1pq5: Difference between revisions

Revision as of 15:31, 21 February 2008

Trypsin at pH 5, 0.85 A

OverviewOverview

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 StructureAbout this Structure

1PQ5 is a Single protein structure of sequence from Fusarium oxysporum with and as ligands. Active as Trypsin, with EC number 3.4.21.4 Full crystallographic information is available from OCA.

ReferenceReference

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 14:31:27 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1pq5.jpg|left|200px]]<br /><applet load="1pq5" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1pq5.jpg|left|200px]]<br /><applet load="1pq5" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1pq5, resolution 0.85&Aring;" />
 '''Trypsin at pH 5, 0.85 A'''<br />
 ==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.
+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==
-PQ5 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 and ARG as [http://en.wikipedia.org/wiki/ligands ligands]. 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PQ5 OCA].
+PQ5 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> and <scene name='pdbligand=ARG:'>ARG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. 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=1PQ5 OCA].
 ==Reference==
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 [[Category: Trypsin]]
 [[Category: Jelsch, C.]]
-[[Category: Lamzin, V.S.]]
+[[Category: Lamzin, V S.]]
 [[Category: Rypniewski, W.]]
 [[Category: Schmidt, A.]]
@@ Line 25: / Line 25: @@
 [[Category: ultra-high resolution]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:01:06 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:31:27 2008''