1pqa
From Proteopedia
(New page: 200px<br /><applet load="1pqa" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pqa, resolution 1.23Å" /> '''Trypsin with PMSF at...) |
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| - | [[Image:1pqa.jpg|left|200px]]<br /><applet load="1pqa" size=" | + | [[Image:1pqa.jpg|left|200px]]<br /><applet load="1pqa" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1pqa, resolution 1.23Å" /> | caption="1pqa, resolution 1.23Å" /> | ||
'''Trypsin with PMSF at atomic resolution'''<br /> | '''Trypsin with PMSF at atomic resolution'''<br /> | ||
==Overview== | ==Overview== | ||
| - | A series of crystal structures of trypsin, containing either an | + | A series of crystal structures of trypsin, containing either an autoproteolytic cleaved peptide fragment or a covalently bound inhibitor, were determined at atomic and ultra-high resolution and subjected to ab initio quantum chemical calculations and multipole refinement. Quantum chemical calculations reproduced the observed active site crystal structure with severe deviations from standard stereochemistry and indicated the protonation state of the catalytic residues. Multipole refinement directly revealed the charge distribution in the active site and proved the validity of the ab initio calculations. The combined results confirmed the catalytic function of the active site residues and the two water molecules acting as the nucleophile and the proton donor. The crystal structures represent snapshots from the reaction pathway, close to a tetrahedral intermediate. The de-acylation of trypsin then occurs in true SN2 fashion. |
==About this Structure== | ==About this Structure== | ||
| - | 1PQA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] Full crystallographic information is available from [http:// | + | 1PQA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PQA OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Trypsin]] | [[Category: Trypsin]] | ||
[[Category: Jelsch, C.]] | [[Category: Jelsch, C.]] | ||
| - | [[Category: Lamzin, V | + | [[Category: Lamzin, V S.]] |
[[Category: Rypniewski, W.]] | [[Category: Rypniewski, W.]] | ||
[[Category: Schmidt, A.]] | [[Category: Schmidt, A.]] | ||
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[[Category: trypsin]] | [[Category: trypsin]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:31:23 2008'' |
Revision as of 12:31, 21 February 2008
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Trypsin with PMSF at atomic resolution
Overview
A series of crystal structures of trypsin, containing either an autoproteolytic cleaved peptide fragment or a covalently bound inhibitor, were determined at atomic and ultra-high resolution and subjected to ab initio quantum chemical calculations and multipole refinement. Quantum chemical calculations reproduced the observed active site crystal structure with severe deviations from standard stereochemistry and indicated the protonation state of the catalytic residues. Multipole refinement directly revealed the charge distribution in the active site and proved the validity of the ab initio calculations. The combined results confirmed the catalytic function of the active site residues and the two water molecules acting as the nucleophile and the proton donor. The crystal structures represent snapshots from the reaction pathway, close to a tetrahedral intermediate. The de-acylation of trypsin then occurs in true SN2 fashion.
About this Structure
1PQA is a Single protein structure of sequence from Fusarium oxysporum with as ligand. Active as Trypsin, with EC number 3.4.21.4 Full crystallographic information is available from OCA.
Reference
Trypsin revisited: crystallography AT (SUB) atomic resolution and quantum chemistry revealing details of catalysis., Schmidt A, Jelsch C, Ostergaard P, Rypniewski W, Lamzin VS, J Biol Chem. 2003 Oct 31;278(44):43357-62. Epub 2003 Aug 22. PMID:12937176
Page seeded by OCA on Thu Feb 21 14:31:23 2008
