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1pip

From Proteopedia

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[[Image:1pip.gif|left|200px]]<br /><applet load="1pip" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1pip, resolution 1.7&Aring;" />
 
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'''CRYSTAL STRUCTURE OF PAPAIN-SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE COMPLEX AT 1.7 ANGSTROMS RESOLUTION: NONCOVALENT BINDING MODE OF A COMMON SEQUENCE OF ENDOGENOUS THIOL PROTEASE INHIBITORS'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF PAPAIN-SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE COMPLEX AT 1.7 ANGSTROMS RESOLUTION: NONCOVALENT BINDING MODE OF A COMMON SEQUENCE OF ENDOGENOUS THIOL PROTEASE INHIBITORS==
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Succinyl-Gln-Val-Val-Ala-Ala-p-nitroanilide corresponding to a common sequence of endogenous thiol protease inhibitors is a noncompetitive reversible inhibitor of papain. In order to elucidate the binding mode of the inhibitor at the atomic level, its complex with papain was crystallized at ca. pH 7.0 using the hanging drop method, and the crystal structure was analyzed at 1.7-A resolution. The crystal has space group P2(1)2(1)2(1), with a = 43.09, b = 102.32, c = 49.69 A, and Z = 4. A total of 47,215 observed reflections were collected on the imaging plates using the same single crystal, and 19,833 unique reflections with Fo &gt; sigma (Fo) were used for structure determination and refinement. The papain structure was determined by use of the atomic coordinates of papain previously reported, and then refined by the X-PLOR program. The inhibitor molecule was located on a difference Fourier map and fitted into the electron density with the aid of computer graphics. The complex structure was finally refined to R = 19.6% including 118 solvent molecules. The X-ray analysis of the complex crystal shows that the inhibitor is located at the R-domain side, not in the center of the binding site created by the R- and L-domains of papain. Such a binding mode of the inhibitor explains well the biological behavior that the inhibitor exhibits against papain. Comparison with the structure of papain-stefin B complex indicates that the structure of the Gln-Val-Val-Ala-Gly sequence itself is not necessarily the essential requisite for inhibitory activity.(ABSTRACT TRUNCATED AT 250 WORDS)
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<StructureSection load='1pip' size='340' side='right'caption='[[1pip]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1pip]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Carica_papaya Carica papaya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PIP 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">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</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=NIT:4-NITROANILINE'>NIT</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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=1pip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pip OCA], [https://pdbe.org/1pip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pip RCSB], [https://www.ebi.ac.uk/pdbsum/1pip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pip ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PAPA1_CARPA PAPA1_CARPA]
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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/pi/1pip_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=1pip ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1PIP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Carica_papaya Carica papaya]. Active as [http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PIP OCA].
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*[[Papain|Papain]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of papain-succinyl-Gln-Val-Val-Ala-Ala-p-nitroanilide complex at 1.7-A resolution: noncovalent binding mode of a common sequence of endogenous thiol protease inhibitors., Yamamoto A, Tomoo K, Doi M, Ohishi H, Inoue M, Ishida T, Yamamoto D, Tsuboi S, Okamoto H, Okada Y, Biochemistry. 1992 Nov 24;31(46):11305-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1445868 1445868]
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[[Category: Carica papaya]]
[[Category: Carica papaya]]
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[[Category: Papain]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Doi M]]
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[[Category: Doi, M.]]
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[[Category: Inoue M]]
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[[Category: Inoue, M.]]
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[[Category: Ishida T]]
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[[Category: Ishida, T.]]
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[[Category: Ohishi H]]
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[[Category: Ohishi, H.]]
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[[Category: Okada Y]]
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[[Category: Okada, Y.]]
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[[Category: Okamoto H]]
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[[Category: Okamoto, H.]]
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[[Category: Tomoo K]]
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[[Category: Tomoo, K.]]
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[[Category: Tsuboi S]]
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[[Category: Tsuboi, S.]]
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[[Category: Yamamoto A]]
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[[Category: Yamamoto, A.]]
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[[Category: Yamamoto D]]
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[[Category: Yamamoto, D.]]
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[[Category: hydrolase(thiol protease)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:29:08 2008''
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Current revision

CRYSTAL STRUCTURE OF PAPAIN-SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE COMPLEX AT 1.7 ANGSTROMS RESOLUTION: NONCOVALENT BINDING MODE OF A COMMON SEQUENCE OF ENDOGENOUS THIOL PROTEASE INHIBITORS

PDB ID 1pip

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