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==Structure of SCP-B a member of the Eqolisin family of Peptidases in a complex with a Tripeptide Ala-Ile-His== | |||
<StructureSection load='1s2k' size='340' side='right'caption='[[1s2k]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1s2k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Scytalidium_lignicola Scytalidium lignicola]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S2K FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | |||
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TYR:TYROSINE'>TYR</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s2k OCA], [https://pdbe.org/1s2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s2k RCSB], [https://www.ebi.ac.uk/pdbsum/1s2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s2k ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PRTB_SCYLI PRTB_SCYLI] | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s2/1s2k_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1s2k ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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<ref>PMID:14993599</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1s2k" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Pepsin|Pepsin]] | |||
== References == | |||
== | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Scytalidium lignicola]] | [[Category: Scytalidium lignicola]] | ||
[[Category: Cherney MM]] | |||
[[Category: Fujinaga M]] | |||
[[Category: Cherney | [[Category: James MN]] | ||
[[Category: Fujinaga | [[Category: Oda K]] | ||
[[Category: James | [[Category: Oyama H]] | ||
[[Category: Oda | |||
[[Category: Oyama | |||
Latest revision as of 09:11, 23 August 2023
Structure of SCP-B a member of the Eqolisin family of Peptidases in a complex with a Tripeptide Ala-Ile-HisStructure of SCP-B a member of the Eqolisin family of Peptidases in a complex with a Tripeptide Ala-Ile-His
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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