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1s2b

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(New page: 200px<br /><applet load="1s2b" size="450" color="white" frame="true" align="right" spinBox="true" caption="1s2b, resolution 2.1&Aring;" /> '''Structure of SCP-B th...)
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[[Image:1s2b.jpg|left|200px]]<br /><applet load="1s2b" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1s2b, resolution 2.1&Aring;" />
 
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'''Structure of SCP-B the first member of the Eqolisin family of Peptidases to have its structure determined'''<br />
 
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==Overview==
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==Structure of SCP-B the first member of the Eqolisin family of Peptidases to have its structure determined==
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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.
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<StructureSection load='1s2b' size='340' side='right'caption='[[1s2b]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1s2b]] is a 1 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=1S2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S2B FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s2b OCA], [https://pdbe.org/1s2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s2b RCSB], [https://www.ebi.ac.uk/pdbsum/1s2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s2b ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PRTB_SCYLI PRTB_SCYLI]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s2/1s2b_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1s2b ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S2B OCA].
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*[[Pepsin|Pepsin]]
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__TOC__
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==Reference==
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</StructureSection>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14993599 14993599]
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[[Category: Large Structures]]
[[Category: Scytalidium lignicola]]
[[Category: Scytalidium lignicola]]
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[[Category: Scytalidopepsin B]]
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[[Category: Cherney MM]]
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[[Category: Single protein]]
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[[Category: Fujinaga M]]
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[[Category: Cherney, M.M.]]
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[[Category: James MN]]
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[[Category: Fujinaga, M.]]
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[[Category: Oda K]]
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[[Category: James, M.N.]]
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[[Category: Oyama H]]
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[[Category: Oda, K.]]
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[[Category: Oyama, H.]]
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[[Category: beta sandwich]]
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[[Category: carboxyl peptidase]]
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[[Category: eqolisin family]]
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[[Category: protease]]
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[[Category: proteinase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:02:59 2007''
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Current revision

Structure of SCP-B the first member of the Eqolisin family of Peptidases to have its structure determined

PDB ID 1s2b

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