Sandbox Reserved 468: Difference between revisions

Matrix Metalloproteinase-1 (MMP-1)is a collagenase made up of two monomers. Collagenases are enzymes that break down the bonds in collagen. MMP-1 in humans is encoded by the MMP1 gene. Interestingly, MMP-1 was actually the first vertebrate collagenase both purified to homogeneity as a protein, and cloned as a cDNA [1].

MMP-1 belongs to a family of enzymes known as Matrix metalloproteinases (MMPs). These enzymes are known as zinc-dependent endopeptidases because of the zinc ions involved in their catalytic sites. The MMPs belong to a larger family of proteins known as the metzincin superfamily. MMPs are capable of degrading all kinds of extracellular matrix proteins as well as a number of other bioactive molecules. They are known to be involved in the cleavage of cell surface receptors, the release of apoptotic ligands (such as the FAS ligand), and chemokine/cytokine in/activation. MMPs are also thought to play a major role on cell behaviors such as cell proliferation, migration (adhesion/dispersion), differentiation, angiogenesis, apoptosis,host defense, embryonic development, reproduction, and tissue remodeling. MMPs are also involved in disease processes, such as arthritis and metastasis [5].  

MMP's were first described in vertebrates in 1962 but have also been found in invertebrates and plants. They are distinguished from other endopeptidases by their dependence on metal ions as cofactors, their ability to degrade extracellular matrix, and their specific evolutionary DNA sequence. MMPs are typically secreted as inactive proproteins which are later activated when cleaved by another protease [2][3].

The structure of human MMP-1 was determined to have two monomeric structures (chains A and B). However, it is believed that this dimer is not physiologically relevant, as it was found that human MMP-1 is a monomer in solution. The structure of MMP-1, just like the other members of matrix metalloproteinases family, is formed by three different domains. The structure consists of a <scene name='Sandbox_Reserved_468/Catalytic_domain/3'>Catalytic Domain</scene>, a variable Linker Region and the <scene name='Sandbox_Reserved_468/Linker_region/1'>Hemopexin-like domain</scene>. The catalytic domain of one monomer contacts the hemopexin-like domain of the other monomer. These structures were determined by using X-ray crystallography and NMR [2][3].

The Catalytic Domains of all MMPs share very similar characteristics, having the same general shape and a diameter of ~40Å. The <scene name='Sandbox_Reserved_468/Catalytic_domain/3'>Catalytic Domain</scene> of MMP-1 is composed of five highly twisted β-strands, three α-helix and a total of eight loops, enclosing a total of five metal ions, three Ca2+ and two Zn2+, one of which with catalytic role [2]. The Catalytic Domain (CAT) of MMP-1 starts with the F100 as the first amino-acid of the N-terminal loop of the CAT domain. This is different from the first published x-ray structure of the CAT domain which showed the truncated form of this domain, where the first 7 amino-acids are not present [6].

In MMPs, the catalytic domain is followed by a stretch of 15–65 amino acid residues referred to as the linker or the hinge region. The length of this region varies between MMPs and does not have a well-determined structure. This region is typically rich in proline residues. Interestingly, the replacement of those with alanine drastically reduced the collagenolytic activity of certain MMPs, which may indicate that the presence of the correct linker structure is important for collagenolysis [4].

The <scene name='Sandbox_Reserved_468/Linker_region/1'>Hemopexin-like domain</scene> starts with Cys259 and forms a complete circle by joining to Cys447 using a disulfide bond that connects and gives this domain the characteristic four-bladed β-propeller structure. β-Propeller structures provide a large flat surface that is thought to be involved in protein-protein interactions. This determines substrate specificity and is the site for interaction with TIMP’s (tissue inhibitor of metalloproteinases). Each blade starts near the periphery with a <scene name='Sandbox_Reserved_468/Calcium_channel/2'>Calcium channel</scene>, in which the Asp residues (Asp266, Asp359 and Asp408) coordinate the central calcium ion through their carbonyl oxygen atom. Glu310 provides the fourth coordination thus completing the acidic patch at the entrance of the central, solvent-accessible channel. The side-chains of these residues form salt bridges to the neighbouring β-strands holding the entrance of the central channel together. Three water molecules are found trapped in the center of this channel but these molecules are not involved in this process. Two of the water molecules are at positions corresponding to the sodium and chloride ion in the proMMP-1 structure. The water molecule corresponding to the sodium ion is at hydrogen-bonding distances to the carbonyl oxygen atom of Ile268, Ala312, Ala361 and Val410 [3].

In the first mechanism, Browner M.F. and colleagues proposed the base-catalysis mechanism, carried out by the conserved glutamate residue and the Zn2+ ion [5][6].  

In the third mechanism, the Manzetti-mechanism, Manzetti Sergio and colleagues provided evidence that a coordination between water and zinc during catalysis was unlikely, and suggested a third mechanism wherein a histidine participates in catalysis by allowing the Zn2+ ion to assume a quasi-penta coordinated state, via its dissociation from it. In this state, the Zn2+ ion is coordinated with the two oxygen atoms from the catalytic glutamic acid, the substrate's carbonyl oxygen atom, and the two histidine residues, and can polarize the glutamic acid's oxygen atom, proximate the scissile bond, and induce it to act as reversible electron donor. This forms an oxyanion transition state. At this stage, a water molecule acts on the dissociated scissile bond and completes the hydrolyzation of the substrate [5][6].