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. Author manuscript; available in PMC: 2012 Mar 11.
Published in final edited form as: J Mol Biol. 2010 Dec 9;406(5):713–729. doi: 10.1016/j.jmb.2010.12.005

Figure 2.

Figure 2

Classification of metalloendopeptidase structures and MMPs by sequence-order-independent surface similarity. A). Hierarchical tree of the binding pockets of 156 metalloendopeptidase enzymes based on their structural alignment in a sequence-order-independent fasion. Eight distinct clusters of binding pockets can be seen (shaded rectangles) and are labeled accordingly. From left to right: bontoxilysin #1, bontoxilysin #2, serratia-protease, astacin, thermolysin, pep-lys mepase, reprolysin, and MMP. The left most unshaded cluster consist of mostly other proteins or domains mislabeled as metzincins. B). A detailed view of the MMP clusters. These clusters are largely in agreement with the conventional classification of MMPs, with the MMP class labeled for each clade. MMP-3 formed two separate clusters (MMP-3A and MMP-3B). From left to right: MMP-3A, MMP-3B, MMP-12 & 13, MMP-11 & 7, MMP-9, MMP-8, and MMP-1