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2jgp
From Proteopedia
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==Structure of the TycC5-6 PCP-C bidomain of the tyrocidine synthetase TycC== | ==Structure of the TycC5-6 PCP-C bidomain of the tyrocidine synthetase TycC== | ||
| - | <StructureSection load='2jgp' size='340' side='right' caption='[[2jgp]], [[Resolution|resolution]] 1.85Å' scene=''> | + | <StructureSection load='2jgp' size='340' side='right'caption='[[2jgp]], [[Resolution|resolution]] 1.85Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | [[2jgp]] is a 1 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[2jgp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevibacillus_brevis Brevibacillus brevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JGP FirstGlance]. <br> |
| - | <b>[[Ligand|Ligands:]]</b> <scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>< | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2jgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jgp OCA], [https://pdbe.org/2jgp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jgp RCSB], [https://www.ebi.ac.uk/pdbsum/2jgp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jgp ProSAT]</span></td></tr> |
| - | <b>Resources:</b> <span class='plainlinks'>[ | + | </table> |
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/TYCC_BREPA TYCC_BREPA] Incorporates six amino acids (for tyrocidine A, Asn, Gln, Tyr, Val, Orn, and Leu) in their L-configuration into the peptide product. | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
| - | [[Image:Consurf_key_small.gif|right]] | + | [[Image:Consurf_key_small.gif|200px|right]] |
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jg/2jgp_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jg/2jgp_consurf.spt"</scriptWhenChecked> |
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | + | </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=2jgp ConSurf]. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
The crystal structure of the bidomain PCP-C from modules 5 and 6 of the nonribosomal tyrocidine synthetase TycC was determined at 1.8 A resolution. The bidomain structure reveals a V-shaped condensation domain, the canyon-like active site groove of which is associated with the preceding peptidyl carrier protein (PCP) domain at its donor side. The relative arrangement of the PCP and the peptide bond-forming condensation (C) domain places the active sites approximately 50 A apart. Accordingly, this PCP-C structure represents a conformational state prior to peptide transfer from the donor-PCP to the acceptor-PCP domain, implying the existence of additional states of PCP-C domain interaction during catalysis. Additionally, PCP-C exerts a mode of cyclization activity that mimics peptide bond formation catalyzed by C domains. Based on mutational data and pK value analysis of active site residues, it is suggested that nonribosomal peptide bond formation depends on electrostatic interactions rather than on general acid/base catalysis. | The crystal structure of the bidomain PCP-C from modules 5 and 6 of the nonribosomal tyrocidine synthetase TycC was determined at 1.8 A resolution. The bidomain structure reveals a V-shaped condensation domain, the canyon-like active site groove of which is associated with the preceding peptidyl carrier protein (PCP) domain at its donor side. The relative arrangement of the PCP and the peptide bond-forming condensation (C) domain places the active sites approximately 50 A apart. Accordingly, this PCP-C structure represents a conformational state prior to peptide transfer from the donor-PCP to the acceptor-PCP domain, implying the existence of additional states of PCP-C domain interaction during catalysis. Additionally, PCP-C exerts a mode of cyclization activity that mimics peptide bond formation catalyzed by C domains. Based on mutational data and pK value analysis of active site residues, it is suggested that nonribosomal peptide bond formation depends on electrostatic interactions rather than on general acid/base catalysis. | ||
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Structural and functional insights into a peptide bond-forming bidomain from a nonribosomal peptide synthetase.,Samel SA, Schoenafinger G, Knappe TA, Marahiel MA, Essen LO Structure. 2007 Jul;15(7):781-92. PMID:17637339<ref>PMID:17637339</ref> | Structural and functional insights into a peptide bond-forming bidomain from a nonribosomal peptide synthetase.,Samel SA, Schoenafinger G, Knappe TA, Marahiel MA, Essen LO Structure. 2007 Jul;15(7):781-92. PMID:17637339<ref>PMID:17637339</ref> | ||
| - | From | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| + | </div> | ||
| + | <div class="pdbe-citations 2jgp" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Brevibacillus brevis]] | [[Category: Brevibacillus brevis]] | ||
| - | [[Category: Essen | + | [[Category: Large Structures]] |
| - | [[Category: Knappe | + | [[Category: Essen L-O]] |
| - | [[Category: Marahiel | + | [[Category: Knappe TA]] |
| - | [[Category: Samel | + | [[Category: Marahiel MA]] |
| - | [[Category: Schoenafinger | + | [[Category: Samel SA]] |
| - | + | [[Category: Schoenafinger G]] | |
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Current revision
Structure of the TycC5-6 PCP-C bidomain of the tyrocidine synthetase TycC
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