3oqv: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
Line 3: Line 3:
<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 ==
== Structural highlights ==
<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>
<table><tr><td colspan='2'>[[3oqv]] 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=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" id="ligandDat"><scene name='pdbligand=DTD:DITHIANE+DIOL'>DTD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.9&#8491;</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='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='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>
<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>
</table>
== Function ==
== Function ==
[[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> 
[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 ==
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<ref>PMID:21296757</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3oqv" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 11455]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Charbonnier, J B]]
[[Category: Streptomyces noursei]]
[[Category: Gondry, M]]
[[Category: Charbonnier JB]]
[[Category: Ledu, M H]]
[[Category: Gondry M]]
[[Category: Sauguet, L]]
[[Category: Ledu MH]]
[[Category: Aminoacyl-trna]]
[[Category: Sauguet L]]
[[Category: Cyclodipeptide synthase]]
[[Category: Protein binding]]
[[Category: Rossmann fold]]

Latest revision as of 10:35, 21 February 2024

AlbC, a cyclodipeptide synthase from Streptomyces noursei

3oqv, resolution 1.90Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=3oqv&oldid=4066977"