|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structures of the first condensation domain of the CDA synthetase== | | ==Crystal structures of the first condensation domain of the CDA synthetase== |
| - | <StructureSection load='4jn3' size='340' side='right' caption='[[4jn3]], [[Resolution|resolution]] 1.69Å' scene=''> | + | <StructureSection load='4jn3' size='340' side='right'caption='[[4jn3]], [[Resolution|resolution]] 1.69Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4jn3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Strco Strco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JN3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JN3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4jn3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor_A3(2) Streptomyces coelicolor A3(2)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JN3 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.69Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jn5|4jn5]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SCO3230 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=100226 STRCO])</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=4jn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jn3 OCA], [https://pdbe.org/4jn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jn3 RCSB], [https://www.ebi.ac.uk/pdbsum/4jn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jn3 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4jn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jn3 OCA], [http://pdbe.org/4jn3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jn3 RCSB], [http://www.ebi.ac.uk/pdbsum/4jn3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jn3 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| Line 22: |
Line 21: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Strco]] | + | [[Category: Large Structures]] |
| - | [[Category: Bloudoff, K]] | + | [[Category: Bloudoff K]] |
| - | [[Category: Schmeing, T M]] | + | [[Category: Schmeing TM]] |
| - | [[Category: Biosynthetic protein]]
| + | |
| - | [[Category: Calcium-dependent antibiotic]]
| + | |
| - | [[Category: Coa dependant acyltransferase superfamily]]
| + | |
| - | [[Category: Nonribosomal peptide synthetase]]
| + | |
| - | [[Category: Nrps condensation domain]]
| + | |
| - | [[Category: Peptide bond formation]]
| + | |
| Structural highlights
Publication Abstract from PubMed
Nonribosomal peptide synthetases (NRPSs) are large modular macromolecular machines that produce small peptide molecules with wide-ranging biological activities, such as antibiotics and green chemicals. The condensation (C) domain is responsible for amide bond formation, the central chemical step in nonribosomal peptide synthesis. Here we present two crystal structures of the first condensation domain of the calcium-dependent antibiotic (CDA) synthetase (CDA-C1) from Streptomyces coelicolor, determined at resolutions 1.8A and 2.4A. The conformations adopted by CDA-C1 are quite similar in these two structures yet distinct from those seen in other NRPS C domain structures. HPLC-based reaction assays show that this CDA-C1 construct is catalytically active, and small-angle X-ray scattering experiments suggest that the conformation observed in these crystal structures could faithfully represent the conformation in solution. We have performed targeted molecular dynamics simulations, normal mode analyses and energy-minimized linear interpolation to investigate the conformational changes required to transition between the observed structures. We discuss the implications of these conformational changes in the synthetic cycle and of the observation that the "latch" that covers the active site is consistently formed in all studied C domains.
Crystal Structures of the First Condensation Domain of CDA Synthetase Suggest Conformational Changes during the Synthetic Cycle of Nonribosomal Peptide Synthetases.,Bloudoff K, Rodionov D, Schmeing TM J Mol Biol. 2013 Jun 10. pii: S0022-2836(13)00363-X. doi:, 10.1016/j.jmb.2013.06.003. PMID:23756159[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bloudoff K, Rodionov D, Schmeing TM. Crystal Structures of the First Condensation Domain of CDA Synthetase Suggest Conformational Changes during the Synthetic Cycle of Nonribosomal Peptide Synthetases. J Mol Biol. 2013 Jun 10. pii: S0022-2836(13)00363-X. doi:, 10.1016/j.jmb.2013.06.003. PMID:23756159 doi:10.1016/j.jmb.2013.06.003
|
