PDB 1JK3 deposited: 2001-07-11 modified: 2011-07-13
Title Crystal structure of human MMP-12 (Macrophage Elastase) at true atomic resolution
Authors Bode, W., Braun, M., Huber, R., Kocourek, A., Lang, R., Maskos, K., Tschesche, H.
Structure factors resolution 1.09 rfactor 0.16742 rfree 0.19572
DPI 0.10 theoretical min: 0.03

The macrophage elastase enzyme (MMP-12) expressed mainly in alveolar macrophages has been identified in the mouse lung as the main destructive agent associated with cigarette smoking, which gives rise to emphysema, both directly via elastin degradation and indirectly by disturbing the proteinase/antiproteinase balance via inactivation of the alpha1-proteinase inhibitor (alpha1-PI), the antagonist of the leukocyte elastase. The catalytic domain of human recombinant MMP-12 has been crystallized in complex with the broad-specificity inhibitor batimastat (BB-94). The crystal structure analysis of this complex, determined using X-ray data to 1.1 A and refined to an R-value of 0.165, reveals an overall fold similar to that of other MMPs. However, the S-shaped double loop connecting strands III and IV is fixed closer to the beta-sheet and projects its His172 side-chain further into the rather hydrophobic active-site cleft, defining the S3 and the S1-pockets and separating them from each other to a larger extent than is observed in other MMPs. The S2-site is planar, while the characteristic S1'-subsite is a continuous tube rather than a pocket, in which the MMP-12-specific Thr215 replaces a Val residue otherwise highly conserved in almost all other MMPs. This alteration might allow MMP-12 to accept P1' Arg residues, making it unique among MMPs. The active-site cleft of MMP-12 is well equipped to bind and efficiently cleave the AlaMetPhe-LeuGluAla sequence in the reactive-site loop of alpha1-PI, as occurs experimentally. Similarities in contouring and particularly a common surface hydrophobicity both inside and distant from the active-site cleft explain why MMP-12 shares many substrates with matrilysin (MMP-7). The MMP-12 structure is an excellent template for the structure-based design of specific inhibitors for emphysema therapy and for the construction of mutants to clarify the role of this MMP.

J.Mol.Biol. 2001 Sep; 312(4):731-742 doi:10.1006/jmbi.2001.4954

Cross References
Database source Identifier Description
PubMed 11575928 JMOBAK
Biomolecule Structure Assembly Serial Assembly Type Conformational State Chains Ligands Atoms
1JK3/1 1JK3 1 monomer 0 1 6 1403
1JK3/2 1JK3 2 dimer 0 2 11 2806
1JK3/3 1JK3 3 dimer 0 2 12 2810