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Structure of the C-terminally truncated human ProMMP9, a gelatin-binding matrix metalloproteinase
Patricia A Elkins1, Yen Sen Ho, Ward W Smith
1GlaxoSmithKline, King of Prussia, Pennsylvania 19406, USA. patricia_a_elkins@gsk.com
Abstract:
The X-ray crystal structure of the proform of human matrix metalloproteinase MMP9 has been solved to 2.5 A resolution. The construct includes the prodomain, the catalytic domain and three FnII (fibronectin type II) domains. The prodomain is inserted into the active-site cleft, blocking access to the catalytic zinc. Comparison with the crystal structure of the most closely related MMP, MMP2, indicates that the conformations of residues in the active-site cleft and in the cysteine-switch peptide of the prodomain are highly conserved and that design of MMP9-specific inhibitors will be challenging. In common with MMP2, the MMP9 S1' inhibitor-binding pocket is large compared with that of other MMPs. One small point of difference in the S1' binding pockets of MMP9 and MMP2 may provide an opportunity to explore the design of specific inhibitors. The side chain of Arg424 in MMP9 is angled slightly away from the S1' pocket when compared with the corresponding residue in MMP2, Thr424. The secondary structure of the FnII domains is conserved between the two closely related MMPs, although the second FnII domain makes no contact with the catalytic domain in MMP9, while the same domain in MMP2 has a substantial area of interaction with the catalytic domain.
Insights
The crystal structure of human matrix metalloproteinase MMP9 reveals its prodomain blocks the active site. Designing MMP9-specific inhibitors is challenging due to conserved active-site features shared with MMP2.
Area of Science:
- Biochemistry
- Structural Biology
- Enzymology
Background:
- Matrix metalloproteinases (MMPs) are crucial enzymes involved in extracellular matrix remodeling.
- Human matrix metalloproteinase-9 (MMP9) plays significant roles in physiological and pathological processes.
- Understanding the structural basis of MMP9 is essential for developing targeted therapeutics.
Purpose of the Study:
- To determine the X-ray crystal structure of the proform of human MMP9.
- To compare the structural features of MMP9 with its close homolog, MMP2.
- To identify potential targets for the design of MMP9-specific inhibitors.
Main Methods:
- X-ray crystallography was used to solve the structure of the MMP9 proform to 2.5 A resolution.
- The structure included the prodomain, catalytic domain, and three fibronectin type II (FnII) domains.
- Comparative structural analysis was performed with the known structure of MMP2.
Main Results:
- The prodomain of MMP9 occupies the active-site cleft, inhibiting catalytic activity.
- Key active-site residues and the cysteine-switch peptide show high conservation between MMP9 and MMP2.
- The S1' inhibitor-binding pocket in MMP9 is large, similar to MMP2, but a subtle difference at residue 424 (Arg in MMP9, Thr in MMP2) may offer a design opportunity.
- The second FnII domain in MMP9 does not interact with the catalytic domain, unlike in MMP2.
Conclusions:
- The structural similarity between MMP9 and MMP2 presents a challenge for developing specific inhibitors.
- A minor difference in the S1' pocket, specifically the orientation of Arg424, could be exploited for inhibitor design.
- The distinct interaction of the second FnII domain in MMP9 compared to MMP2 warrants further investigation.