Mononuclear structures enzymes

The first zinc enzyme to be discovered was carbonic anhydrase in 1940, followed by car-boxypeptidase A some 14 years later. They both represent the archetype of mono-zinc enzymes, with a central catalytically active Zn2+ atom bound to three protein ligands, and the fourth site occupied by a water molecule. Yet, despite the overall similarity of catalytic zinc sites with regard to their common tetrahedral [(XYZ)Zn2+-OH2] structure, these mononuclear zinc enzymes catalyse a wide variety of reactions, as pointed out above. The mechanism of action of the majority of zinc enzymes centres around the zinc-bound water molecule,... 

The class of mononuclear dioxygenases [30] can e.g. perform hydroperoxidation of lipids, the cleavage of catechol and dihydroxylation of aromatics. A prominent example is naphthalene dioxygenase, which was the first identified by its crystal structure. It contains iron and a Rieske (2Fe-2S) cluster and is commonly referred to as a Rieske-type dioxygenase [33]. The iron in this case is flanked by two histidines and one aspartic acid residue. Among the mononuclear iron enzymes, the 2-His-l-carboxylate is a common motif, which flanks one-side of the iron in a triangle and plays an important role in dioxygen activation [34] (Fig. 4.17). 

DMSO) reductase and biotin-S-oxidoreduc-tase, as well as the bacterial dissimilatory (or respiratory) nitrate reductases (Hille 1996) (Table 18.8). The mononuclear molybdenum enzymes possess a pterin cofactor and may be categorized based on the structure of their molybdenum center... 

R Hille. The mononuclear molybdenum enzymes. Chem Rev 96 2757-2816 1996. NA Turner, RC Bray, GP Diakun. Information from E.X.A.F.S. spectroscopy on the structures of different forms of molybdenum in xanthine oxidase and the catalytic mechanism of the enzyme. Biochem J 260 563, 1989. 

In this chapter, we will review computational studies of DMSOR, SO and XO. Our emphasis will be on the computational methods and what is needed to obtain reliable results. We will also compare the properties of Mo and W enzymes and discuss the active-site design of the three families of mononuclear Mo enzymes. A more general review of computational studies of Mo/W enzymes was published in 2011, a recent review considers the XO family, whereas structural and functional models of MoAV en mes have been reviewed several times recently. " ... 

Drennan and co-workers have identified the dioxygen binding site on iron in hydroxypropylphosphonic acid epoxidase (HppE), an unusual mononuclear iron enzyme that used dioxygen to catalyse the oxidative epoxida-tion of (S)-2-hydroxypropylphosphonic acid (715) to epoxide (716) and converted (i )-2-hydroxypropylphosphonic acid (717) to 2-oxo-propylphos-phonic acid (718) (Scheme 181). These structures illustrated how HppE was... 

There are hundreds of iron-containing enzymes. In general, the iron can exist as (a) a mononuclear site, in which it is coordinated by a tetrapyrrole structure (hemes) or strictly by amino acid residues that donate oxo, nitrogen, or sulfur ligands (b) a dinuclear site in which the irons are bridged by oxo, nitrogen, or sulfur coordination (c) a trinuclear site as in the 3Fe-4S clusters or (d) a tetranuclear site as in the [4Fe-4S] clusters. 

Figure 17.3 Anatomy of a redox enzyme representation of the X-ray crystallographic structure of Trametes versicolor laccase III (PDB file IKYA) [Bertrand et al., 2002]. The protein is represented in green lines and the Cu atoms are shown as gold spheres. Sugar moieties attached to the surface of the protein are shown in red. A molecule of 2,5-xyhdine that co-crystallized with the protein (shown in stick form in elemental colors) is thought to occupy the broad-specificity hydrophobic binding pocket where organic substrates ate oxidized by the enzyme. Electrons from substrate oxidation are passed to the mononuclear blue Cu center and then to the trinuclear Cu active site where O2 is reduced to H2O. (See color insert.)...

Nickel is found in thiolate/sulflde environment in the [NiFe]-hydrogenases and in CODH/ACS.33 In addition, either a mononuclear Ni-thiolate site or a dinuclear cysteine-S bridged structure are assumed plausible for the new class of Ni-containing superoxide dismutases, NiSOD (A).34 [NiFe]-hydrogenase catalyzes the two-electron redox chemistry of dihydrogen. Several crystal structures of [NiFe]-hydrogenases have demonstrated that the active site of the enzyme consists of a heterodinuclear Ni—Fe unit bound to thiolate sulfurs of cysteine residues with a Ni—Fe distance below 3 A (4) 35-39 This heterodinuclear active site has been the target of extensive model studies, which are summarized in Section 6.3.4.12.5. 

The zinc acetate complex of tris(3-/-butyl-5-methylpyrazol-l-yl)borate was prepared as a structural model for carbonic anhydrase and comparison with the enzyme active site structures confirmed that the complexes are excellent structural models.239 A mononuclear zinc hydroxide complex can also be formed with the tris(pyrazolyl) borate ligand system as a structural model for carbonic anhydrase.240... 

Synthesis of functional models of carbonic anhydrase has been attempted with the isolation of an initial mononuclear zinc hydroxide complex with the ligand hydrotris(3-t-butyl-5-methyl-pyrazolyl)borate. Vahrenkamp and co-workers demonstrate the functional as well as the structural analogy to the enzyme carbonic anhydrase. A reversible uptake of carbon dioxide was observed, although the unstable bicarbonate complex rapidly forms a dinuclear bridged complex. In addition, coordinated carbonate esters have been formed and hydrolyzed, and inhibition by small ions noted.462 A number of related complexes are discussed in the earlier Section 6.8.4. 

Zinc is a constituent of over 300 enzymes with much research into the coordination of zinc to the protein backbone, and how its chemistry is modulated by the donor set and environment.2 As well as the Lewis acid catalysis properties in enzymes, the structural role in zinc finger proteins has been a major area of research since the late 1990s. A number of reviews on zinc physiology, enzymology, and proteins in general have been published.978-981 There is extensive analysis available to classify the mononuclear sites in zinc proteins and identification of structural relationships of the extended environment.982,983... 

Hegg, E. L. and L. Que (1997). The 2-His-l-carboxylate facial triad-An emerging structural motif in mononuclear non-heme iron(II) enzymes. Eur. J. Biochem. 250(3) 625-629. 

One last class of mononuclear non-haem iron enzyme that we have not yet considered, consists of the microbial superoxide dismutases with Fe(III) at their active site. The crystal structure of the E. coli enzyme shows a coordination geometry reminiscent of protocatechuate 3,4-dioxygenase, with four endogenous protein ligands, three His and one Asp residue, and one bound water molecule (Carlioz et ah, 1988). 

Amino acid is one of the most important biological ligands. Researches on the coordination of metal-amino acid complexes will help us better understand the complicated behavior of the active site in a metal enzyme. Up to now many Ln-amino acid complexes [50] and 1 1 or 1 2 transition metal-amino acid complexes [51] with the structural motifs of mononuclear entity or chain have been synthesized. Recently, a series of polynuclear lanthanide clusters with amino acid as a ligand were reported (most of them display a Ln404-cubane structural motif) [52]. It is also well known that amino acids are useful ligands for the construction of polynuclear copper clusters [53-56], Several studies on polynuclear transition metal clusters with amino acids as ligands, such as [C03] [57,58], [Co2Pt2] [59], [Zn6] [60], and [Fe ] [61] were also reported. 

Figure 7. Traces of the a-carbon polypeptide backbone of domains 1 and 6 in the hCP structure. Domain 1 is shown (shaded) on the left hand side of the diagram this domain contributes four histidine residues (not shown) to the trinuclear cluster copper atoms are depicted as black spheres. Domain 6 is on the right hand side of the figure and also contributes four histidine residues to the cluster. The portion of the polypeptide chain colored black is that which is missing in the truncated enzyme. This polypeptide, residues 991 to 1046 inclusive, includes two histidine residues bound to the trinuclear copper center and three residues bound to the mononuclear copper in domain 6 these residues are depicted in black. The absence of the C-terminal polypeptide would also remove over 50% of the interdomain hydrogen-bond and iron-pair interactions observed in the intact enzyme.

Figure 13.21 Mononuclear non-haem iron enzymes from each of the five families in structures which are poised for attack by 02. (a) The extradiol-cleaving catechol dioxygenase, 2,3-dihydroxy-biphenyl 1,2-dioxygenase (b) the Rieske dioxygenase, naphthalene 1,2-dioxygenase (c) isopenicillin N-synthase (d) the ot-ketoglutarate dependent enzyme clavaminate synthase and (e) the pterin-dependent phenylalanine hydroxylase. (From Koehntop et al., 2005. With kind permission of Springer Science and Business Media.)...

Copper enzymes are involved in reactions with a large number of other, mostly inorganic substrates. In addition to its role in oxygen and superoxide activation described above, copper is also involved in enzymes that activate methane, nitrite and nitrous oxide. The structure of particulate methane mono-oxygenase from the methanotrophic bacteria Methylococcus capsulatus has been determined at a resolution of 2.8 A. It is a trimer with an a3P33 polypeptide arrangement. Two metal centres, modelled as mononuclear and dinuclear copper, are located in the soluble part of each P-subunit, which resembles CcOx subunit II. A third metal centre, occupied by Zn in the crystal, is located within the membrane. 

---