Currently a total of 23 enzymes out of 29 MMPs have been identified in humans. Five MMPs are shorter isoforms of full-length enzymes, and one is annotated as MMP-like1 protein. Additionally, several plant and nonvertebrate MMPs have been found and characterized.
All MMP family members share a similar multidomain structure. The general structural pattern consists of a prodomain, a catalytic domain, a hinge region, and a hemo-pexin domain. The prodomain comprises a signal peptide [of about 20 amino acids (aa)] and a propeptide region, of about 80 aa. The signal peptide is cleaved off the molecule during its transport through the endoplasmic reticulum for cell release. The propeptide contains two specific regions, which as based on their biochemical properties, mechanistically account for the activation of the zymogen (i.e., latent form) to the active MMP. These two regions consist of a protease-sensitive sequence located in the second out of three helices and a unique, cysteine-switch motif PRCGXPD, within the peptide tail.
The catalytic domain (of about 170aa) consists of five b-sheet and three a-helix structures linked by a connecting loop. Three calcium ions and one structural zinc atom strengthen and stabilize the structure. The active site with its characteristic metal-binding motif HEXGHXXGXXH is located near the C-terminus, a highly conserved (56% to 64%) portion of the protein. The second zinc atom, also known as the active zinc, is coordinated by three histidines present within this motif. The substrate binding region is located adjacent to the active site. Unlike the active site, the binding pocket reveals a high level of sequence variability among the different MMP classes, and thus accounts for the specificity of substrate recognition by the MMPs.
The hemopexin-like domain consists of four hemopexin-like repeats (containing about 210 aa) and occupies the C-terminal part of the molecule. Each repeat has a four-bladed b-propeller fold, with a single stabilizing disulfide bond between blades I and IV. Because these domains are also found in many other proteins, for instance in integrins, it is thought that they can also be involved in protein-protein interactions. The hemopexin domain connects to the catalytic domain via a proline-rich polypeptide hinge region of
10 to 70aa. The hemopexin-like domains are determinants of substrate specificity of each enzyme The function of the hinge region is not fully understood.
Although all MMP family members have a similar overall structural motif, their molecular weight ranges from 28,000 to 92,000 da and suggests the existence of different levels and patterns of glycosylation, as well as some structural diversity. Whereas some enzymes lack certain domains, others have additional inserts that modulate but not drastically alter their functions. For instance, MMP-7 and MMP-26 lack the hemopexin domain, whereas MMP-2 and MMP-9 have an insert of three fibronectin type II domains in the vicinity of the catalytic site. NMR studies have indicated that the inserts consist of two antiparallel b-sheets, connected with a short a-helix. and are stabilized by two disulfide bonds. Domains 2 and 3 are thought to be structurally flexible, which can facilitate simultaneous interactions with multiple sites in the ECM.
Several members of the MMP family exhibit additional structural features that allow classifying them into a separate subgroup of membrane-type MMPs (MT-MMPs). Within their polypeptide linker that connects the prodomain with the catalytic domain, there is a sequence R-X-R/K-R, which seems to be essential for specific post-translational processing of these proteinases. Also, their C-terminal region has a 70 to 100aa hydrophobic polypeptide tail that inserts in the cell membrane, terminating with a short cytoplasmic tail. These enzymes are anchored in a cell membrane. So far, six membrane-type proteases have been characterized .
Each MMP exhibits a unique set of structural and functional characteristics. For instance, MMP-23 lacks the cys-teine switch motif and the hemopexin domain. Instead, it has a unique cysteine and proline-rich region, the IL-1 type
11 receptor-like domain, and a furin-susceptible region. MMP-23 is activated in the Golgi-like MT-MMP, but it does not have a transmembrane domain. It is released in active form, but it may associate to the cell membrane via the N-terminal part of the propeptide.
MMPs can be grouped according to different common properties, varying from primary sequence homologies, substrate specificity, or site of action. One such approach is based on grouping by DNA homology using the resources of the human genome project database, or as based on the search for proteins with homologous catalytic domain of MMPs. Relevant amino acid sequences were detected after analyses of alignments that revealed 29 different proteins stemming out from the same ancestor. Based on this approach, MMPs could be ordered into five subfamilies: nonfurin-regulated MMPs, gelatinases, transmembrane MMPs, GPI-anchored, and others. A similar clustering, with minor differences, was obtained when catalytic domain or hemopexin sequences were compared .
Based on the differences in substrate specificity, MMPs can be classified into six subgroups: collagenases, gelatinases, stromyelisins, matrilysins, membrane-type MMPs, and others . Based on the site of action, there are two groups of enzymes: secreted into the extracellular matrix and transmembrane proteins. Table I summarizes groups of MMPs.
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