Zinc binding residues

The recruitment of zinc for a structural role, or to activate an enzyme, has been observed. The zinc ion induces the dimerization of human growth hormone (hGH), with two Zn ions associated per dimer of hGH. This is confirmed by replacement of possible zinc binding residues resulting in weakened binding of the zinc ion. Formation of a zinc-hGH dimeric complex may be important for storage of hGH in secretory granules.975 In a toxic role, anthrax lethal factor is one of the three components of the secreted toxin and is a zinc-dependent protease that cleaves a protein kinase and causes lysis of macrophages.976... 

Fig. 3.13. The 3D structure of neprilysin (enkephalinase, EC 3.4.24.11) obtained from ldmt.pdb [79]. This structure was determined for the enkephal-inase-phosphoramidon complex, but the inhibitor has been removed to unmask the catalytic center, a) Structure of the enzyme, with the Glu and the two His residues of the HEXXH zinc-binding motif shown in blue, b) Zoom on the catalytic center, revealing the spatial arrangement of the zinc-binding residues.

In addition, three enzymes involved in DNA replication, including DNA primases, prokaryotic DNA topoisomerase I and some hexameric DNA helicases, are also classic zinc-ribbon proteins. In bacteriophage DNA primases, mutations of the zinc-binding residues abrogate the synthesis of RNA primers for lagging strand DNA synthesis. Strikingly, each subunit of the mini-chromosomal maintenance (MCM) protein, a heterohexameric helicase that initiates DNA replication in S. cerevisiae, contains an independently folded zinc-ribbon domain that appears to stabilize the dodecameric structure (a dimer of hexamers) of this replication complex. ... 

Figure 7. The structure of thermolysin. Ribbon representation of the structure of thermolysin (silver, Brookhaven Databank [53] code 3TLN) shown with a bound inhibitor (green). The catalytic zinc atom (cyan) and structural calcium atoms (magenta) are shown. The active site is located between the N-terminal zinc protease domain and the alpha helical C-terminal domain. Zinc binding residues are in blue and the residue assisting catalysis is shown in red.

Figure 1.9 Examples of functionally important intrinsic metal atoms in proteins, (a) The di-iron center of the enzyme ribonucleotide reductase. Two iron atoms form a redox center that produces a free radical in a nearby tyrosine side chain. The iron atoms are bridged by a glutamic acid residue and a negatively charged oxygen atom called a p-oxo bridge. The coordination of the iron atoms is completed by histidine, aspartic acid, and glutamic acid side chains as well as water molecules, (b) The catalytically active zinc atom in the enzyme alcohol dehydrogenase. The zinc atom is coordinated to the protein by one histidine and two cysteine side chains. During catalysis zinc binds an alcohol molecule in a suitable position for hydride transfer to the coenzyme moiety, a nicotinamide, [(a) Adapted from P. Nordlund et al., Nature 345 593-598, 1990.)...

Figure 10.5 Comparison of the sequence-specific binding to DNA of six different zinc fingers. Residues in the N-terminus of the a helix in the finger regions are numbered 1 to 6. The residue immediately preceding the a helix is numbered -1. Amino acid residues and nucleotides that make sequence-specific contacts are colored. In spite of the structural similarities between the zinc fingers and their overall mode of binding, there is no simple rule that governs which bases the fingers contact.

His 118, Glu 146, His 128, His 142, Trpl, and His 14 as zinc binding ligands has been supported by a series of site-directed mutagenesis studies in which each of these residues was replaced with Ala each mutant bound only two zinc ions [35,64]. 

Independently, Ruan etal. (1990) demonstrated that unnatural metal-ligating residues may likewise be utilized toward the stabilization of short a helices by transition metal ions (including Zn " ")—these investigators reported that an 11-mer is converted from the random coil conformation to about 80% a helix by the addition of Cd at 4°C. These results suggest that the engineering of zinc-binding sites in small peptides or large proteins may be a powerful approach toward the stabilization of protein secondary structure. 

The engineering of zinc-binding sites in a-helical peptides, where metal binding stabilizes protein tertiary structure, has been reported by Handel and DeGrado (1990). In these experiments zinc-binding sites are incorporated into a dimeric helix-loop—helix peptide (H3 2) and a protein composed of four helices connected by three short loop sequences (H3 4). a model of one subunit of the H3 2 dimer is found in Fig. 47. In addition to metal complexation by two histidine residues at positions n and n+4 of one a helix, the metal is coordinated by a third histidine residue of an adjacent a helix. The composition of the zinc coordination polyhedron is like that of carbonic anhydrase (i.e., Hiss), and spectroscopic results suggest that all three histidine residues are involved in zinc complexation. This work sets an important foundation... 

The zinc binding element plays, above aU, a structuring role by ensuring that the recognition hehx is correctly oriented and stabUized. The zinc ion does not contact the DNA directly. In Zif268 the zinc motif participates directly in the DNA-binding via formation of a H-bond between the His residue of the zinc complex and the N7 of a G C base pair of the DNA. 

The function of zinc ions may be either catalytic or stractural. Enzymes with a co-catalytic center of two or even three zinc ions in close proximity are also known. In a new type of zinc-binding site, the protein interface, zinc ions are fixed at the interface of two proteins with the aid of amino acid residues. The ligand residues are usually His, Asp, Glu or Cys, which interact via nitrogen, oxygen or sulfur donors with the metal ion. In catalytic binding sites. His coordination dominates and an additional reactive water molecule is bound. 

The MMPs consist of one or more structural domains (Figure 1). The first domain, the propeptide domain, confers a self-inhibitory action on the full-length MMP. The second domain contains the active site residues and is referred to as the catalytic domain. The catalytic domain is characterized by the conserved zinc-binding sequence (HEXGHXXGXXHS), which also contains the glutamate residue that is essential for activity [17]. The MMPs are activated by cleavage of the prodomain. All MMPs contain these first two domains. Matrilysin, the simplest of the MMPs, is an example of a two-domain enzyme, where the active enzyme consists solely of the catalytic domain. 

---