1ycm

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(New page: 200px<br /> <applet load="1ycm" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ycm" /> '''Solution Structure of matrix metalloprotein...)
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[[Image:1ycm.gif|left|200px]]<br />
 
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<applet load="1ycm" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ycm" />
 
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'''Solution Structure of matrix metalloproteinase 12 (MMP12) in the presence of N-Isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid (NNGH)'''<br />
 
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==Overview==
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==Solution Structure of matrix metalloproteinase 12 (MMP12) in the presence of N-Isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid (NNGH)==
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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.
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<StructureSection load='1ycm' size='340' side='right'caption='[[1ycm]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ycm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YCM FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NGH:N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL+HYDROXAMIC+ACID'>NGH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ycm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycm OCA], [https://pdbe.org/1ycm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ycm RCSB], [https://www.ebi.ac.uk/pdbsum/1ycm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ycm ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/MMP12_HUMAN MMP12_HUMAN] May be involved in tissue injury and remodeling. Has significant elastolytic activity. Can accept large and small amino acids at the P1' site, but has a preference for leucine. Aromatic or hydrophobic residues are preferred at the P1 site, with small hydrophobic residues (preferably alanine) occupying P3.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yc/1ycm_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ycm ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==Disease==
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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<ref>PMID:15809432</ref>
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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]]
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1YCM 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YCM OCA].
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</div>
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<div class="pdbe-citations 1ycm" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15809432 15809432]
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*[[Matrix metalloproteinase 3D structures|Matrix metalloproteinase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Macrophage elastase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Bertini I]]
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[[Category: Bertini, I.]]
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[[Category: Calderone V]]
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[[Category: Calderone, V.]]
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[[Category: Cosenza M]]
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[[Category: Cosenza, M.]]
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[[Category: Fragai M]]
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[[Category: Fragai, M.]]
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[[Category: Lee YM]]
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[[Category: Lee, Y.M.]]
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[[Category: Luchinat C]]
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[[Category: Luchinat, C.]]
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[[Category: Mangani S]]
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[[Category: Mangani, S.]]
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[[Category: Terni B]]
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[[Category: SPINE, Structural.Proteomics.in.Europe.]]
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[[Category: Turano P]]
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[[Category: Terni, B.]]
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[[Category: Turano, P.]]
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[[Category: CA]]
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[[Category: NGH]]
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[[Category: ZN]]
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[[Category: calcium]]
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[[Category: macrophage metalloelastase]]
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[[Category: mmp-12]]
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[[Category: nngh]]
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[[Category: solution structure]]
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[[Category: spine]]
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[[Category: structural genomics]]
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[[Category: structural proteomics in europe]]
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[[Category: zinc]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 20:17:59 2007''
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Current revision

Solution Structure of matrix metalloproteinase 12 (MMP12) in the presence of N-Isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid (NNGH)

PDB ID 1ycm

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