Rubredoxin active site

Figure 17 X-Ray structure of the active site of the rubredoxin from Clostridium pasteurianum...

The most ordered surface waters are those around charged side chains or in surface crevices. Occasionally those crevices can be very deep, such as the active site pocket in carbonic anhydrase, which extends about 15 A in from the surface, with a network of water molecules (Lindskog f al., 1971). The well-ordered waters at the protein surface are usually part of an approximately tetrahedral (but sometimes planar trigonal) network of hydrogen bonds to the protein and to other waters. An example from rubredoxin is shown in Fig. 60. 

Blue copper proteins, 36 323, 377-378, see also Azurin Plastocyanin active site protonations, 36 396-398 charge, 36 398-401 classification, 36 378-379 comparison with rubredoxin, 36 404 coordinated amino acid spacing, 36 399 cucumber basic protein, 36 390 electron transfer routes, 36 403-404 electron transport, 36 378 EXAFS studies, 36 390-391 functional role, 36 382-383 occurrence, 36 379-382 properties, 36 380 pseudoazurin, 36 389-390 reduction potentials, 36 393-396 self-exchange rate constants, 36 401-403 UV-VIS spectra, 36 391-393 Blue species... 

Active Site Structure of Rubredoxin There are several non-heme iron-sulphur proteins that are involved in electron transfer. They contain distinct iron-sulphur clusters composed of iron atoms, sulphydryl groups from cysteine residues and inorganic or labile sulphur atoms or sulphide ions. The labile sulphur is readily removed by washing with acid. The cysteine moieties are incorporated within the protein chain and are thus not labile. The simplest type of cluster is bacteria rubredoxin, (Cys-S)4 Fe (often abbreviated FelSO where S stands for inorganic sulphur), and contains only non labile sulphur. It is a bacterial protein of uncertain function with a molecular weight of 6000. The single iron atom is at the centre of a tetrahedron of four cysteine ligands (Fig.). 

The function of the electron-mediating proteins which contain a single redox active site (e.g., rubredoxin, azurins, flavodoxins, plasto-cyanins) is mainly related to the first aspect. Still, the pronounced specificity encountered in their function in biological energy conversion processes indicates that their redox center, often a transition metal ion, is embedded in an evolutionarily optimized polypeptide envelope. The... 

This structural unit occurs in the one-iron proteins, rubredoxins (Rd), obtained from bacteria, in which the active site is [Fe(S-Cys)4], where S-Cys is a cysteinyl residue of the protein chain [structure (38) of Figure 6]. These proteins have molecular weights typically about 6000. The variety, of physical investigations (magnetic susceptibility,210 ESR,211 Mossbauer,212 optical absorption,207,213 MCD214) have demonstrated that the two redox states, Rdox and Rered, coupled by one-electron... 

Rubredoxin is a small protein which has one Fe ion (molecular weight 6000), as is schematically illustrated in Fig. 3. Jensen s group has revealed fairly precise structural features of the active site of Clostridium pasteurianum and Desulfovibrio vulgaris rubredoxins (10, 11). The simple model complex [Fe(S2-o-xyl)2], 2 has been synthesized and analyzed crystallographically by Holm s group (12). Geometry of the FeS4 core of the oxidized rubredoxin seems to be almost identical to that... 

Fig. 4. The crystallographic structure within 5 A of the active site of Desulfovibrio vulgaris rubredoxin (6, 11). Heavy lines represent peptide backbone chains.

The difference in redox potential and in thermal stability between native rubredoxin and the simple model complexes has been suggested to be brought about by the different protein environments (18). This is as yet unproved, however. The amino acid sequences of many rubredoxins isolated from various sources have been determined, as shown in Fig. 5 (19). A sequence around the Fe active site, Cys-X-Y-Cys, is an invariant fragment and primarily determines the chemical and physical properties. For example, C. pasteurianum rubredoxin has such sequences, Cys6-Thr-Val-Cys9 and Cys39-Pro-Leu-Cys42. 

Fe-S Bond Lengths and Fe-S-C Angles of the Active Site of Clostridium pasteurianum Rubredoxin with 1.2-A Refinement X-Ray Analysis... 

The active site of rubredoxin (Rd), (I) (Figure 1), consists of one Fe ion tetrahedraUy coordinated by four cysteine thiolate ligands. The iron core serves as the electron-transport site of rubredoxin proteins. 

Negative-ion gas-phase photoelectron spectroscopy has also recently been nsed to evalnate the reorganization energies of tetrahedrally coordinated Fe+ anions that serve as models for the active sites of mononuclear iron sulfur proteins such as rubredoxin that cycles between high spin Fe+ and high spin... 

The iron sulfide complex (10) resembles the active sites of oxidized rubredoxins nonheme iron-sulfur proteins. The complex catalyzes the reductions of aromatic nitro compounds to A -arylhydroxylamines by thiol (equation 11 ). The method offers a facile, high yield approach to N-arylhydroxylamines. For example, p-dinitrobenzene was reduced to p-nitrophenylhydroxylamine in 92% yield. 

UV-VIS Spectra Reduction Potentials Active-Site Protonations Charge on Proteins Self-Exchange Rate Constants Electron Transfer Routes Comparison with Rubredoxin Summary References... 

A new member of the family of nonheme diiron enzymes recently discovered is called rubrerythrin. This metalloprotein is formally classified as an oxidoreductase (rubredoxin oxygen oxidoreductase). The diiron(III,III) active site structure is displayed in Figure 2(f). This biomolecule possesses two histidines coordinated to one iron and one histidine coordinated to the second iron. A carboxylate bridges the two irons and there are carboxylate ligands also coordinated to each iron. The purpose of this enzyme in the strict anaerobe is to safely reduce oxygen to water. 

Nature has also replaced a catalytic metal to create a new function. For example, rubredoxin oxidase contains an iron in the active site and catalyzes electron transfer. The amino acid sequence of ji-lactamase is related to that of rubredoxin oxidase, indicating that they evolved from a common ancestor. ji-Lactamase contains a zinc ion in the active site and detoxifies p-lactam antibiotics by hydrolysis of the P-lactam ring. Evolutionary pressure from the use of P-lactam antibiotics hkely caused rubredoxin oxidase to bind a different metal to create a new function [28]. 

Fig. 4 Reaction pathways for superoxide dismutases and superoxide reductases. Shown in black are the two possible pathways leading to oxidation of the active site by superoxide, producing peroxide this half of the catalytic cycle is common to SOR and SOD. Shown in gray is the re-reductive path specific to SOD, and which in SOR is replaced by a single-electron transfer from the specialized redox protein, rubredoxin. M may be Fe (n = 2, in SOR, or in SOD), Ni, Mn (n = 2, in SOD), or Cu (n = 1, in SOD)...

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