2qaa
From Proteopedia
(Difference between revisions)
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| - | [[Image:2qaa.jpg|left|200px]] | + | [[Image:2qaa.jpg|left|200px]] |
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| - | '''Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3''' | + | {{Structure |
| + | |PDB= 2qaa |SIZE=350|CAPTION= <scene name='initialview01'>2qaa</scene>, resolution 1.23Å | ||
| + | |SITE= <scene name='pdbsite=AC1:So4+Binding+Site+For+Residue+B+911'>AC1</scene>, <scene name='pdbsite=AC2:So4+Binding+Site+For+Residue+A+912'>AC2</scene>, <scene name='pdbsite=AC3:So4+Binding+Site+For+Residue+A+913'>AC3</scene>, <scene name='pdbsite=AC4:So4+Binding+Site+For+Residue+B+914'>AC4</scene>, <scene name='pdbsite=AC5:So4+Binding+Site+For+Residue+B+915'>AC5</scene>, <scene name='pdbsite=AC6:Cl+Binding+Site+For+Residue+A+941'>AC6</scene>, <scene name='pdbsite=AC7:Cl+Binding+Site+For+Residue+B+942'>AC7</scene>, <scene name='pdbsite=AC8:Cl+Binding+Site+For+Residue+B+943'>AC8</scene>, <scene name='pdbsite=AC9:Cl+Binding+Site+For+Residue+B+944'>AC9</scene>, <scene name='pdbsite=BC1:Cl+Binding+Site+For+Residue+A+945'>BC1</scene>, <scene name='pdbsite=BC2:Cl+Binding+Site+For+Residue+B+946'>BC2</scene>, <scene name='pdbsite=BC3:Cl+Binding+Site+For+Residue+A+950'>BC3</scene>, <scene name='pdbsite=BC4:Cl+Binding+Site+For+Residue+B+952'>BC4</scene>, <scene name='pdbsite=BC5:Cl+Binding+Site+For+Residue+B+954'>BC5</scene>, <scene name='pdbsite=BC6:Cl+Binding+Site+For+Residue+A+957'>BC6</scene>, <scene name='pdbsite=BC7:TYR+Binding+Site+For+Residue+A+1'>BC7</scene>, <scene name='pdbsite=BC8:LEU+Binding+Site+For+Residue+A+2'>BC8</scene>, <scene name='pdbsite=BC9:TYR+Binding+Site+For+Residue+B+1'>BC9</scene>, <scene name='pdbsite=CC1:LEU+Binding+Site+For+Residue+B+2'>CC1</scene>, <scene name='pdbsite=CC2:Edo+Binding+Site+For+Residue+A+921'>CC2</scene>, <scene name='pdbsite=CC3:Edo+Binding+Site+For+Residue+A+922'>CC3</scene>, <scene name='pdbsite=CC4:Edo+Binding+Site+For+Residue+A+923'>CC4</scene>, <scene name='pdbsite=CC5:Edo+Binding+Site+For+Residue+B+924'>CC5</scene>, <scene name='pdbsite=CC6:Epe+Binding+Site+For+Residue+A+961'>CC6</scene>, <scene name='pdbsite=CC7:Gol+Binding+Site+For+Residue+A+901'>CC7</scene>, <scene name='pdbsite=CC8:Gol+Binding+Site+For+Residue+B+902'>CC8</scene>, <scene name='pdbsite=CC9:Gol+Binding+Site+For+Residue+B+903'>CC9</scene>, <scene name='pdbsite=DC1:Gol+Binding+Site+For+Residue+B+904'>DC1</scene>, <scene name='pdbsite=DC2:Acy+Binding+Site+For+Residue+A+931'>DC2</scene>, <scene name='pdbsite=DC3:Acy+Binding+Site+For+Residue+B+932'>DC3</scene> and <scene name='pdbsite=DC4:Acy+Binding+Site+For+Residue+A+933'>DC4</scene> | ||
| + | |LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</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> and <scene name='pdbligand=ACY:ACETIC ACID'>ACY</scene> | ||
| + | |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] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2QAA is a [ | + | 2QAA 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=2QAA OCA]. |
==Reference== | ==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:// | + | 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] |
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Streptogrisin B]] | [[Category: Streptogrisin B]] | ||
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[[Category: TYR]] | [[Category: TYR]] | ||
[[Category: alpha helix]] | [[Category: alpha helix]] | ||
| - | [[Category: beta | + | [[Category: beta barrel]] |
[[Category: chymotrypsin-type serine peptidase]] | [[Category: chymotrypsin-type serine peptidase]] | ||
[[Category: hydrolase]] | [[Category: hydrolase]] | ||
| - | [[Category: second tetrahedral | + | [[Category: second tetrahedral intermediate]] |
| - | [[Category: single amino | + | [[Category: single amino acid]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:23:36 2008'' |
Revision as of 16:23, 20 March 2008
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| , resolution 1.23Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , and | ||||||
| Ligands: | , , , , , and | ||||||
| Activity: | Streptogrisin B, with EC number 3.4.21.81 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3
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
2QAA is a Single protein structure of sequence from Streptomyces griseus. 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
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