Solution structure of the catalytic domain of human stromelysin complexed with a hydrophobic inhibitor

Stromelysin, a representative matrix metalloproteinase and target of drug development efforts, plays a prominent role in the pathological proteolysis associated with arthritis and secondarily in that of cancer metastasis and invasion. To provide a structural template to aid the development of therap...

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Bibliographic Details
Published in:Protein science 1995-12, Vol.4 (12), p.2487-2498
Main Authors: Van Doren, Steven R., Kurochkin, Alexander V., Hu, Weidong, Ye, Qi‐Zhuang, Johnson, Linda L., Hupe, Donald J., Zuiderweg, ERIK R.P.
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Binding Sites
Catalysis
catalytic domain
Chemical Phenomena
Chemistry, Physical
Collagenases - chemistry
Enzyme Inhibitors - metabolism
Humans
hydroxamate
Hydroxamic Acids - chemistry
Hydroxamic Acids - metabolism
Magnetic Resonance Spectroscopy
Matrix Metalloproteinase 3
Metalloendopeptidases - antagonists & inhibitors
Metalloendopeptidases - chemistry
Metalloendopeptidases - metabolism
Models, Molecular
Molecular Sequence Data
Molecular Structure
multidimensional NMR
protein structure
Protein Structure, Secondary
Solutions
stromelysin
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Summary:Stromelysin, a representative matrix metalloproteinase and target of drug development efforts, plays a prominent role in the pathological proteolysis associated with arthritis and secondarily in that of cancer metastasis and invasion. To provide a structural template to aid the development of therapeutic inhibitors, we have determined a medium‐resolution structure of a 20‐kDa complex of human stromelysin's catalytic domain with a hydrophobic peptidic inhibitor using multinuclear, multidimensional NMR spectroscopy. This domain of this zinc hydrolase contains a mixed β‐sheet comprising one antiparallel strand and four parallel strands, three helices, and a methionine‐containing turn near the catalytic center. The ensemble of 20 structures was calculated using, on average, 8 interresidue NOE restraints per residue for the 166‐residue protein fragment complexed with a 4‐residue substrate analogue. The mean RMS deviation (RMSD) to the average structure for backbone heavy atoms is 0.91 A and for all heavy atoms is 1.42 Å. The structure has good stereochemical properties, including its backbone torsion angles. The β‐sheet and α‐helices of the catalytic domains of human stromelysin (NMR model) and human fibroblast collagenase (X‐ray crystallographic model of Lovejoy B et al., 1994b, Biochemistry 55:8207‐8217) superimpose well, having a pairwise RMSD for backbone heavy atoms of 2.28 Å when three loop segments are disregarded. The hydroxamate‐substituted inhibitor binds across the hydrophobic active site of stromelysin in an extended conformation. The first hydrophobic side chain is deeply buried in the principal S1' subsite, the second hydrophobic side chain is located on the opposite side of the inhibitor backbone in the hydrophobic S2' surface subsite, and a third hydrophobic side chain (P3') lies at the surface.
ISSN:0961-8368
1469-896X
DOI:10.1002/pro.5560041205