2qa9

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[[Image:2qa9.png|left|200px]]
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==Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2==
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<StructureSection load='2qa9' size='340' side='right' caption='[[2qa9]], [[Resolution|resolution]] 1.18&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2qa9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QA9 FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Streptogrisin_B Streptogrisin B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.81 3.4.21.81] </span></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qa9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qa9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qa9 RCSB], [http://www.ebi.ac.uk/pdbsum/2qa9 PDBsum]</span></td></tr>
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<table>
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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/qa/2qa9_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/chain_selection.php?pdb_ID=2ata 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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Streptogrisin B (SGPB) has served as one of the models for studying the catalytic activities of serine peptidases. Here we report its native crystal structures at pH 4.2 at a resolution of 1.18A, and at pH 7.3 at a resolution of 1.23A. Unexpectedly, outstanding electron density peaks occurred in the active site and the substrate-binding region of SGPB in the computed maps at both pHs. The densities at pH 4.2 were assigned as a tetrapeptide, Asp-Ala-Ile-Tyr, whereas those at pH 7.3 were assigned as a tyrosine molecule and a leucine molecule existing at equal occupancies in both of the SGPB molecules in the asymmetric unit. Refinement with relaxed geometric restraints resulted in molecular structures representing mixtures of the second tetrahedral intermediates and the enzyme-product complexes of SGPB existing in a pH-dependent equilibrium. Structural comparisons with the complexes of SGPB with turkey ovomucoid third domain (OMTKY3) and its variants have shown that, upon the formation of the tetrahedral intermediate, residues Glu192A to Gly193 of SGPB move towards the alpha-carboxylate O of residue P1 of the bound species, and adjustments in the side-chain conformational angles of His57 and Ser195 of SGPB favor the progression of the catalytic mechanism of SGPB.
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{{STRUCTURE_2qa9| PDB=2qa9 | SCENE= }}
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1.2A-resolution crystal structures reveal the second tetrahedral intermediates of streptogrisin B (SGPB).,Lee TW, James MN Biochim Biophys Acta. 2008 Feb;1784(2):319-34. Epub 2007 Nov 29. PMID:18157955<ref>PMID:18157955</ref>
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===Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2===
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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{{ABSTRACT_PUBMED_18157955}}
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== References ==
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<references/>
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==About this Structure==
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__TOC__
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[[2qa9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QA9 OCA].
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</StructureSection>
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==Reference==
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<ref group="xtra">PMID:018157955</ref><references group="xtra"/>
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[[Category: Streptogrisin B]]
[[Category: Streptogrisin B]]
[[Category: Streptomyces griseus]]
[[Category: Streptomyces griseus]]

Revision as of 18:37, 30 September 2014

Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2

2qa9, resolution 1.18Å

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