1s2b
From Proteopedia
(New page: 200px<br /><applet load="1s2b" size="450" color="white" frame="true" align="right" spinBox="true" caption="1s2b, resolution 2.1Å" /> '''Structure of SCP-B th...) |
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| - | [[Image:1s2b.jpg|left|200px]]<br /><applet load="1s2b" size=" | + | [[Image:1s2b.jpg|left|200px]]<br /><applet load="1s2b" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1s2b, resolution 2.1Å" /> | caption="1s2b, resolution 2.1Å" /> | ||
'''Structure of SCP-B the first member of the Eqolisin family of Peptidases to have its structure determined'''<br /> | '''Structure of SCP-B the first member of the Eqolisin family of Peptidases to have its structure determined'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The molecular structure of the pepstatin-insensitive carboxyl peptidase | + | The molecular structure of the pepstatin-insensitive carboxyl peptidase from Scytalidium lignicolum, formerly known as scytalidopepsin B, was solved by multiple isomorphous replacement phasing methods and refined to an R factor of 0.230 (R(free) = 0.246) at 2.1-A resolution. In addition to the structure of the unbound peptidase, the structure of a product complex of cleaved angiotensin II bound in the active site of the enzyme was also determined. We propose the name scytalidocarboxyl peptidase B (SCP-B) for this enzyme. On the basis of conserved, catalytic residues identified at the active site, we suggest the name Eqolisin for the enzyme family. The previously uninvestigated SCP-B fold is that of a beta-sandwich; each sheet has seven antiparallel strands. A tripeptide product, Ala-Ile-His, bound in the active site of SCP-B has allowed for identification of the catalytic residues and the residues in subsites S1, S2, and S3, which are important for substrate binding. The most likely hydrolytic mechanism involves nucleophilic attack of a general base (Glu-136)-activated water (OH(-)) on the si-face of the scissile peptide carbonylcarbon atom to form a tetrahedral intermediate. Electrophilic assistance and oxyanion stabilization is provided by the side-chain amide of Gln-53. Protonation of the leaving-group nitrogen is accomplished by the general acid function of the protonated carboxyl group of Glu-136. |
==About this Structure== | ==About this Structure== | ||
| - | 1S2B is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Scytalidium_lignicola Scytalidium lignicola]. Active as [http://en.wikipedia.org/wiki/Scytalidopepsin_B Scytalidopepsin B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.32 3.4.23.32] Full crystallographic information is available from [http:// | + | 1S2B is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Scytalidium_lignicola Scytalidium lignicola]. Active as [http://en.wikipedia.org/wiki/Scytalidopepsin_B Scytalidopepsin B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.32 3.4.23.32] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S2B OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Scytalidopepsin B]] | [[Category: Scytalidopepsin B]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Cherney, M | + | [[Category: Cherney, M M.]] |
[[Category: Fujinaga, M.]] | [[Category: Fujinaga, M.]] | ||
| - | [[Category: James, M | + | [[Category: James, M N.]] |
[[Category: Oda, K.]] | [[Category: Oda, K.]] | ||
[[Category: Oyama, H.]] | [[Category: Oyama, H.]] | ||
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[[Category: proteinase]] | [[Category: proteinase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:57:09 2008'' |
Revision as of 12:57, 21 February 2008
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Structure of SCP-B the first member of the Eqolisin family of Peptidases to have its structure determined
Overview
The molecular structure of the pepstatin-insensitive carboxyl peptidase from Scytalidium lignicolum, formerly known as scytalidopepsin B, was solved by multiple isomorphous replacement phasing methods and refined to an R factor of 0.230 (R(free) = 0.246) at 2.1-A resolution. In addition to the structure of the unbound peptidase, the structure of a product complex of cleaved angiotensin II bound in the active site of the enzyme was also determined. We propose the name scytalidocarboxyl peptidase B (SCP-B) for this enzyme. On the basis of conserved, catalytic residues identified at the active site, we suggest the name Eqolisin for the enzyme family. The previously uninvestigated SCP-B fold is that of a beta-sandwich; each sheet has seven antiparallel strands. A tripeptide product, Ala-Ile-His, bound in the active site of SCP-B has allowed for identification of the catalytic residues and the residues in subsites S1, S2, and S3, which are important for substrate binding. The most likely hydrolytic mechanism involves nucleophilic attack of a general base (Glu-136)-activated water (OH(-)) on the si-face of the scissile peptide carbonylcarbon atom to form a tetrahedral intermediate. Electrophilic assistance and oxyanion stabilization is provided by the side-chain amide of Gln-53. Protonation of the leaving-group nitrogen is accomplished by the general acid function of the protonated carboxyl group of Glu-136.
About this Structure
1S2B is a Single protein structure of sequence from Scytalidium lignicola. Active as Scytalidopepsin B, with EC number 3.4.23.32 Full crystallographic information is available from OCA.
Reference
The molecular structure and catalytic mechanism of a novel carboxyl peptidase from Scytalidium lignicolum., Fujinaga M, Cherney MM, Oyama H, Oda K, James MN, Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3364-9. Epub 2004 Mar 1. PMID:14993599
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