Are there enzymes found in nature or the man made world that can help break down metals?
There are bacteria, which can assist the proces of rust.

"Some sulfate-reducing bacteria produce hydrogen sulfide, which can cause sulfide stress cracking. Acidithiobacillus bacteria produce sulfuric acid; Acidothiobacillus thiooxidans frequently damages sewer pipes. Ferrobacillus ferrooxidans directly oxidizes iron to iron oxides and iron hydroxides; the rusticles forming on RMS Titanic wreck are caused by bacterial activity. Other bacteria produce various acids, both organic and mineral, or ammonia." (http://en.wikipedia.org/wiki/Microbial_corrosion)

As you see, many of these active ingredients, like hydrogen sulfide, sulfuric acid, other acids or ammonia are not enzymes per se, although they are produced by enzymatic processes in bacteria.

Closer to your specification is Ferrobacillus ferrooxidans (synonyms: Acidithiobacillus ferrooxidans, Thiobacillus ferrooxidans, Ferrobacillus sulfooxidans), which directly acts on iron by enzymes associated with the cell membrane: 

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Figure 1. Schematic representation of ferrous iron oxidation by the Gram-negative autotrophic acidophile, At. ferrooxidans. Controlled influx of protons is used to generate ATP via the membrane-bound ATP synthetase complex (ATPase). Iron oxidation is mediated by a cytochrome located on the outer membrane and electrons transferred via periplasmic cytochromes and rusticyanin either to a terminal oxidase (“downhill pathway,” indicated in brown text and by **) where they are used to reduce oxygen, or used to reduce NAD+ (“uphill pathway,” indicated red text and by *) in a reaction also driven by the proton motive force across the inner membrane (Bonnefoy and Holmes, 2011). Source: Johnson et al. 2012.