2qa9

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:27, 30 August 2023) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2qa9.jpg|left|200px]]
 
-
{{Structure
+
==Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2==
-
|PDB= 2qa9 |SIZE=350|CAPTION= <scene name='initialview01'>2qa9</scene>, resolution 1.18&Aring;
+
<StructureSection load='2qa9' size='340' side='right'caption='[[2qa9]], [[Resolution|resolution]] 1.18&Aring;' scene=''>
-
|SITE= <scene name='pdbsite=AC1:Cl+Binding+Site+For+Residue+E+411'>AC1</scene>, <scene name='pdbsite=AC2:So4+Binding+Site+For+Residue+E+421'>AC2</scene>, <scene name='pdbsite=AC3:So4+Binding+Site+For+Residue+E+422'>AC3</scene>, <scene name='pdbsite=AC4:Edo+Binding+Site+For+Residue+E+431'>AC4</scene>, <scene name='pdbsite=AC5:Edo+Binding+Site+For+Residue+E+432'>AC5</scene>, <scene name='pdbsite=AC6:Edo+Binding+Site+For+Residue+E+433'>AC6</scene>, <scene name='pdbsite=AC7:Edo+Binding+Site+For+Residue+E+434'>AC7</scene> and <scene name='pdbsite=AC8:Gol+Binding+Site+For+Residue+E+401'>AC8</scene>
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
+
<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>
-
|ACTIVITY= [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]
+
</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>
-
|GENE=
+
<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>
-
}}
+
<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>
-
 
+
</table>
-
'''Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/PRTB_STRGR PRTB_STRGR] Has a primary specificity for large aliphatic or aromatic amino acids.
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[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/2qa9_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2qa9 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.
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.
-
==About this Structure==
+
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>
-
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].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
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]
+
</div>
-
[[Category: Single protein]]
+
<div class="pdbe-citations 2qa9" style="background-color:#fffaf0;"></div>
-
[[Category: Streptogrisin B]]
+
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Streptomyces griseus]]
[[Category: Streptomyces griseus]]
-
[[Category: James, M N.G.]]
+
[[Category: James MNG]]
-
[[Category: Lee, T W.]]
+
[[Category: Lee TW]]
-
[[Category: CL]]
+
-
[[Category: EDO]]
+
-
[[Category: GOL]]
+
-
[[Category: SO4]]
+
-
[[Category: alpha helix]]
+
-
[[Category: beta barrel]]
+
-
[[Category: chymotrypsin-type serine peptidase]]
+
-
[[Category: hydrolase]]
+
-
[[Category: second tetrahedral intermediate]]
+
-
[[Category: tetrapeptide]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:23:37 2008''
+

Current revision

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

PDB ID 2qa9

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2qa9"
Personal tools