This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3oqh

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:18, 21 February 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==Crystal structure of B. licheniformis CDPS yvmC-BLIC==
==Crystal structure of B. licheniformis CDPS yvmC-BLIC==
-
<StructureSection load='3oqh' size='340' side='right' caption='[[3oqh]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+
<StructureSection load='3oqh' size='340' side='right'caption='[[3oqh]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3oqh]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacld Bacld]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OQH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OQH FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3oqh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_licheniformis_DSM_13_=_ATCC_14580 Bacillus licheniformis DSM 13 = ATCC 14580]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OQH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OQH FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.901&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3oqi|3oqi]], [[3oqj|3oqj]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BL00817, BLi03566, yvmC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=279010 BACLD])</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=3oqh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oqh OCA], [https://pdbe.org/3oqh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oqh RCSB], [https://www.ebi.ac.uk/pdbsum/3oqh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oqh 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=3oqh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oqh OCA], [http://pdbe.org/3oqh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3oqh RCSB], [http://www.ebi.ac.uk/pdbsum/3oqh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3oqh ProSAT]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/CDLS_BACLD CDLS_BACLD]] Involved in the biosynthesis of pulcherrimin, a red extracellular pigment. 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-Leu-L-Leu) (cLL) from L-leucyl-tRNA(Leu). Can also incorporate various nonpolar residues, such as L-phenylalanine, L-leucine and methionine, into cyclodipeptides.<ref>PMID:19430487</ref> <ref>PMID:21325056</ref>
+
[https://www.uniprot.org/uniprot/CDLS_BACLD CDLS_BACLD] Involved in the biosynthesis of pulcherrimin, a red extracellular pigment. 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-Leu-L-Leu) (cLL) from L-leucyl-tRNA(Leu). Can also incorporate various nonpolar residues, such as L-phenylalanine, L-leucine and methionine, into cyclodipeptides.<ref>PMID:19430487</ref> <ref>PMID:21325056</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Cyclodipeptides are secondary metabolites biosynthesized by many bacteria and exhibit a wide array of biological activities. Recently, a new class of small proteins, named cyclodipeptide synthases (CDPS), which are unrelated to the typical nonribosomal peptide synthetases, was shown to generate several cyclodipeptides, using aminoacyl-tRNAs as substrates. The Mycobacterium tuberculosis CDPS, Rv2275, was found to generate cyclodityrosine through the formation of an aminoacyl-enzyme intermediate and to have a structure and oligomeric state similar to those of the class Ic aminoacyl-tRNA synthetases (aaRSs). However, the poor sequence conservation among CDPSs has raised questions about the architecture and catalytic mechanism of the identified homologs. Here we report the crystal structures of Bacillus licheniformis CDPS YvmC-Blic, in the apo form and complexed with substrate mimics, at 1.7-2.4-A resolutions. The YvmC-Blic structure also exhibits similarity to the class Ic aaRSs catalytic domain. Our mutational analysis confirmed the importance of a set of residues for cyclodileucine formation among the conserved residues localized in the catalytic pocket. Our biochemical data indicated that YvmC-Blic binds tRNA and generates cyclodileucine as a monomer. We were also able to detect the presence of an aminoacyl-enzyme reaction intermediate, but not a dipeptide tRNA intermediate, whose existence was postulated for Rv2275. Instead, our results support a sequential catalytic mechanism for YvmC-Blic, with the successive attachment of two leucine residues on the enzyme via a conserved serine residue. Altogether, our findings suggest that all CDPS enzymes share a common aaRS-like architecture and a catalytic mechanism involving the formation of an enzyme-bound intermediate.
+
-
 
+
-
Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog.,Bonnefond L, Arai T, Sakaguchi Y, Suzuki T, Ishitani R, Nureki O Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):3912-7. Epub 2011 Feb 15. PMID:21325056<ref>PMID:21325056</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3oqh" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Bacld]]
+
[[Category: Bacillus licheniformis DSM 13 = ATCC 14580]]
-
[[Category: Arai, T]]
+
[[Category: Large Structures]]
-
[[Category: Bonnefond, L]]
+
[[Category: Arai T]]
-
[[Category: Ishitani, R]]
+
[[Category: Bonnefond L]]
-
[[Category: Nureki, O]]
+
[[Category: Ishitani R]]
-
[[Category: Suzuki, T]]
+
[[Category: Nureki O]]
-
[[Category: Ligase]]
+
[[Category: Suzuki T]]
-
[[Category: Rossmann fold]]
+
-
[[Category: Trna]]
+

Current revision

Crystal structure of B. licheniformis CDPS yvmC-BLIC

PDB ID 3oqh

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3oqh"
Personal tools