5kgn: Difference between revisions
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==1.95A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (2d)== | ==1.95A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (2d)== | ||
<StructureSection load='5kgn' size='340' side='right' caption='[[5kgn]], [[Resolution|resolution]] 1.95Å' scene=''> | <StructureSection load='5kgn' size='340' side='right'caption='[[5kgn]], [[Resolution|resolution]] 1.95Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5kgn]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KGN OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5kgn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KGN FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DTY:D-TYROSINE'>DTY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5kgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kgn OCA], [https://pdbe.org/5kgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kgn RCSB], [https://www.ebi.ac.uk/pdbsum/5kgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kgn 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/GPMI_CAEEL GPMI_CAEEL] Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate.<ref>PMID:15234973</ref> <ref>PMID:17897734</ref> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >1012 members. Functional analysis of the ligands, named ipglycermides, demonstrates sub-nanomolar inhibition of iPGM with complete selectivity over dPGM. The crystal structure of an iPGM macrocyclic peptide complex illuminated an allosteric, locked-open inhibition mechanism placing the cyclic peptide at the bi-domain interface. This binding mode aligns the pendant lariat cysteine thiolate for coordination with the iPGM transition metal ion cluster. The extended charged, hydrophilic binding surface interaction rationalizes the persistent challenges these enzymes have presented to small-molecule screening efforts highlighting the important roles of macrocyclic peptides in expanding chemical diversity for ligand discovery. | |||
Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases.,Yu H, Dranchak P, Li Z, MacArthur R, Munson MS, Mehzabeen N, Baird NJ, Battalie KP, Ross D, Lovell S, Carlow CK, Suga H, Inglese J Nat Commun. 2017 Apr 3;8:14932. doi: 10.1038/ncomms14932. PMID:28368002<ref>PMID:28368002</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5kgn" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Phosphoglycerate mutase 3D structures|Phosphoglycerate mutase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Caenorhabditis elegans]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Synthetic construct]] | ||
[[Category: | [[Category: Battaile KP]] | ||
[[Category: | [[Category: Carlow T]] | ||
[[Category: | [[Category: Dranchak P]] | ||
[[Category: | [[Category: Inglese J]] | ||
[[Category: | [[Category: Li Z]] | ||
[[Category: | [[Category: Lovell S]] | ||
[[Category: | [[Category: MacArthur R]] | ||
[[Category: | [[Category: Mehzabeen N]] | ||
[[Category: | [[Category: Suga H]] | ||
[[Category: | [[Category: Yu H]] | ||