2qa9
From Proteopedia
(New page: 200px<br /><applet load="2qa9" size="350" color="white" frame="true" align="right" spinBox="true" caption="2qa9, resolution 1.18Å" /> '''Crystal structure of...) |
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caption="2qa9, resolution 1.18Å" /> | caption="2qa9, resolution 1.18Å" /> | ||
'''Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2'''<br /> | '''Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2'''<br /> | ||
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| + | ==Overview== | ||
| + | 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== | ==About this Structure== | ||
| - | 2QA9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 2QA9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus] with <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=EDO:'>EDO</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Known structural/functional Sites: <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>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QA9 OCA]. |
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| + | ==Reference== | ||
| + | 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://ispc.weizmann.ac.il//pmbin/getpm?pmid=18157955 18157955] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Streptogrisin B]] | [[Category: Streptogrisin B]] | ||
| - | [[Category: Streptomyces | + | [[Category: Streptomyces griseus]] |
[[Category: James, M.N.G.]] | [[Category: James, M.N.G.]] | ||
[[Category: Lee, T.W.]] | [[Category: Lee, T.W.]] | ||
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[[Category: tetrapeptide]] | [[Category: tetrapeptide]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 13 08:18:13 2008'' |
Revision as of 06:18, 13 February 2008
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Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2
Overview
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
2QA9 is a Single protein structure of sequence from Streptomyces griseus with , , and as ligands. Active as Streptogrisin B, with EC number 3.4.21.81 Known structural/functional Sites: , , , , , , and . Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Wed Feb 13 08:18:13 2008
