1tm5: Difference between revisions

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-[[Image:1tm5.jpg|left|200px]]
- {{Structure
+==crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 M59A mutant==
-|PDB= 1tm5 |SIZE=350|CAPTION= <scene name='initialview01'>1tm5</scene>, resolution 1.45&Aring;
+<StructureSection load='1tm5' size='340' side='right'caption='[[1tm5]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene> and <scene name='pdbligand=1PE:PENTAETHYLENE GLYCOL'>1PE</scene>
+<table><tr><td colspan='2'>[[1tm5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens] and [https://en.wikipedia.org/wiki/Hordeum_vulgare_subsp._vulgare Hordeum vulgare subsp. vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TM5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TM5 FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.45&#8491;</td></tr>
-|GENE= APR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1390 Bacillus amyloliquefaciens])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1tm5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tm5 OCA], [https://pdbe.org/1tm5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tm5 RCSB], [https://www.ebi.ac.uk/pdbsum/1tm5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tm5 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/tm/1tm5_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=1tm5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A series of mutants of chymotrypsin inhibitor 2 (CI2), at residues that interact with the inhibited enzyme subtilisin BPN', were studied to determine the relative importance of intermolecular contacts on either side of the scissile bond. Mutants were tested for inhibition of subtilisin, rates of hydrolysis by subtilisin, and ability to acylate subtilisin. Additionally, crystal structures of the mutant CI2 complexes with subtilisin were obtained. Ordered water molecules were found to play an important role in inhibitor recognition, and features of the crystal structures, in combination with biochemical data, support a transition-state stabilization role for the P(1) residue in subtilisin catalysis. Consistent with the proposed mechanism of inhibition, in which rapid acylation is followed by religation, leaving-group contacts with the enzyme were found to be more critical determinants of inhibition than acylating-group contacts in the mutants studied here.
-'''crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 M59A mutant'''
+Binding, proteolytic, and crystallographic analyses of mutations at the protease-inhibitor interface of the subtilisin BPN'/chymotrypsin inhibitor 2 complex.,Radisky ES, Kwan G, Karen Lu CJ, Koshland DE Jr Biochemistry. 2004 Nov 2;43(43):13648-56. PMID:15504027<ref>PMID:15504027</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1tm5" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-A series of mutants of chymotrypsin inhibitor 2 (CI2), at residues that interact with the inhibited enzyme subtilisin BPN', were studied to determine the relative importance of intermolecular contacts on either side of the scissile bond. Mutants were tested for inhibition of subtilisin, rates of hydrolysis by subtilisin, and ability to acylate subtilisin. Additionally, crystal structures of the mutant CI2 complexes with subtilisin were obtained. Ordered water molecules were found to play an important role in inhibitor recognition, and features of the crystal structures, in combination with biochemical data, support a transition-state stabilization role for the P(1) residue in subtilisin catalysis. Consistent with the proposed mechanism of inhibition, in which rapid acylation is followed by religation, leaving-group contacts with the enzyme were found to be more critical determinants of inhibition than acylating-group contacts in the mutants studied here.
+*[[Chymotrypsin inhibitor 3D structures|Chymotrypsin inhibitor 3D structures]]
+*[[Subtilisin 3D structures|Subtilisin 3D structures]]
-==About this Structure==
+== References ==
-TM5 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens] and [http://en.wikipedia.org/wiki/Hordeum_vulgare_subsp._vulgare Hordeum vulgare subsp. vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TM5 OCA].
+<references/>
+__TOC__
-==Reference==
+</StructureSection>
-Binding, proteolytic, and crystallographic analyses of mutations at the protease-inhibitor interface of the subtilisin BPN'/chymotrypsin inhibitor 2 complex., Radisky ES, Kwan G, Karen Lu CJ, Koshland DE Jr, Biochemistry. 2004 Nov 2;43(43):13648-56. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15504027 15504027]
 [[Category: Bacillus amyloliquefaciens]]
 [[Category: Hordeum vulgare subsp. vulgare]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Subtilisin]]
+[[Category: Karen Lu CJ]]
-[[Category: Jr., D E.Koshland.]]
+[[Category: Koshland Jr DE]]
-[[Category: Kwan, G.]]
+[[Category: Kwan G]]
-[[Category: Lu, C J.Karen.]]
+[[Category: Radisky ES]]
-[[Category: Radisky, E S.]]
-[[Category: 1PE]]
-[[Category: CA]]
-[[Category: CIT]]
-[[Category: NA]]
-[[Category: inhibitor]]
-[[Category: serine protease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:20:13 2008''