1jaq: Difference between revisions

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New page: left|200px<br /> <applet load="1jaq" size="450" color="white" frame="true" align="right" spinBox="true" caption="1jaq, resolution 2.4Å" /> '''COMPLEX OF 1-HYDROXY...
 
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[[Image:1jaq.gif|left|200px]]<br />
<applet load="1jaq" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1jaq, resolution 2.4&Aring;" />
'''COMPLEX OF 1-HYDROXYLAMINE-2-ISOBUTYLMALONYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)'''<br />


==Overview==
==COMPLEX OF 1-HYDROXYLAMINE-2-ISOBUTYLMALONYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)==
Matrix metalloproteinases (MMPs) are a family of zinc endopeptidases, involved in tissue remodeling. They have also been implicated in various, disease processes including tumour invasion and joint destruction and are, therefore attractive targets for inhibitor design. For rational drug, design, information of inhibitor binding at the atomic level is essential., Recently, we have published the refined high-resolution crystal structure, of the catalytic domain of human neutrophil collagenase (HNC) complexed, with the inhibitor Pro-Leu-Gly-NHOH, which is a mimic for the unprimed, (P3-P1) residues of a bound peptide substrate. We have now determined two, additional HNC complexes formed with the thiol inhibitor, HSCH2CH(CH2Ph)CO-L-Ala-Gly-NH2 and another hydroxamate inhibitor, HONHCOCH(iBu)CO-L-Ala-Gly-NH2, which were both refined to R-values of, 0.183/0.198 at 0.240/0.225-nm resolution. The inhibitor thiol and, hydroxamate groups ligand the catalytic zinc, giving rise to a slightly, distorted tetrahedral and trigonal-bipyramidal coordination sphere, respectively. The thiol inhibitor diastereomer with S-configuration at the, P1' residue (corresponding to an L-amino acid analog) binds to HNC. Its, peptidyl moiety mimics binding of primed (P1'-P3') residues of the, substrate. In combination with our first structure a continuous, hexapeptide corresponding to a peptide substrate productively bound to HNC, was constructed and energy-minimized. Proteolytic cleavage of this, Michaelis complex is probably general base-catalyzed as proposed for, thermolysin, i.e. a glutamate assists nucleophilic attack of a water, molecule. Although there are many structural and mechanistic similarities, to thermolysin, substrate binding to MMPs differs due to the interactions, beyond S1'-P1'. While thermolysin binds substrates with a kink at P1', substrates are bound in an extended conformation in the collagenases. This, property explains the tolerance of thermolysin for D-amino acid residues, at the P1' position, in contrast to the collagenases. The third inhibitor, HONHCOCH(iBu)CO-L-Ala-Gly-NH2, unexpectedly binds in a different manner, than anticipated from its design and binding mode in thermolysin. Its, hydroxamate group obviously interacts with the catalytic zinc in a, favourable bidentate manner, but in contrast its isobutyl (iBu) side chain, remains outside of the S1' pocket, presumably due to severe constraints, imposed by the adjacent planar hydroxamate group. Instead, the C-terminal, Ala-Gly-NH2 tail adopts a bent conformation and inserts into this S1', pocket, presumably in a non-optimized manner. Both the isobutyl side chain, and the C-terminal peptide tail could be replaced by other, better fitting, groups.(ABSTRACT TRUNCATED AT 250 WORDS)
<StructureSection load='1jaq' size='340' side='right'caption='[[1jaq]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1jaq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JAQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JAQ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=01S:N-[(2R)-2-(HYDROXYCARBAMOYL)-4-METHYLPENTANOYL]-L-ALANYLGLYCINAMIDE'>01S</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jaq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jaq OCA], [https://pdbe.org/1jaq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jaq RCSB], [https://www.ebi.ac.uk/pdbsum/1jaq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jaq ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MMP8_HUMAN MMP8_HUMAN] Can degrade fibrillar type I, II, and III collagens.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ja/1jaq_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1jaq ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1JAQ 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 CA, ZN and HMI as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Neutrophil_collagenase Neutrophil collagenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.34 3.4.24.34] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JAQ OCA].
*[[Matrix metalloproteinase 3D structures|Matrix metalloproteinase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
X-ray structures of human neutrophil collagenase complexed with peptide hydroxamate and peptide thiol inhibitors. Implications for substrate binding and rational drug design., Grams F, Reinemer P, Powers JC, Kleine T, Pieper M, Tschesche H, Huber R, Bode W, Eur J Biochem. 1995 Mar 15;228(3):830-41. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7737183 7737183]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Neutrophil collagenase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Bode W]]
[[Category: Bode, W.]]
[[Category: Grams F]]
[[Category: Grams, F.]]
[[Category: Huber R]]
[[Category: Huber, R.]]
[[Category: Kleine T]]
[[Category: Kleine, T.]]
[[Category: Piper M]]
[[Category: Piper, M.]]
[[Category: Powers JC]]
[[Category: Powers, J.C.]]
[[Category: Reinemer P]]
[[Category: Reinemer, P.]]
[[Category: Tschesche H]]
[[Category: Tschesche, H.]]
[[Category: CA]]
[[Category: HMI]]
[[Category: ZN]]
[[Category: metalloprotease]]
[[Category: metzincins]]
[[Category: zinc-endopeptidase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 17:39:10 2007''

Latest revision as of 10:38, 7 February 2024

COMPLEX OF 1-HYDROXYLAMINE-2-ISOBUTYLMALONYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)COMPLEX OF 1-HYDROXYLAMINE-2-ISOBUTYLMALONYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)

Structural highlights

1jaq is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MMP8_HUMAN Can degrade fibrillar type I, II, and III collagens.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1jaq, resolution 2.40Å

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