MMP-3の触媒ドメインはTIMP(英語版)(tissue inhibitor of metalloproteinase)によって阻害される。TIMPのN末端領域は、MMP-3の活性部位の溝にペプチド基質のように結合する。TIMPのCys1残基は触媒亜鉛とキレートを形成し、触媒グルタミン酸残基(Glu202)のカルボン酸酸素の1つと水素結合を形成する。これらの相互作用によって酵素の機能に必要不可欠な、亜鉛に結合した水分子が追い出される。TIMPによる水分子の喪失と活性部位の遮断によって、酵素反応は不可能となる[21]。
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