Journal:JBIC:19

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

Maja Martic, Ida Noémi Jakab-Simon, Lærke Tvedebrink Haahr, Wilfred Raymond Hagen and Hans Erik Mølager Christensen^[1]

Molecular Tour
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 monomeric form [Figure (1) of the monomer, chain A] shows that the silver(I) ion is part of the cluster (clearly seen on the electron density map), as predicted from previous spectroscopic and electrochemical studies [Figure (2) of the cluster with electron density map around it]. The heterometal is coordinated to the three inorganic sulfides of the cluster and to the thiolate group of residue 14 [highlight and label residue Cys14 on Figure2; label also the other coord. residues, i.e. Cys11, Cys17 and Cys56 with a pale color], replacing the aboriginal Fe ion in the all-iron coordinated [Fe4S4] D14C variant (2Z8Q) [if possible, here it should be an animated figure (3) with the overall structures of the monomeric protein, showing the exchange between the Ag ion in this heterometallic cluster and the Fe ion coordinated to the same S-ligands in Pf Fd D14C [Fe₄S₄]-cluster (presented in http://proteopedia.org/w/Journal:JBIC:10)]and completing the incomplete cuboidal cluster present in the [Fe₃S₄] WT Pf Fd (PDB: 1sj1) and its D14C (PDB: 3pni) variant. Structure alignment of backbone atoms from the heterometallic [AgFe₃S₄] protein and the homometallic [Fe₄S₄] D14C variant (2z8q) shows very minor differences, 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. More significant difference can be seen in the superimposed Fe – S clusters [Figure (4) is the enlarged 3D image of the superimposed [AgFe₃S₄] (atom colors corresponding to yellow: S, orange: Fe, gray: Ag) and [Fe₄S₄] (purple) clusters] 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, because to the longer Ag – S bond lengths compared to Fe – S bonds. However, the S – Ag – S bond angles are still close to the expected 90° for a primitive cubic system.

Codes:

Blue: indicates approx. which words should be highlighted in the text for the link with the 3D images Black: description of the figure, in Italic the one we don’t know if they can do it or not.