1z3j: Difference between revisions
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'''Solution Structure of MMP12 in the presence of N-isobutyl-N-4-methoxyphenylsulfonyl]glycyl hydroxamic acid (NNGH)'''<br /> | '''Solution Structure of MMP12 in the presence of N-isobutyl-N-4-methoxyphenylsulfonyl]glycyl hydroxamic acid (NNGH)'''<br /> | ||
==Overview== | ==Overview== | ||
The structures of the catalytic domain of matrix metalloproteinase 12 in | The structures of the catalytic domain of matrix metalloproteinase 12 in the presence of acetohydroxamic acid and N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid have been solved by x-ray diffraction in the crystalline state at 1.0 and 1.3-A resolution, respectively, and compared with the previously published x-ray structure at 1.2-A resolution of the adduct with batimastat. The structure of the N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid adduct has been solved by NMR in solution. The three x-ray structures and the solution structure are similar but not identical to one another, the differences being sizably higher in the loops. We propose that many of the loops show a dynamical behavior in solution on a variety of time scales. Different conformations of some flexible regions of the protein can be observed as "frozen" in different crystalline environments. The mobility in solution studied by NMR reveals conformational equilibria in accessible time scales, i.e., from 10(-5) s to ms and more. Averaging of some residual dipolar couplings is consistent with further motions down to 10(-9) s. Finally, local thermal motions of each frozen conformation in the crystalline state at 100 K correlate well with local motions on the picosecond time scale. Flexibility/conformational heterogeneity in crucial parts of the catalytic domain is a rule rather than an exception in matrix metalloproteinases, and its extent may be underestimated by inspection of one x-ray structure. Backbone flexibility may play a role in the difficulties encountered in the design of selective inhibitors, whereas it may be a requisite for substrate binding and broad substrate specificity. | ||
==Disease== | ==Disease== | ||
Known diseases associated with this structure: Cardiomyopathy, dilated, 1G OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=188840 188840]], Cardiomyopathy, familial hypertrophic OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=188840 188840]], Muscular dystrophy, limb-girdle, type 2J OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=188840 188840]], Myopathy, proximal, with early respiratory muscle involvement OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=188840 188840]], Tibial muscular dystrophy, tardive OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=188840 188840]] | Known diseases associated with this structure: Cardiomyopathy, dilated, 1G OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=188840 188840]], Cardiomyopathy, familial hypertrophic OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=188840 188840]], Muscular dystrophy, limb-girdle, type 2J OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=188840 188840]], Myopathy, early-onset, with fatal cardiomyopathy OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=188840 188840]], Myopathy, proximal, with early respiratory muscle involvement OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=188840 188840]], Tibial muscular dystrophy, tardive OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=188840 188840]] | ||
==About this Structure== | ==About this Structure== | ||
1Z3J is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with ZN, CA and NGH as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Macrophage_elastase Macrophage elastase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.65 3.4.24.65] Full crystallographic information is available from [http:// | 1Z3J is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=NGH:'>NGH</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Macrophage_elastase Macrophage elastase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.65 3.4.24.65] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z3J OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Cosenza, M.]] | [[Category: Cosenza, M.]] | ||
[[Category: Fragai, M.]] | [[Category: Fragai, M.]] | ||
[[Category: Lee, Y | [[Category: Lee, Y M.]] | ||
[[Category: Luchinat, C.]] | [[Category: Luchinat, C.]] | ||
[[Category: Mangani, S.]] | [[Category: Mangani, S.]] | ||
| Line 36: | Line 35: | ||
[[Category: zinc]] | [[Category: zinc]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:11:47 2008'' | ||
Revision as of 17:11, 21 February 2008
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Solution Structure of MMP12 in the presence of N-isobutyl-N-4-methoxyphenylsulfonyl]glycyl hydroxamic acid (NNGH)
OverviewOverview
The structures of the catalytic domain of matrix metalloproteinase 12 in the presence of acetohydroxamic acid and N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid have been solved by x-ray diffraction in the crystalline state at 1.0 and 1.3-A resolution, respectively, and compared with the previously published x-ray structure at 1.2-A resolution of the adduct with batimastat. The structure of the N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid adduct has been solved by NMR in solution. The three x-ray structures and the solution structure are similar but not identical to one another, the differences being sizably higher in the loops. We propose that many of the loops show a dynamical behavior in solution on a variety of time scales. Different conformations of some flexible regions of the protein can be observed as "frozen" in different crystalline environments. The mobility in solution studied by NMR reveals conformational equilibria in accessible time scales, i.e., from 10(-5) s to ms and more. Averaging of some residual dipolar couplings is consistent with further motions down to 10(-9) s. Finally, local thermal motions of each frozen conformation in the crystalline state at 100 K correlate well with local motions on the picosecond time scale. Flexibility/conformational heterogeneity in crucial parts of the catalytic domain is a rule rather than an exception in matrix metalloproteinases, and its extent may be underestimated by inspection of one x-ray structure. Backbone flexibility may play a role in the difficulties encountered in the design of selective inhibitors, whereas it may be a requisite for substrate binding and broad substrate specificity.
DiseaseDisease
Known diseases associated with this structure: Cardiomyopathy, dilated, 1G OMIM:[188840], Cardiomyopathy, familial hypertrophic OMIM:[188840], Muscular dystrophy, limb-girdle, type 2J OMIM:[188840], Myopathy, early-onset, with fatal cardiomyopathy OMIM:[188840], Myopathy, proximal, with early respiratory muscle involvement OMIM:[188840], Tibial muscular dystrophy, tardive OMIM:[188840]
About this StructureAbout this Structure
1Z3J is a Single protein structure of sequence from Homo sapiens with , and as ligands. Active as Macrophage elastase, with EC number 3.4.24.65 Full crystallographic information is available from OCA.
ReferenceReference
Conformational variability of matrix metalloproteinases: beyond a single 3D structure., Bertini I, Calderone V, Cosenza M, Fragai M, Lee YM, Luchinat C, Mangani S, Terni B, Turano P, Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5334-9. Epub 2005 Apr 4. PMID:15809432
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