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Substrate hydrolysis by matrix metalloproteinase-9.

S J Kridel1, E Chen, L P Kotra

  • 1Program On Cell Adhesion and the Cancer Research Center, Burnham Institute, La Jolla, California 92037, USA.

The Journal of Biological Chemistry
|March 30, 2001
PubMed
Summary
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Matrix metalloproteinase-9 (MMP-9) exhibits unique substrate preferences, particularly for arginine at P(2) and P(1) positions. This specificity helps differentiate its function from other MMPs, revealing potential new physiological substrates.

Area of Science:

  • Biochemistry
  • Enzymology
  • Proteomics

Background:

  • Matrix metalloproteinases (MMPs) share similar catalytic cleft architectures, questioning substrate specificity.
  • Understanding MMP substrate recognition is crucial for deciphering their diverse biological roles.

Purpose of the Study:

  • To define the substrate recognition profile of matrix metalloproteinase-9 (MMP-9) using an unbiased approach.
  • To identify unique sequence motifs and subsites critical for MMP-9 substrate selectivity.

Main Methods:

  • Employed an unbiased phage display strategy to identify MMP-9 substrates.
  • Analyzed substrate sequences to determine consensus recognition motifs and subsite preferences.
  • Queried protein databases using identified MMP-9 motifs to find potential physiological substrates.

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Main Results:

  • Identified three distinct substrate groups binding to different subsites within the MMP-9 catalytic pocket.
  • Determined a prevalent motif Pro-X-X-Hy-(Ser/Thr) (P3 to P2'), similar to collagen cleavage sites.
  • MMP-9 demonstrated selectivity over MMP-7 and MMP-13, with unique preferences for Arg at P(2) and P(1), and Ser/Thr at P(2').

Conclusions:

  • Substrate selectivity for MMP-9 is determined by key interactions beyond P(3) and P(1') subsites.
  • The identified consensus MMP-9 recognition motif revealed a limited list of putative physiological substrates.
  • These findings provide a foundation for generating testable hypotheses regarding MMP-9's physiological functions.