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MMP8

MMP-8, also called, Neutrophil collagenase or Collagenase 2, is a zinc-dependent and calcium-dependent enzyme. It belongs to the matrix metalloproteinase (MMP) family which is involved in the breakdown of extracellular matrix in embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. The gene coding this family is localized on the chromosome 11 of Homo sapiens .

spinqualitylabelsall models MMP-8 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Classification EC 3.4.24.34 This classification means that this enzyme: - is a hydrolase: it hydrolyzes covalent bonds - is an endopeptidase: cleaves peptide bond - cleaves interstitial collagens in the triple helical domain (at a site about three-fourths away from the N-terminus) The difference between this classification and EC 3.4.24.7 is that this enzyme cleaves type III collagen more slowly than type I. To see [1] [2] [3] [4] pockets [5] Structure and domains MMP8 is composed of several domains: a propeptide, a catalytic domain, a hinge region, and a C-terminal hemopexinlike domain. Thanks to X-ray crystallography, the structure of the catalytic domain of MMP8 has been solved with 1,7 Å resolution (2OY4). This domain consists of three alpha helixes and five beta sheets. Pocket interaction Ca2+ CA pocket interaction The active site of the enzyme is composed by two Gly residues (169 and 171) next to two Asp residues (137 and 173). This enzyme binds 3 CA ions per subunit. maintain a Zn2+ atom coordinated with three water molecules. One of them is as well bound to the Glu residue thanks to a hydrogen bond. The second Zn2+ atom is not involved in the active site. At first, the Gly 206 residue of the substrate binds the active site thanks to the Zn2+ atom. When it binds it takes the place of unstable water molecules and establishes stabilizing interactions with the active site thanks to its C terminal part. Then, the Ala 182 residue of the enzyme makes a hydrogen bond with the NH group of the substrate: this allows the substrate to enter the cavity of the catalytic site. The rest of the protein is stabilized by 4 hydrogen bonds with the amino acid located in the cavity. Zn2+ ZN pocket interaction The active site of the enzyme is composed by one Asp residue (149) next to three His residues (147, 162 and 175). This enzyme binds 2ZN ions per subunit. maintain a Zn2+ atom coordinated with three water molecules. One of them is as well bound to the Glu residue thanks to a hydrogen bond. The second Zn2+ atom is not involved in the active site. At first, the Gly 206 residue of the substrate binds the active site thanks to the Zn2+ atom. When it binds it takes the place of unstable water molecules and establishes stabilizing interactions with the active site thanks to its C terminal part. Then, the Ala 182 residue of the enzyme makes a hydrogen bond with the NH group of the substrate: this allows the substrate to enter the cavity of the catalytic site. The rest of the protein is stabilized by 4 hydrogen bonds with the amino acid located in the cavity. The conserved cysteine present in the cysteine-switch motif (89-96) binds the catalytic zinc ion, thus inhibiting the enzyme. The dissociation of the cysteine from the zinc ion upon the activation-peptide release activates the enzyme. Catalytic domain It seems to have 163 residues involved in the catalytic domain: Met80-Gly242. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC394940/?page=1). The catalytic zinc ion is situated at the bottom of the active-site. The other zinc ion and the two calcium ions are packed against the top of the beta sheet and presumably function to stabilize the catalytic domain. The polypeptide folding and in particular the zinc environment of the collagenase catalytic domain bear a close ressemblance to the astacins and the snake venom metalloproteinases. The catalytic domain alone has proteolytic activity against other protein substrates and synthetic substrates. S1' pocket Homopexin domain The hemopexin domain has two conserved cysteines that are disulfide bonded. Mutation of those cysteines to alanines or reduction and alkylation destroys collagenolytic activity (K. Suzuki and H.Nagase, unpublished results). Mechanism To express collagenolytic activity, they have to retain both the catalytic and hemopexin domains. It is not clear how the hemopexin domain help to cleave triple-helical collagens because the isolated hemopexin domains of MMP-8 does not bind to collagen. The binding of collagenases to collagen must partially unwind triple helix to allow cleavage of the individual alpha chains. Since heat-denatured collagens (gelatins) are poorer substrates at 37°C , interaction of collagenase to interstitial collagen must induce conformational change in alpha chain of collagen that fits the substrate binding site of the catalytic domain, but the molecular basis of this mechanism is not known. In this model the peptide lies antiparallel to the edge strand IV by forming a number of hydrogen bonds. The N-terminal Pro at P3 (the third residue on the left of the scissile bond) interacts with the hydrophobic cleft formed by side chains of His162, Ser151, and Phe164, whereas Leu at P2 (the second residue on the right of the scissile bond) interacts with a shallow groove lined by His201, Ala206 and His207. The dominant interactions between the peptide and the enzyme are made by the phenyl side chain of the inhibitor and the large hydrophobic S1' pocket (located to the right of the catalytic zinc) formed by side chains of His197, Val194, Tyr219, and the main chain segment of Pro217-Asn-Tyr219. The side chain of P2� Ala points away from the enzyme and the C-terminal, P3� Gly is located crossover segments Gly158-Leu160 and Pro217-Tyr219. Function Like all the MMPs, MMP8 is secreted as inactive proproteins and then activated after a cleavage by extracellular proteinases. Indeed, it can't be activated without removal of the activation peptide. cleave the helical collagen molecule at a single Gly-Ile/Leu bond in each alpha-chain of the molecule. The cleavage generates fragments that spontaneously lose their helical conformation, denature to gelatin, and become soluble. The gelatin is then susceptible to attack by gelatinases and other proteases metalloendopeptidase activity = mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. Disease Overexpression of MMP8, or inadequate control by TIMPs, can be associated with a lot of pathological conditions: psoriasis, sclerosis, osteoarthritis, rheumatoid arthritis, osteoporosis, Alzheimer's disease, tumor growh and metastasis. Structural highlights This is a sample scene created with SAT to color by Group, and another to make a transparent representation of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

References

RESSOURCE : Image:2oy4 mm1.pdb ( la structure du monomère )