We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.
2qaa
From Proteopedia
(Difference between revisions)
(New page: 200px<br /><applet load="2qaa" size="350" color="white" frame="true" align="right" spinBox="true" caption="2qaa, resolution 1.23Å" /> '''Crystal structure of...) |
|||
| (15 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | [[Image:2qaa.jpg|left|200px]]<br /><applet load="2qaa" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="2qaa, resolution 1.23Å" /> | ||
| - | '''Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3'''<br /> | ||
| - | == | + | ==Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3== |
| - | + | <StructureSection load='2qaa' size='340' side='right'caption='[[2qaa]], [[Resolution|resolution]] 1.23Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | [ | + | <table><tr><td colspan='2'>[[2qaa]] 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=2QAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QAA 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]] 1.23Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</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=2qaa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qaa OCA], [https://pdbe.org/2qaa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qaa RCSB], [https://www.ebi.ac.uk/pdbsum/2qaa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qaa ProSAT]</span></td></tr> |
| - | + | </table> | |
| - | + | == Function == | |
| - | [ | + | [https://www.uniprot.org/uniprot/PRTB_STRGR PRTB_STRGR] Has a primary specificity for large aliphatic or aromatic amino acids. |
| - | + | == 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/qa/2qaa_consurf.spt"</scriptWhenChecked> |
| - | [[ | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2qaa ConSurf]. | |
| - | + | <div style="clear:both"></div> | |
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 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. | ||
| - | + | 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> | |
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 2qaa" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Streptomyces griseus]] | ||
| + | [[Category: James MNG]] | ||
| + | [[Category: Lee TW]] | ||
Current revision
Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3
| |||||||||||
