7dgl: Difference between revisions
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The | ==The Ni-bound dimeric structure of K78H/G80A/H82A myoglobin== | ||
<StructureSection load='7dgl' size='340' side='right'caption='[[7dgl]], [[Resolution|resolution]] 1.91Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7dgl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DGL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DGL 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]] 1.91Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</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=7dgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dgl OCA], [https://pdbe.org/7dgl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dgl RCSB], [https://www.ebi.ac.uk/pdbsum/7dgl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dgl ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/MYG_HORSE MYG_HORSE] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The metal active site is precisely designed in metalloproteins. Here we applied 3D domain swapping, a phenomenon in which a partial protein structure is exchanged between molecules, to introduce metal sites in proteins. We designed multiple metal-binding sites specific to domain-swapped myoglobin (Mb) with His mutation. Stable dimeric Mbs with metal-binding sites were obtained by shifting the His position and introducing two Ala residues in the hinge region (K78H/G80A/H82A and K79H/G80A/H81A Mbs). The absorption and circular dichroism spectra of the monomer and dimer of K78H/G80A/H82A and K79H/G80A/H81A Mbs were similar to the corresponding spectra, respectively, of wild-type Mb. No negative peak due to dimer-to-monomer dissociation was observed below the denaturation temperature in the differential scanning calorimetry thermograms of K78H/G80A/H82A and K79H/G80A/H81A Mbs, whereas the dimer dissociates into monomers at 68 degrees C for wild-type Mb. These results show that the two mutants were stable in the dimer state. Metal ions bound to the metal-binding sites containing the introduced His in the domain-swapped Mb dimers. Co(2+)-bound and Ni(2+)-bound K78H/G80A/H82A Mb exhibited octahedral metal-coordination structures, where His78, His81, Glu85, and three H2O/OH(-) molecules coordinated to the metal ion. On the other hand, Co(2+)-bound and Zn(2+)-bound K79H/G80A/H81A Mb exhibited tetrahedral metal-coordination structures, where His79, His82, Asp141, and a H2O/OH(-) molecule coordinated to the metal ion. The Co(2+)-bound site exists deep inside the protein in the K79H/G80A/H81A Mb dimer, which may allow the unique tetrahedral coordination for the Co(2+) ion. These results show that we can utilize domain swapping to construct artificial metalloproteins. | |||
Rational design of metal-binding sites in domain-swapped myoglobin dimers.,Nagao S, Idomoto A, Shibata N, Higuchi Y, Hirota S J Inorg Biochem. 2021 Jan 28;217:111374. doi: 10.1016/j.jinorgbio.2021.111374. PMID:33578251<ref>PMID:33578251</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7dgl" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: Nagao | *[[Myoglobin 3D structures|Myoglobin 3D structures]] | ||
[[Category: | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Equus caballus]] | |||
[[Category: Large Structures]] | |||
[[Category: Higuchi Y]] | |||
[[Category: Hirota S]] | |||
[[Category: Idomoto A]] | |||
[[Category: Nagao S]] | |||
[[Category: Shibata N]] | |||
Latest revision as of 19:33, 29 November 2023
The Ni-bound dimeric structure of K78H/G80A/H82A myoglobinThe Ni-bound dimeric structure of K78H/G80A/H82A myoglobin
Structural highlights
FunctionMYG_HORSE Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles. Publication Abstract from PubMedThe metal active site is precisely designed in metalloproteins. Here we applied 3D domain swapping, a phenomenon in which a partial protein structure is exchanged between molecules, to introduce metal sites in proteins. We designed multiple metal-binding sites specific to domain-swapped myoglobin (Mb) with His mutation. Stable dimeric Mbs with metal-binding sites were obtained by shifting the His position and introducing two Ala residues in the hinge region (K78H/G80A/H82A and K79H/G80A/H81A Mbs). The absorption and circular dichroism spectra of the monomer and dimer of K78H/G80A/H82A and K79H/G80A/H81A Mbs were similar to the corresponding spectra, respectively, of wild-type Mb. No negative peak due to dimer-to-monomer dissociation was observed below the denaturation temperature in the differential scanning calorimetry thermograms of K78H/G80A/H82A and K79H/G80A/H81A Mbs, whereas the dimer dissociates into monomers at 68 degrees C for wild-type Mb. These results show that the two mutants were stable in the dimer state. Metal ions bound to the metal-binding sites containing the introduced His in the domain-swapped Mb dimers. Co(2+)-bound and Ni(2+)-bound K78H/G80A/H82A Mb exhibited octahedral metal-coordination structures, where His78, His81, Glu85, and three H2O/OH(-) molecules coordinated to the metal ion. On the other hand, Co(2+)-bound and Zn(2+)-bound K79H/G80A/H81A Mb exhibited tetrahedral metal-coordination structures, where His79, His82, Asp141, and a H2O/OH(-) molecule coordinated to the metal ion. The Co(2+)-bound site exists deep inside the protein in the K79H/G80A/H81A Mb dimer, which may allow the unique tetrahedral coordination for the Co(2+) ion. These results show that we can utilize domain swapping to construct artificial metalloproteins. Rational design of metal-binding sites in domain-swapped myoglobin dimers.,Nagao S, Idomoto A, Shibata N, Higuchi Y, Hirota S J Inorg Biochem. 2021 Jan 28;217:111374. doi: 10.1016/j.jinorgbio.2021.111374. PMID:33578251[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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