1yjb: Difference between revisions

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-{{Seed}}
-[[Image:1yjb.png|left|200px]]
-<!--
+==SUBTILISIN BPN' 8397+1 (E.C. 3.4.21.14) (MUTANT WITH MET 50 REPLACED BY PHE, ASN 76 REPLACED BY ASP, GLY 169 REPLACED BY ALA, GLN 206 REPLACED BY CYS, ASN 218 REPLACED BY SER AND LYS 256 REPLACED BY TYR) (M50F, N76D, G169A, Q206C, N218S, AND K256Y) IN 35% DIMETHYLFORMAMIDE==
-The line below this paragraph, containing "STRUCTURE_1yjb", creates the "Structure Box" on the page.
+<StructureSection load='1yjb' size='340' side='right'caption='[[1yjb]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1yjb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YJB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YJB FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
-{{STRUCTURE_1yjb|  PDB=1yjb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yjb OCA], [https://pdbe.org/1yjb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yjb RCSB], [https://www.ebi.ac.uk/pdbsum/1yjb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yjb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SUBT_BACAM SUBT_BACAM] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides. Has a high substrate specificity to fibrin.<ref>PMID:12524032</ref>
+== 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/yj/1yjb_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1yjb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The serine protease subtilisin BPN' is a useful catalyst for peptide synthesis when dissolved in high concentrations of a water-miscible organic co-solvent such as N,N-dimethylformamide (DMF). However, in 50% DMF, the k(cat) for amide hydrolysis is two orders of magnitude lower than in aqueous solution. Surprisingly, the k(cat) for ester hydrolysis is unchanged in 50% DMF. To explain this alteration in activity, the structure of subtilisin 8397+1 was determined in 20, 35, and 50% (v/v) DMF to 1.8 A resolution. In 50% DMF, the imidazole ring of His64, the central residue of the catalytic triad, has rotated approximately 180 degrees around the Cbeta-Cgamma bond. Two new water molecules in the active site stabilize the rotated conformation. This rotation places His64 in an unfavorable geometry to interact with the other members of the catalytic triad, Ser221 and Asp32. NMR experiments confirm that the characteristic resonance due to the low barrier hydrogen bond between the His64 and Asp32 is absent in 50% DMF. These experiments provide a clear structural basis for the change in activity of serine proteases in organic co-solvents.
-===SUBTILISIN BPN' 8397+1 (E.C. 3.4.21.14) (MUTANT WITH MET 50 REPLACED BY PHE, ASN 76 REPLACED BY ASP, GLY 169 REPLACED BY ALA, GLN 206 REPLACED BY CYS, ASN 218 REPLACED BY SER AND LYS 256 REPLACED BY TYR) (M50F, N76D, G169A, Q206C, N218S, AND K256Y) IN 35% DIMETHYLFORMAMIDE===
+Breaking the low barrier hydrogen bond in a serine protease.,Kidd RD, Sears P, Huang DH, Witte K, Wong CH, Farber GK Protein Sci. 1999 Feb;8(2):410-7. PMID:10048334<ref>PMID:10048334</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1yjb" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10048334}}, adds the Publication Abstract to the page
+*[[Subtilisin 3D structures|Subtilisin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10048334 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10048334}}
+__TOC__
+</StructureSection>
-==About this Structure==
-YJB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YJB OCA].
-==Reference==
-Breaking the low barrier hydrogen bond in a serine protease., Kidd RD, Sears P, Huang DH, Witte K, Wong CH, Farber GK, Protein Sci. 1999 Feb;8(2):410-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10048334 10048334]
 [[Category: Bacillus amyloliquefaciens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Subtilisin]]
+[[Category: Farber GK]]
-[[Category: Farber, G K.]]
+[[Category: Kidd RD]]
-[[Category: Kidd, R D.]]
-[[Category: Hydrolase]]
-[[Category: Serine protease]]
-[[Category: Signal]]
-[[Category: Sporulation]]
-[[Category: Zymogen]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 05:17:13 2008''