3s7t - Revision history

OCA at 10:41, 22 June 2022

2022-06-22T10:41:46Z

←Older revision		Revision as of 10:41, 22 June 2022
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	==Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic==		==Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic==
-	<StructureSection load='3s7t' size='340' side='right' caption='[[3s7t]], [[Resolution\|resolution]] 2.81Å' scene=''>	+	<StructureSection load='3s7t' size='340' side='right'caption='[[3s7t]], [[Resolution\|resolution]] 2.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s7t]] 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=3S7T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3S7T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s7t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacld Bacld]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S7T FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oqh\|3oqh]], [[3oqi\|3oqi]], [[3oqj\|3oqj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3oqh\|3oqh]], [[3oqi\|3oqi]], [[3oqj\|3oqj]]</div></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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BL00817, BLi03566, yvmC ([https://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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3s7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s7t OCA], [~~http~~://pdbe.org/3s7t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3s7t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3s7t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3s7t 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=3s7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s7t OCA], [https://pdbe.org/3s7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s7t RCSB], [https://www.ebi.ac.uk/pdbsum/3s7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s7t 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Bacld]]		[[Category: Bacld]]
		+	[[Category: Large Structures]]
	[[Category: Bonnefond, L]]		[[Category: Bonnefond, L]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]

OCA at 05:03, 5 August 2016

2016-08-05T05:03:47Z

←Older revision		Revision as of 05:03, 5 August 2016
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		+
	==Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic==		==Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic==
	<StructureSection load='3s7t' size='340' side='right' caption='[[3s7t]], [[Resolution\|resolution]] 2.81Å' scene=''>		<StructureSection load='3s7t' size='340' side='right' caption='[[3s7t]], [[Resolution\|resolution]] 2.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s7t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_licheniformis Bacillus licheniformis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S7T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s7t]] 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=3S7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S7T FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oqh\|3oqh]], [[3oqi\|3oqi]], [[3oqj\|3oqj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oqh\|3oqh]], [[3oqi\|3oqi]], [[3oqj\|3oqj]]</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=~~1402 Bacillus licheniformis~~])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s7t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s7t RCSB], [http://www.ebi.ac.uk/pdbsum/3s7t PDBsum]</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=3s7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s7t OCA], [http://pdbe.org/3s7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s7t RCSB], [http://www.ebi.ac.uk/pdbsum/3s7t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s7t ProSAT]</span></td></tr>
	</table>		</table>
		+	== 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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 19:
	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 3s7t" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus licheniformis~~]]	+	[[Category: Bacld]]
	[[Category: Bonnefond, L]]		[[Category: Bonnefond, L]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]

OCA at 07:29, 21 December 2014

2014-12-21T07:29:33Z

←Older revision		Revision as of 07:29, 21 December 2014
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-	~~{{STRUCTURE_3s7t\| PDB=3s7t \| SCENE= }}~~	+	==Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic==
-	===Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic===	+	<StructureSection load='3s7t' size='340' side='right' caption='[[3s7t]], [[Resolution\|resolution]] 2.81Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21325056}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3s7t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S7T FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oqh\|3oqh]], [[3oqi\|3oqi]], [[3oqj\|3oqj]]</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=1402 Bacillus licheniformis])</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=3s7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s7t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s7t RCSB], [http://www.ebi.ac.uk/pdbsum/3s7t PDBsum]</span></td></tr>
		+	</table>
		+	<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.

-	~~==About this Structure==~~	+	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>
-	~~[[3s7t]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3S7T OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:021325056</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus licheniformis]]		[[Category: Bacillus licheniformis]]
-	[[Category: Bonnefond, L.]]	+	[[Category: Bonnefond, L]]
-	[[Category: Ishitani, R.]]	+	[[Category: Ishitani, R]]
-	[[Category: Nureki, O.]]	+	[[Category: Nureki, O]]
	[[Category: Cyclodipeptide]]		[[Category: Cyclodipeptide]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]
	[[Category: Trna]]		[[Category: Trna]]

OCA at 08:03, 16 May 2013

2013-05-16T08:03:30Z

←Older revision		Revision as of 08:03, 16 May 2013
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-	[[Image:3s7t.jpg\|left\|200px]]
-
-	<!--
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	{{STRUCTURE_3s7t\| PDB=3s7t \| SCENE= }}		{{STRUCTURE_3s7t\| PDB=3s7t \| SCENE= }}
-
	===Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic===		===Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic===
-
-
-	<!--
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	==Reference==		==Reference==
-	<ref group="xtra">PMID:021325056</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021325056</ref><references group="xtra"/><references/>
	[[Category: Bacillus licheniformis]]		[[Category: Bacillus licheniformis]]
	[[Category: Bonnefond, L.]]		[[Category: Bonnefond, L.]]

OCA at 16:38, 22 June 2011

2011-06-22T16:38:47Z

←Older revision		Revision as of 16:38, 22 June 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3s7t.jpg\|left\|200px]]

-	The ~~entry 3s7t~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3s7t", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3s7t\| PDB=3s7t \| SCENE= }}

-	~~Authors: Bonnefond, L., Ishitani, R., Nureki O~~.	+	===Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic===

-	~~Description~~: ~~Crystal~~ structure ~~of SeMet B~~. licheniformis ~~CDPS YvmC~~-~~Blic~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21325056}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21325056 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21325056}}
		+
		+	==About this Structure==
		+	[[3s7t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S7T OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021325056</ref><references group="xtra"/>
		+	[[Category: Bacillus licheniformis]]
		+	[[Category: Bonnefond, L.]]
		+	[[Category: Ishitani, R.]]
		+	[[Category: Nureki, O.]]
		+	[[Category: Cyclodipeptide]]
		+	[[Category: Ligase]]
		+	[[Category: Rossmann fold]]
		+	[[Category: Trna]]

OCA: Protected "3s7t" [edit=sysop:move=sysop]

2011-06-01T05:29:28Z

Protected "3s7t" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:29, 1 June 2011

OCA: New page: '''Unreleased structure''' The entry 3s7t is ON HOLD Authors: Bonnefond, L., Ishitani, R., Nureki O. Description: Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic

2011-06-01T05:29:28Z

New page: '''Unreleased structure''' The entry 3s7t is ON HOLD Authors: Bonnefond, L., Ishitani, R., Nureki O. Description: Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic

New page

'''Unreleased structure'''

The entry 3s7t is ON HOLD

Authors: Bonnefond, L., Ishitani, R., Nureki O.

Description: Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic