NH---S hydrogen bonds in Peptococcus aerogenes ferredoxin, Clostridium pasteurianum rubredoxin, and Chromatium high potential iron protein.

Abstract

Results from refinement of the crystal structures of P. aerogenes ferredoxin and C pasteurianum rubredoxin determined by x-ray diffraction show that there are 15-18 NHOS bonds in the former and six in the latter with lengths in the range 3.1-3.9 A. Earlier tritium exchange experiments are consistent with the presence of these hydrogen onds in the ferredoxin structure and show that more peptide hydrogen atoms are available for exchange in apoferredoxin than in intact ferredoxin. Four types of NH-S bonds are observed and two of these are geometrically similar to the two.types of 310 NH-O bonds. The existence of more NH-S bonds in ferredoxin than in high potential iron protein suggests why the -2 form of the Fe4S4 cluster is preferred in ferredoxin over the -1 form found in high potential iron protein. From comparison of Cys-X-Y-Cys sequences in rubredoxin, terredoxin, and high potential iron protein we suggest that two Cys-X-Y-Cys-Z sequences, where Z may have conformation angles similar to glycine, are required to make a oneiron cluster, no more than one Cys-X-Y-Cys-Z-Gly sequence is required to form a Fe2S2 ferredoxin, and a Cys-X-Y-Cys-Gly sequence where Y has a conformation such that the cysteines bond to different iron atoms is necessary to form the tetrameric cluster.The properties of iron-sulfur proteins raise an intriguing question: How does the protein structure contribute to the various observed forms of iron-sulfur centers? Iron-sulfur proteins include: (i) rubredoxin (Rb) with one Fe, no inorganic sulfur, and four cysteines; (ii) plant-type ferredoxins with two irons, two inorganic sulfur atoms, and at least four cysteines; and (iii) bacterial-type ferredoxin with one or more tetrameric clusters having four iron atoms, four inorganic sulfur atoms, and four cysteinyl sulfur atoms (1). The latter clusters are found both in Peptococcus aerogenes ferredoxin (Fd) (2) and in high potential iron protein (HiPIP) (3), a bacterial protein with unknown function which is reduced approximately +300 mV, in contrast to ferredoxin, which is reduced at the very low potential of about -400 mV. According to the three-state hypothesis (4), three oxidation states are accessible to the tetrameric cluster, one pair of which is preferred in HiPIP, another pair, of lower potential, in Fd. It has been demonstrated that the cluster in HiPIP can be "superreduced" in the presence of the denaturant dimethyl sulfoxide to the lowest state accessible to Fd (5), while the cluster in ferredoxin can be "superoxidized" in the presence of K3Fe(CN)6 (6). Studies with model compounds for tetrameric clusters have indicated that the -2/-3 reduction step analogous to reduction of ferredoxin operates at a much more negative potential than is observed for the proteins (7). Thus the protein portion of the iron-sulfur proteins has at least two functions that are important for cluster formation and activity: It provides an environment which favors one form of iron-sulfur center over another (i.e., 1 Fe, 2 Fe-2 S, 4 Fe-4 S) and, in the case o...

The coordination chemistry of the structural zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations

“…Similar hydrogen bonds have been observed in several other proteins containing a metal bound to sulphur atoms, e.g. ferredoxins (Adman et al, 1975).…”

Reactivity of the Two Essential Cysteine Residues of the Periplasmic Mercuric Ion-binding Protein, MerP

“…In reduced MerP, the amide of M12 appears to be close enough to hydrogen bond with, and stabilize the thiolate of MerP. In the set of 20 NMR structures of reduced MerP, the S-amideN Met12 and S-amideH Met12 average distances are 3.24 and 2.61 Å, respectively, within the limits of 3.25-3.55 and 2.3-2.6 Å, respectively, expected for S-N Hbonds (45,46). Unlike in DsbA, where His-32 appears to help stabilize the thiolate anion at C30 (38,44), there are no charged residues in the vicinity of Cys-17 in MerP.…”

Hydrogen Bonding with Sulfur

“…This compares closely to other non-TMT compounds, which feature a similar range of distances: 3.36 Å in methyl dithiocarbazate and 3.0-3.5 Å in the active centers of ferredoxins. 20 …”