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1q5p

From Proteopedia

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(New page: 200px<br /><applet load="1q5p" size="450" color="white" frame="true" align="right" spinBox="true" caption="1q5p, resolution 1.6&Aring;" /> '''S156E/S166D variant o...)
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[[Image:1q5p.jpg|left|200px]]<br /><applet load="1q5p" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1q5p, resolution 1.6&Aring;" />
 
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'''S156E/S166D variant of Bacillus lentus subtilisin'''<br />
 
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==Overview==
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==S156E/S166D variant of Bacillus lentus subtilisin==
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The properties of the transition state for serine protease-catalyzed, hydrolysis of an amide bond were determined for a series of subtilisin, variants from Bacillus lentus. There is no significant change in the, structure of the enzyme upon introduction of charged mutations, S156E/S166D, suggesting that changes in catalytic activity reflect global, properties of the enzyme. The effect of charged mutations on the pK(a) of, the active site histidine-64 N(epsilon)(2)-H was correlated with changes, in the second-order rate constant k(cat)/K(m) for hydrolysis of, tetrapeptide anilides at low ionic strength with a Bronsted slope alpha =, 1.1. The solvent isotope effect (D)2(O)(k(cat)/K(m))(1) = 1.4 +/- 0.2., These results are consistent with a rate-limiting breakdown of the, tetrahedral intermediate in the acylation step with hydrogen bond, stabilization of the departing amine leaving group. There is an increase, in the ratio of hydrolysis of succinyl-Ala-Ala-Pro-Phe-anilides for, p-nitroaniline versus aniline leaving groups with variants with more basic, active site histidines that can be described by the interaction, coefficient p(xy) = delta beta(lg)/delta pK(a) (H64) = 0.15. This is, attributed to increased hydrogen bonding of the active site imidazolium, N-H to the more basic amine leaving group as well as electrostatic, destabilization of the transition state. A qualitative characterization of, the transition state is presented in terms of a reaction coordinate, diagram that is defined by the structure-reactivity parameters.
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<StructureSection load='1q5p' size='340' side='right'caption='[[1q5p]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1q5p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lederbergia_lenta Lederbergia lenta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q5P 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]] 1.6&#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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SEB:O-BENZYLSULFONYL-SERINE'>SEB</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1q5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q5p OCA], [https://pdbe.org/1q5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q5p RCSB], [https://www.ebi.ac.uk/pdbsum/1q5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q5p ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SUBS_LEDLE SUBS_LEDLE] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides.
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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/q5/1q5p_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=1q5p 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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1Q5P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_lentus Bacillus lentus] with SO4 and CA as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Q5P OCA].
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*[[Subtilisin 3D structures|Subtilisin 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Do enzymes change the nature of transition states? Mapping the transition state for general acid-base catalysis of a serine protease., Bott RR, Chan G, Domingo B, Ganshaw G, Hsia CY, Knapp M, Murray CJ, Biochemistry. 2003 Sep 16;42(36):10545-53. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12962477 12962477]
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[[Category: Large Structures]]
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[[Category: Bacillus lentus]]
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[[Category: Lederbergia lenta]]
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[[Category: Single protein]]
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[[Category: Bott RR]]
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[[Category: Subtilisin]]
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[[Category: Chan G]]
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[[Category: Bott, R.R.]]
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[[Category: Domingo B]]
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[[Category: Chan, G.]]
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[[Category: Ganshaw G]]
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[[Category: Domingo, B.]]
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[[Category: Hsia CY]]
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[[Category: Ganshaw, G.]]
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[[Category: Knapp M]]
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[[Category: Hsia, C.Y.]]
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[[Category: Murray CJ]]
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[[Category: Knapp, M.]]
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[[Category: Murray, C.J.]]
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[[Category: CA]]
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[[Category: SO4]]
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[[Category: altered flexibility]]
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[[Category: serine protease]]
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[[Category: site-specific variant]]
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[[Category: subtilisin]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:24:19 2007''
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Current revision

S156E/S166D variant of Bacillus lentus subtilisin

PDB ID 1q5p

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