3vsb: Difference between revisions

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-[[Image:3vsb.png|left|200px]]
-<!--
+==SUBTILISIN CARLSBERG D-NAPHTHYL-1-ACETAMIDO BORONIC ACID INHIBITOR COMPLEX==
-The line below this paragraph, containing "STRUCTURE_3vsb", creates the "Structure Box" on the page.
+<StructureSection load='3vsb' size='340' side='right'caption='[[3vsb]], [[Resolution|resolution]] 2.60&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'>[[3vsb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VSB 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]] 2.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SBD:D-NAPHTHYL-1-ACETAMIDO+BORONIC+ACID+ALANINE'>SBD</scene></td></tr>
-{{STRUCTURE_3vsb|  PDB=3vsb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vsb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsb OCA], [https://pdbe.org/3vsb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vsb RCSB], [https://www.ebi.ac.uk/pdbsum/3vsb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vsb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SUBC_BACLI SUBC_BACLI] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides (Ref.4, PubMed:11109488). Shows high specificity for aromatic and hydrophobic amino acids in the P1 substrate position (PubMed:11109488). May play an important role in the degradation of feather keratin (PubMed:11109488).<ref>PMID:11109488</ref> <ref>PMID:4967581</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/vs/3vsb_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=3vsb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In order to probe the structural basis of stereoselectivity in the serine protease family, a series of enantiomeric boronic acids RCH2CH(NHCOCH3)B(OH)2 has been synthesized and kinetically characterized as transition-state analog inhibitors using alpha-chymotrypsin and subtilisin Carlsberg as model systems. When the R-substituent in this series was changed from a p-chlorophenyl to a 1-naphthyl group, alpha-chymotrypsin, but not subtilisin, reversed its usual preference for l-enantiomers and bound more tightly to the D-enantiomer [Martichonok, V., &amp; Jones, J. B. (1996) J. Am. Chem. Soc. 118, 950-958]. The structural factors responsible for the differences in stereoselectivity between the two enzymes have been explored by X-ray crystallographic examination of subtilisin Carlsberg and gamma-chymotrypsin complexes of the L- and D-enantiomers of p-chlorophenyl and 1-naphthyl boronic acid derivatives. In both enzymes, the L-isomers of the inhibitors, which are more closely related to the natural L-amino acid substrates, form tetrahedral adducts, covalently linking the central boron atom and Ogamma of the catalytic serine. The d-isomers, however, differ in the way they interact with subtilisin or gamma-chymotrypsin. With subtilisin, both the D-p-chlorophenyl and D-1-naphthyl inhibitor complexes form covalent Ser Ogamma-to-boron bonds, but with gamma-chymotrypsin, the same inhibitors lead to novel tetrahedral adducts covalently linking both Ser195 Ogamma and His57 Nepsilon2 covalently via the boron atom.
-===SUBTILISIN CARLSBERG D-NAPHTHYL-1-ACETAMIDO BORONIC ACID INHIBITOR COMPLEX===
+Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes.,Stoll VS, Eger BT, Hynes RC, Martichonok V, Jones JB, Pai EF Biochemistry. 1998 Jan 13;37(2):451-62. PMID:9425066<ref>PMID:9425066</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_9425066}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3vsb" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 9425066 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_9425066}}
-==About this Structure==
-[[3vsb]] is a 1 chain structure of [[Subtilisin]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSB OCA].
 ==See Also==
-*[[Subtilisin]]
+*[[Subtilisin 3D structures|Subtilisin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:9425066</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus licheniformis]]
-[[Category: Subtilisin]]
+[[Category: Large Structures]]
-[[Category: Eger, B T.]]
+[[Category: Eger BT]]
-[[Category: Hynes, R C.]]
+[[Category: Hynes RC]]
-[[Category: Jones, J B.]]
+[[Category: Jones JB]]
-[[Category: Martichonok, V.]]
+[[Category: Martichonok V]]
-[[Category: Pai, E F.]]
+[[Category: Pai EF]]
-[[Category: Stoll, V S.]]
+[[Category: Stoll VS]]
-[[Category: Boronic acid inhibitor]]
-[[Category: Hydrolase]]
-[[Category: Serine protease]]