Journal:JBIC:19

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=== Heterometallic [AgFe₃S₄] ferredoxin variants – synthesis, characterization and the first crystal structure of an engineered heterometallic iron-sulfur protein ===

=== Heterometallic [AgFe₃S₄] ferredoxin variants – synthesis, characterization and the first crystal structure of an engineered heterometallic iron-sulfur protein ===

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<b>Molecular Tour</b><br>

<b>Molecular Tour</b><br>

The crystal structure of the ''Pyrococcus furiosus'' (Pf) ferredoxin (Fd) D14C variant with the novel [AgFe₃S₄] heterometallic cluster was determined to 1.95 Å resolution (PBD entry [[4dhv]]), being the first reported structure of an engineered heterometallic iron-sulfur protein.

The crystal structure of the ''Pyrococcus furiosus'' (Pf) ferredoxin (Fd) D14C variant with the novel [AgFe₃S₄] heterometallic cluster was determined to 1.95 Å resolution (PBD entry [[4dhv]]), being the first reported structure of an engineered heterometallic iron-sulfur protein.

The crystal structure of the <scene name='Journal:JBIC:19/Cv/4'>monomeric form</scene> shows that the <scene name='Journal:JBIC:19/Cv/6'>silver (I) ion is part of the cluster</scene> (clearly seen on the electron density map), as predicted from previous spectroscopic and electrochemical studies. The heterometal is coordinated to the <scene name='Journal:JBIC:19/Cv/5'>three inorganic sulfides of the cluster</scene> and to the <scene name='Journal:JBIC:19/Cv/7'>thiolate group of residue 14</scene> (residues <scene name='Journal:JBIC:19/Cv/8'>Cys11, Cys17 and Cys56</scene> are coordinated with Fe ions of heterometal), <scene name='Journal:JBIC:19/Cv/9'>replacing the aboriginal Fe ion in the all-iron coordinated</scene> [Fe₄S₄] D14C variant ([[2z8q]], <span style="color:cyan;background-color:black;font-weight:bold;">heterometallic [AgFe₃S₄] protein is in cyan</span> and <span style="color:lime;background-color:black;font-weight:bold;">homometallic [Fe₄S₄] is in green</span>) and completing the incomplete cuboidal cluster present in the [Fe₃S₄] WT Pf Fd (PDB: [[1sj1]]) and its D14C (PDB: [[3pni]]) variant (for more details see also [http://proteopedia.org/w/Journal:JBIC:10 "Crystal structures of the all cysteinyl coordinated D14C variant of ''Pyrococcus furiosus'' ferredoxin: (4Fe-4S) <-> (3Fe-4S) cluster conversion"]). Structure alignment of backbone atoms from the heterometallic [AgFe₃S₄] protein and the homometallic [Fe₄S₄] D14C variant ([[2z8q]]) shows <scene name='Journal:JBIC:19/Cv/10'>very minor differences</scene>, i.e. the root mean square deviation (RMSD) is 0.4 – 0.7 Å, observed due to the alternate conformation of the main chain atoms, flexible loops and small changes at the N- and C-termini (<span style="color:cyan;background-color:black;font-weight:bold;">heterometallic [AgFe₃S₄] protein is in cyan</span> and <span style="color:lime;background-color:black;font-weight:bold;">homometallic [Fe₄S₄] is in green</span>). <scene name='Journal:JBIC:19/Cv/14'>More significant difference</scene> can be seen in the superimposed Fe–S clusters (atom colors corresponding to <span style="color:yellow;background-color:black;font-weight:bold;">yellow: S</span>, <span style="color:orange;background-color:black;font-weight:bold;">orange: Fe</span>, <span style="color:gray;background-color:black;font-weight:bold;">gray: Ag</span>) from these two variants, which is due to the presence of the second row transition metal ion (Ag) coordinated to the four S-ligands, i.e. the presence of Ag results in a distorted geometry of the cluster compared to the all-iron arrangement, <scene name='Journal:JBIC:19/Cv/12'>because to the longer</scene> Ag – S bond lengths compared to Fe – S bonds. However, the S – Ag – S <scene name='Journal:JBIC:19/Cv/13'>bond angles</scene> are still close to the expected 90° for a primitive cubic system.

The crystal structure of the <scene name='Journal:JBIC:19/Cv/4'>monomeric form</scene> shows that the <scene name='Journal:JBIC:19/Cv/6'>silver (I) ion is part of the cluster</scene> (clearly seen on the electron density map), as predicted from previous spectroscopic and electrochemical studies. The heterometal is coordinated to the <scene name='Journal:JBIC:19/Cv/5'>three inorganic sulfides of the cluster</scene> and to the <scene name='Journal:JBIC:19/Cv/7'>thiolate group of residue 14</scene> (residues <scene name='Journal:JBIC:19/Cv/8'>Cys11, Cys17 and Cys56</scene> are coordinated with Fe ions of heterometal), <scene name='Journal:JBIC:19/Cv/9'>replacing the aboriginal Fe ion in the all-iron coordinated</scene> [Fe₄S₄] D14C variant ([[2z8q]], <span style="color:cyan;background-color:black;font-weight:bold;">heterometallic [AgFe₃S₄] protein is in cyan</span> and <span style="color:lime;background-color:black;font-weight:bold;">homometallic [Fe₄S₄] is in green</span>) and completing the incomplete cuboidal cluster present in the [Fe₃S₄] WT Pf Fd (PDB: [[1sj1]]) and its D14C (PDB: [[3pni]]) variant (for more details see also [http://proteopedia.org/w/Journal:JBIC:10 "Crystal structures of the all cysteinyl coordinated D14C variant of ''Pyrococcus furiosus'' ferredoxin: (4Fe-4S) <-> (3Fe-4S) cluster conversion"]). Structure alignment of backbone atoms from the heterometallic [AgFe₃S₄] protein and the homometallic [Fe₄S₄] D14C variant ([[2z8q]]) shows <scene name='Journal:JBIC:19/Cv/10'>very minor differences</scene>, i.e. the root mean square deviation (RMSD) is 0.4 – 0.7 Å, observed due to the alternate conformation of the main chain atoms, flexible loops and small changes at the N- and C-termini (<span style="color:cyan;background-color:black;font-weight:bold;">heterometallic [AgFe₃S₄] protein is in cyan</span> and <span style="color:lime;background-color:black;font-weight:bold;">homometallic [Fe₄S₄] is in green</span>). <scene name='Journal:JBIC:19/Cv/14'>More significant difference</scene> can be seen in the superimposed Fe–S clusters (atom colors corresponding to <span style="color:yellow;background-color:black;font-weight:bold;">yellow: S</span>, <span style="color:orange;background-color:black;font-weight:bold;">orange: Fe</span>, <span style="color:gray;background-color:black;font-weight:bold;">gray: Ag</span>) from these two variants, which is due to the presence of the second row transition metal ion (Ag) coordinated to the four S-ligands, i.e. the presence of Ag results in a distorted geometry of the cluster compared to the all-iron arrangement, <scene name='Journal:JBIC:19/Cv/12'>because to the longer</scene> Ag – S bond lengths compared to Fe – S bonds. However, the S – Ag – S <scene name='Journal:JBIC:19/Cv/13'>bond angles</scene> are still close to the expected 90° for a primitive cubic system.

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