1pfg
From Proteopedia
(New page: 200px<br /><applet load="1pfg" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pfg, resolution 2.5Å" /> '''Strategy to design in...) |
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| - | [[Image:1pfg.jpg|left|200px]]<br /><applet load="1pfg" size=" | + | [[Image:1pfg.jpg|left|200px]]<br /><applet load="1pfg" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1pfg, resolution 2.5Å" /> | caption="1pfg, resolution 2.5Å" /> | ||
'''Strategy to design inhibitors: Structure of a complex of Proteinase K with a designed octapeptide inhibitor N-Ac-Pro-Ala-Pro-Phe-DAla-Ala-Ala-Ala-NH2 at 2.5A resolution'''<br /> | '''Strategy to design inhibitors: Structure of a complex of Proteinase K with a designed octapeptide inhibitor N-Ac-Pro-Ala-Pro-Phe-DAla-Ala-Ala-Ala-NH2 at 2.5A resolution'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of a complex formed by the interaction between | + | The crystal structure of a complex formed by the interaction between proteinase K and a designed octapeptide amide, N-Ac-Pro-Ala-Pro-Phe-DAla-Ala-Ala-Ala-NH2, has been determined at 2.5 A resolution and refined to an R-factor of 16.7% for 7,430 reflections in the resolution range of 8.0-2.50 A. The inhibitor forms a stable complex through a series of hydrogen bonds and hydrophobic interactions with the protein atoms and water molecules. The inhibitor is hydrolyzed between Phe4I and DAla5I (I indicates the inhibitor). The two fragments are separated by a distance of 3.2 A between the carbonyl carbon of Phe4I and the main-chain nitrogen of DAla5I. The N-terminal tetrapeptide occupies subsites S1-S5 (S5 for acetyl group), whereas the C-terminal part fits into S1'-S5' region (S5' for amide group). It is the first time that such an extended electron density for a designed synthetic peptide inhibitor has been observed in the prime region of an enzyme of the subtilisin family. In fact, the inhibitor fills the recognition site completely. There is only a slight rearrangement of the protein residues to accommodate the inhibitor. Superposition of the present octapeptide inhibitor on the hexapeptide inhibitor studied previously shows an overall homology of the two inhibitors, although the individual atoms are displaced significantly. It suggests the existence of a recognition site with flexible dimensions. Kinetic studies indicate an inhibition rate of 100% by this specifically designed peptide inhibitor. |
==About this Structure== | ==About this Structure== | ||
| - | 1PFG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Engyodontium_album Engyodontium album] with ACE and NH2 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Peptidase_K Peptidase K], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.64 3.4.21.64] Full crystallographic information is available from [http:// | + | 1PFG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Engyodontium_album Engyodontium album] with <scene name='pdbligand=ACE:'>ACE</scene> and <scene name='pdbligand=NH2:'>NH2</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Peptidase_K Peptidase K], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.64 3.4.21.64] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PFG OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Fittkau, S.]] | [[Category: Fittkau, S.]] | ||
[[Category: Peters, K.]] | [[Category: Peters, K.]] | ||
| - | [[Category: Saxena, A | + | [[Category: Saxena, A K.]] |
| - | [[Category: Singh, T | + | [[Category: Singh, T P.]] |
[[Category: ACE]] | [[Category: ACE]] | ||
[[Category: NH2]] | [[Category: NH2]] | ||
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[[Category: proteinase k]] | [[Category: proteinase k]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:28:34 2008'' |
Revision as of 12:28, 21 February 2008
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Strategy to design inhibitors: Structure of a complex of Proteinase K with a designed octapeptide inhibitor N-Ac-Pro-Ala-Pro-Phe-DAla-Ala-Ala-Ala-NH2 at 2.5A resolution
Overview
The crystal structure of a complex formed by the interaction between proteinase K and a designed octapeptide amide, N-Ac-Pro-Ala-Pro-Phe-DAla-Ala-Ala-Ala-NH2, has been determined at 2.5 A resolution and refined to an R-factor of 16.7% for 7,430 reflections in the resolution range of 8.0-2.50 A. The inhibitor forms a stable complex through a series of hydrogen bonds and hydrophobic interactions with the protein atoms and water molecules. The inhibitor is hydrolyzed between Phe4I and DAla5I (I indicates the inhibitor). The two fragments are separated by a distance of 3.2 A between the carbonyl carbon of Phe4I and the main-chain nitrogen of DAla5I. The N-terminal tetrapeptide occupies subsites S1-S5 (S5 for acetyl group), whereas the C-terminal part fits into S1'-S5' region (S5' for amide group). It is the first time that such an extended electron density for a designed synthetic peptide inhibitor has been observed in the prime region of an enzyme of the subtilisin family. In fact, the inhibitor fills the recognition site completely. There is only a slight rearrangement of the protein residues to accommodate the inhibitor. Superposition of the present octapeptide inhibitor on the hexapeptide inhibitor studied previously shows an overall homology of the two inhibitors, although the individual atoms are displaced significantly. It suggests the existence of a recognition site with flexible dimensions. Kinetic studies indicate an inhibition rate of 100% by this specifically designed peptide inhibitor.
About this Structure
1PFG is a Single protein structure of sequence from Engyodontium album with and as ligands. Active as Peptidase K, with EC number 3.4.21.64 Full crystallographic information is available from OCA.
Reference
Strategy to design peptide inhibitors: structure of a complex of proteinase K with a designed octapeptide inhibitor N-Ac-Pro-Ala-Pro-Phe-DAla-Ala-Ala-Ala-NH2 at 2.5 A resolution., Saxena AK, Singh TP, Peters K, Fittkau S, Betzel C, Protein Sci. 1996 Dec;5(12):2453-8. PMID:8976553
Page seeded by OCA on Thu Feb 21 14:28:34 2008
Categories: Engyodontium album | Peptidase K | Single protein | Betzel, C. | Fittkau, S. | Peters, K. | Saxena, A K. | Singh, T P. | ACE | NH2 | Complex | Inhibitor | Octapeptide | Proteinase k
