5es7: Difference between revisions
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
<StructureSection load='5es7' size='340' side='right'caption='[[5es7]], [[Resolution|resolution]] 2.81Å' scene=''> | <StructureSection load='5es7' size='340' side='right'caption='[[5es7]], [[Resolution|resolution]] 2.81Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5es7]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5es7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ES7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ES7 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</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]] 2.805Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</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=5es7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5es7 OCA], [https://pdbe.org/5es7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5es7 RCSB], [https://www.ebi.ac.uk/pdbsum/5es7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5es7 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/LGRA_BREPA LGRA_BREPA] Activates valine (or leucine, but much less frequently), and then glycine and catalyzes the formation of the peptide bond in the first step of peptide synthesis. This enzyme may also play a role in N-formylation of the first amino acid residue in the synthesized dipeptide. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 20: | Line 19: | ||
</div> | </div> | ||
<div class="pdbe-citations 5es7" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5es7" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Linear gramicidin synthase|Linear gramicidin synthase]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Brevibacillus parabrevis]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Aloise | [[Category: Aloise MN]] | ||
[[Category: Reimer | [[Category: Reimer JM]] | ||
[[Category: Schmeing | [[Category: Schmeing TM]] | ||
Latest revision as of 11:20, 12 July 2023
Crystal structure of the F-A domains of the LgrA initiation module soaked with FON, AMPcPP, and valine.Crystal structure of the F-A domains of the LgrA initiation module soaked with FON, AMPcPP, and valine.
Structural highlights
FunctionLGRA_BREPA Activates valine (or leucine, but much less frequently), and then glycine and catalyzes the formation of the peptide bond in the first step of peptide synthesis. This enzyme may also play a role in N-formylation of the first amino acid residue in the synthesized dipeptide. Publication Abstract from PubMedNonribosomal peptide synthetases (NRPSs) are very large proteins that produce small peptide molecules with wide-ranging biological activities, including environmentally friendly chemicals and many widely used therapeutics. NRPSs are macromolecular machines, with modular assembly-line logic, a complex catalytic cycle, moving parts and many active sites. In addition to the core domains required to link the substrates, they often include specialized tailoring domains, which introduce chemical modifications and allow the product to access a large expanse of chemical space. It is still unknown how the NRPS tailoring domains are structurally accommodated into megaenzymes or how they have adapted to function in nonribosomal peptide synthesis. Here we present a series of crystal structures of the initiation module of an antibiotic-producing NRPS, linear gramicidin synthetase. This module includes the specialized tailoring formylation domain, and states are captured that represent every major step of the assembly-line synthesis in the initiation module. The transitions between conformations are large in scale, with both the peptidyl carrier protein domain and the adenylation subdomain undergoing huge movements to transport substrate between distal active sites. The structures highlight the great versatility of NRPSs, as small domains repurpose and recycle their limited interfaces to interact with their various binding partners. Understanding tailoring domains is important if NRPSs are to be utilized in the production of novel therapeutics. Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase.,Reimer JM, Aloise MN, Harrison PM, Schmeing TM Nature. 2016 Jan 14;529(7585):239-42. doi: 10.1038/nature16503. PMID:26762462[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||