|
|
| (3 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Crystal structure of Cyclo(L-leucyl-L-phenylalanyl) synthase== | | ==Crystal structure of Cyclo(L-leucyl-L-phenylalanyl) synthase== |
| - | <StructureSection load='4q24' size='340' side='right' caption='[[4q24]], [[Resolution|resolution]] 2.90Å' scene=''> | + | <StructureSection load='4q24' size='340' side='right'caption='[[4q24]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4q24]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q24 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q24 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4q24]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_noursei Streptomyces noursei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q24 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q24 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XVE:PHENYLMETHYL+N-[(2S)-4-CHLORO-3-OXO-1-PHENYL-BUTAN-2-YL]CARBAMATE'>XVE</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]] 2.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3oqv|3oqv]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XVE:PHENYLMETHYL+N-[(2S)-4-CHLORO-3-OXO-1-PHENYL-BUTAN-2-YL]CARBAMATE'>XVE</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyclo(L-leucyl-L-phenylalanyl)_synthase Cyclo(L-leucyl-L-phenylalanyl) synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.20 2.3.2.20] </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=4q24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q24 OCA], [https://pdbe.org/4q24 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q24 RCSB], [https://www.ebi.ac.uk/pdbsum/4q24 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q24 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=4q24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q24 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q24 RCSB], [http://www.ebi.ac.uk/pdbsum/4q24 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/CLPS_STRNR CLPS_STRNR]] Involved in the biosynthesis of albonoursin (cyclo[(alpha,beta-dehydro-Phe)-(alpha,beta-dehydro-Leu)]), an antibacterial peptide. It uses activated amino acids in the form of aminoacyl-tRNAs (aa-tRNAs) as substrates to catalyze the ATP-independent formation of cyclodipeptides which are intermediates in diketopiperazine (DKP) biosynthetic pathways. Catalyzes the formation of cyclo(L-Phe-L-Leu) (cFL) as major products from L-L-phenylalanyl-tRNA(Phe) and L-leucyl-tRNA(Leu). AlbC can also incorporate various nonpolar residues, such as L-phenylalanine, L-leucine, L-tyrosine and L-methionine, and to a much lesser extent L-alanine and L-valine, into cyclodipeptides. Indeed, ten possible cyclodipeptides composed of L-phenylalanine, L-leucine, L-tyrosine and L-methionine are all synthesized to detectable amounts by AlbC.<ref>PMID:12498889</ref> <ref>PMID:19430487</ref> | + | [https://www.uniprot.org/uniprot/CLPS_STRNR CLPS_STRNR] Involved in the biosynthesis of albonoursin (cyclo[(alpha,beta-dehydro-Phe)-(alpha,beta-dehydro-Leu)]), an antibacterial peptide. It uses activated amino acids in the form of aminoacyl-tRNAs (aa-tRNAs) as substrates to catalyze the ATP-independent formation of cyclodipeptides which are intermediates in diketopiperazine (DKP) biosynthetic pathways. Catalyzes the formation of cyclo(L-Phe-L-Leu) (cFL) as major products from L-L-phenylalanyl-tRNA(Phe) and L-leucyl-tRNA(Leu). AlbC can also incorporate various nonpolar residues, such as L-phenylalanine, L-leucine, L-tyrosine and L-methionine, and to a much lesser extent L-alanine and L-valine, into cyclodipeptides. Indeed, ten possible cyclodipeptides composed of L-phenylalanine, L-leucine, L-tyrosine and L-methionine are all synthesized to detectable amounts by AlbC.<ref>PMID:12498889</ref> <ref>PMID:19430487</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 18: |
Line 18: |
| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4q24" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Favry, E]] | + | [[Category: Large Structures]] |
| - | [[Category: Gondry, M]] | + | [[Category: Streptomyces noursei]] |
| - | [[Category: Mechulam, Y]] | + | [[Category: Favry E]] |
| - | [[Category: Moutiez, M]] | + | [[Category: Gondry M]] |
| - | [[Category: Schmitt, E]] | + | [[Category: Mechulam Y]] |
| - | [[Category: Seguin, J]] | + | [[Category: Moutiez M]] |
| - | [[Category: Thai, R]] | + | [[Category: Schmitt E]] |
| - | [[Category: Aminoacyl-trna]] | + | [[Category: Seguin J]] |
| - | [[Category: Cyclodipeptide synthase]] | + | [[Category: Thai R]] |
| - | [[Category: Rossmann fold]]
| + | |
| - | [[Category: Transferase-transferase inhibitor complex]]
| + | |
| Structural highlights
Function
CLPS_STRNR Involved in the biosynthesis of albonoursin (cyclo[(alpha,beta-dehydro-Phe)-(alpha,beta-dehydro-Leu)]), an antibacterial peptide. It uses activated amino acids in the form of aminoacyl-tRNAs (aa-tRNAs) as substrates to catalyze the ATP-independent formation of cyclodipeptides which are intermediates in diketopiperazine (DKP) biosynthetic pathways. Catalyzes the formation of cyclo(L-Phe-L-Leu) (cFL) as major products from L-L-phenylalanyl-tRNA(Phe) and L-leucyl-tRNA(Leu). AlbC can also incorporate various nonpolar residues, such as L-phenylalanine, L-leucine, L-tyrosine and L-methionine, and to a much lesser extent L-alanine and L-valine, into cyclodipeptides. Indeed, ten possible cyclodipeptides composed of L-phenylalanine, L-leucine, L-tyrosine and L-methionine are all synthesized to detectable amounts by AlbC.[1] [2]
Publication Abstract from PubMed
Cyclodipeptide synthases form cyclodipeptides from two aminoacyl transfer RNAs. They use a ping-pong mechanism that begins with transfer of the aminoacyl moiety of the first aminoacyl tRNA onto a conserved serine, yielding an aminoacyl enzyme. Combining X-ray crystallography, site-directed mutagenesis and affinity labelling of the cyclodipeptide synthase AlbC, we demonstrate that the covalent intermediate reacts with the aminoacyl moiety of the second aminoacyl tRNA, forming a dipeptidyl enzyme, and identify the aminoacyl-binding sites of the aminoacyl tRNAs.
Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases.,Moutiez M, Schmitt E, Seguin J, Thai R, Favry E, Belin P, Mechulam Y, Gondry M Nat Commun. 2014 Oct 6;5:5141. doi: 10.1038/ncomms6141. PMID:25284085[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Lautru S, Gondry M, Genet R, Pernodet JL. The albonoursin gene Cluster of S noursei biosynthesis of diketopiperazine metabolites independent of nonribosomal peptide synthetases. Chem Biol. 2002 Dec;9(12):1355-64. PMID:12498889
- ↑ Gondry M, Sauguet L, Belin P, Thai R, Amouroux R, Tellier C, Tuphile K, Jacquet M, Braud S, Courcon M, Masson C, Dubois S, Lautru S, Lecoq A, Hashimoto S, Genet R, Pernodet JL. Cyclodipeptide synthases are a family of tRNA-dependent peptide bond-forming enzymes. Nat Chem Biol. 2009 Jun;5(6):414-20. doi: 10.1038/nchembio.175. PMID:19430487 doi:http://dx.doi.org/10.1038/nchembio.175
- ↑ Moutiez M, Schmitt E, Seguin J, Thai R, Favry E, Belin P, Mechulam Y, Gondry M. Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases. Nat Commun. 2014 Oct 6;5:5141. doi: 10.1038/ncomms6141. PMID:25284085 doi:http://dx.doi.org/10.1038/ncomms6141
|
