2qa9

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{{Seed}}
 
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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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The line below this paragraph, containing "STRUCTURE_2qa9", creates the "Structure Box" on the page.
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<StructureSection load='2qa9' size='340' side='right'caption='[[2qa9]], [[Resolution|resolution]] 1.18&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2qa9]] is a 2 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=2QA9 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.18&#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=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></td></tr>
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{{STRUCTURE_2qa9| PDB=2qa9 | SCENE= }}
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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=2qa9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qa9 OCA], [https://pdbe.org/2qa9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qa9 RCSB], [https://www.ebi.ac.uk/pdbsum/2qa9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qa9 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PRTB_STRGR PRTB_STRGR] Has a primary specificity for large aliphatic or aromatic amino acids.
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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/main_output.php?pdb_ID=2qa9 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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===Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2===
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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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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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The line below this paragraph, {{ABSTRACT_PUBMED_18157955}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2qa9" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18157955 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18157955}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2QA9 is a [[Single protein]] structure of 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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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/18157955 18157955]
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[[Category: Single protein]]
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[[Category: Streptogrisin B]]
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[[Category: Streptomyces griseus]]
[[Category: Streptomyces griseus]]
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[[Category: James, M N.G.]]
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[[Category: James MNG]]
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[[Category: Lee, T W.]]
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[[Category: Lee TW]]
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[[Category: Alpha helix]]
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[[Category: Beta barrel]]
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[[Category: Chymotrypsin-type serine peptidase]]
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[[Category: Hydrolase]]
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[[Category: Second tetrahedral intermediate]]
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[[Category: Tetrapeptide]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 17:26:24 2008''
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Current revision

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

PDB ID 2qa9

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