5t3d: Difference between revisions

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<StructureSection load='5t3d' size='340' side='right'caption='[[5t3d]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='5t3d' size='340' side='right'caption='[[5t3d]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5t3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4zxj 4zxj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T3D FirstGlance]. <br>
<table><tr><td colspan='2'>[[5t3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4zxj 4zxj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T3D FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=75C:5-({[(2R,3S)-3-AMINO-4-HYDROXY-2-{[2-({N-[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA-ALANYL}AMINO)ETHYL]SULFANYL}BUTYL]SULFONYL}AMINO)-5-DEOXYADENOSINE'>75C</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]] 2.8&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">entF, b0586, JW0578 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=75C:5-({[(2R,3S)-3-AMINO-4-HYDROXY-2-{[2-({N-[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA-ALANYL}AMINO)ETHYL]SULFANYL}BUTYL]SULFONYL}AMINO)-5-DEOXYADENOSINE'>75C</scene></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=5t3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t3d OCA], [http://pdbe.org/5t3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t3d RCSB], [http://www.ebi.ac.uk/pdbsum/5t3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t3d ProSAT]</span></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=5t3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t3d OCA], [https://pdbe.org/5t3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t3d RCSB], [https://www.ebi.ac.uk/pdbsum/5t3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t3d ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/ENTF_ECOLI ENTF_ECOLI]] Activates the carboxylate group of L-serine via ATP-dependent PPi exchange reactions to the aminoacyladenylate, preparing that molecule for the final stages of enterobactin synthesis. Holo-EntF acts as the catalyst for the formation of the three amide and three ester bonds present in the cyclic (2,3-dihydroxybenzoyl)serine trimer enterobactin, using seryladenylate and acyl-holo-EntB (acylated with 2,3-dihydroxybenzoate by EntE).  
[https://www.uniprot.org/uniprot/ENTF_ECOLI ENTF_ECOLI] Activates the carboxylate group of L-serine via ATP-dependent PPi exchange reactions to the aminoacyladenylate, preparing that molecule for the final stages of enterobactin synthesis. Holo-EntF acts as the catalyst for the formation of the three amide and three ester bonds present in the cyclic (2,3-dihydroxybenzoyl)serine trimer enterobactin, using seryladenylate and acyl-holo-EntB (acylated with 2,3-dihydroxybenzoate by EntE).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Many important natural products are produced by multidomain non-ribosomal peptide synthetases (NRPSs). During synthesis, intermediates are covalently bound to integrated carrier domains and transported to neighbouring catalytic domains in an assembly line fashion. Understanding the structural basis for catalysis with non-ribosomal peptide synthetases will facilitate bioengineering to create novel products. Here we describe the structures of two different holo-non-ribosomal peptide synthetase modules, each revealing a distinct step in the catalytic cycle. One structure depicts the carrier domain cofactor bound to the peptide bond-forming condensation domain, whereas a second structure captures the installation of the amino acid onto the cofactor within the adenylation domain. These structures demonstrate that a conformational change within the adenylation domain guides transfer of intermediates between domains. Furthermore, one structure shows that the condensation and adenylation domains simultaneously adopt their catalytic conformations, increasing the overall efficiency in a revised structural cycle. These structures and the single-particle electron microscopy analysis demonstrate a highly dynamic domain architecture and provide the foundation for understanding the structural mechanisms that could enable engineering of novel non-ribosomal peptide synthetases.
 
Structures of two distinct conformations of holo-non-ribosomal peptide synthetases.,Drake EJ, Miller BR, Shi C, Tarrasch JT, Sundlov JA, Allen CL, Skiniotis G, Aldrich CC, Gulick AM Nature. 2016 Jan 14;529(7585):235-8. doi: 10.1038/nature16163. PMID:26762461<ref>PMID:26762461</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5t3d" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Ecoli]]
[[Category: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Drake, E J]]
[[Category: Drake EJ]]
[[Category: Gulick, A M]]
[[Category: Gulick AM]]
[[Category: Miller, B R]]
[[Category: Miller BR]]
[[Category: Sundlov, J A]]
[[Category: Sundlov JA]]
[[Category: Adenylation]]
[[Category: Biosynthetic protein]]
[[Category: Condensation]]
[[Category: Nonribosomal peptide synthetase]]
[[Category: Nrp]]
[[Category: Pcp]]
[[Category: Phosphopantetheine]]
[[Category: Thioesterase]]

Latest revision as of 15:35, 6 March 2024

Crystal structure of holo-EntF a nonribosomal peptide synthetase in the thioester-forming conformation

5t3d, resolution 2.80Å

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