3oqv

From Proteopedia

(Difference between revisions)

Revision as of 10:53, 18 May 2022

AlbC, a cyclodipeptide synthase from Streptomyces noursei

Structural highlights

3oqv is a 1 chain structure with sequence from Atcc 11455. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	albC (ATCC 11455)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 (CDPSs) belong to a newly defined family of enzymes that use aminoacyl-tRNAs (aa-tRNAs) as substrates to synthesize the two peptide bonds of various cyclodipeptides, which are the precursors of many natural products with noteworthy biological activities. Here, we describe the crystal structure of AlbC, a CDPS from Streptomyces noursei. The AlbC structure consists of a monomer containing a Rossmann-fold domain. Strikingly, it is highly similar to the catalytic domain of class-I aminoacyl-tRNA synthetases (aaRSs), especially class-Ic TyrRSs and TrpRSs. AlbC contains a deep pocket, highly conserved among CDPSs. Site-directed mutagenesis studies indicate that this pocket accommodates the aminoacyl moiety of the aa-tRNA substrate in a way similar to that used by TyrRSs to recognize their tyrosine substrates. These studies also suggest that the tRNA moiety of the aa-tRNA interacts with AlbC via at least one patch of basic residues, which is conserved among CDPSs but not present in class-Ic aaRSs. AlbC catalyses its two-substrate reaction via a ping-pong mechanism with a covalent intermediate in which l-Phe is shown to be transferred from Phe-tRNA(Phe) to an active serine. These findings provide insight into the molecular bases of the interactions between CDPSs and their aa-tRNAs substrates, and the catalytic mechanism used by CDPSs to achieve the non-ribosomal synthesis of cyclodipeptides.

Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis.,Sauguet L, Moutiez M, Li Y, Belin P, Seguin J, Le Du MH, Thai R, Masson C, Fonvielle M, Pernodet JL, Charbonnier JB, Gondry M Nucleic Acids Res. 2011 May 1;39(10):4475-89. Epub 2011 Feb 3. PMID:21296757^[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
↑ Sauguet L, Moutiez M, Li Y, Belin P, Seguin J, Le Du MH, Thai R, Masson C, Fonvielle M, Pernodet JL, Charbonnier JB, Gondry M. Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis. Nucleic Acids Res. 2011 May 1;39(10):4475-89. Epub 2011 Feb 3. PMID:21296757 doi:10.1093/nar/gkr027

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3oqv"

@@ Line 1: / Line 1: @@
 ==AlbC, a cyclodipeptide synthase from Streptomyces noursei==
-<StructureSection load='3oqv' size='340' side='right' caption='[[3oqv]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='3oqv' size='340' side='right'caption='[[3oqv]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3oqv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11455 Atcc 11455]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OQV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OQV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3oqv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_11455 Atcc 11455]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OQV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OQV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTD:DITHIANE+DIOL'>DTD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTD:DITHIANE+DIOL'>DTD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">albC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1971 ATCC 11455])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">albC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1971 ATCC 11455])</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=3oqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oqv OCA], [http://pdbe.org/3oqv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3oqv RCSB], [http://www.ebi.ac.uk/pdbsum/3oqv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3oqv 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=3oqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oqv OCA], [https://pdbe.org/3oqv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oqv RCSB], [https://www.ebi.ac.uk/pdbsum/3oqv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oqv ProSAT]</span></td></tr>
 </table>
 == 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;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 24: @@
 </StructureSection>
 [[Category: Atcc 11455]]
+[[Category: Large Structures]]
 [[Category: Charbonnier, J B]]
 [[Category: Gondry, M]]

3oqv

From Proteopedia

Revision as of 10:53, 18 May 2022

AlbC, a cyclodipeptide synthase from Streptomyces noursei

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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