses, the following substrate-SHC-assisted Ni(2+) insertion catalytic mechanism was proposed: Ni(2+) insertion to SHC is promoted by the support of an acetate side chain of SHC.
-The nickel-sirohydrochlorin formation mechanism of the ancestral class II chelatase CfbA in coenzyme F430 biosynthesis.,Fujishiro T, Ogawa S Chem Sci. 2021 Jan 4;12(6):2172-2180. doi: 10.1039/d0sc05439a. PMID:34163982<ref>PMID:34163982</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6m2g" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Methanocaldococcus jannaschii DSM 2661]]
 [[Category: Fujishiro T]]