4gr4 - Revision history

OCA at 11:33, 1 March 2024

OCA — Fri, 01 Mar 2024 11:33:57 GMT

←Older revision		Revision as of 11:33, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4gr4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lydicus Streptomyces lydicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GR4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4gr4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lydicus Streptomyces lydicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GR4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.44Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=4gr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gr4 OCA], [https://pdbe.org/4gr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gr4 RCSB], [https://www.ebi.ac.uk/pdbsum/4gr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gr4 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=4gr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gr4 OCA], [https://pdbe.org/4gr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gr4 RCSB], [https://www.ebi.ac.uk/pdbsum/4gr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gr4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/D1GLU5_9ACTN D1GLU5_9ACTN]		[https://www.uniprot.org/uniprot/D1GLU5_9ACTN D1GLU5_9ACTN]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The biosynthesis of non-ribosomally formed peptides (NRPs), which include important antibiotics such as vancomycin, requires the activation of amino acids through adenylate formation. The biosynthetic gene clusters of NRPs frequently contain genes for small, so-called MbtH-like proteins. Recently it was discovered that these MbtH-like proteins are required for some of the adenylation reactions in NRP biosynthesis, but the mechanism of their interaction with the adenylating enzymes has remained unknown. In this study, we determined the structure of SlgN1, a 3-methylaspartate adenylating enzyme involved in the biosynthesis of the hybrid polyketide/NRP antibiotic streptolydigin. SlgN1 contains an MbtH-like domain at its N-terminus, and our analysis defines the parameters required for an interaction between MbtH-like domains and an adenylating enzyme. Highly conserved tryptophan residues of the MbtH-like domain critically contribute to this interaction. W25 and W35 form a cleft on the surface of the MbtH-like domain, which accommodates the alanine side chain of A433 of the adenylating domain. Mutation of A433 to glutamate abolished the activity of SlgN1. Mutation of S23 of the MbtH-like domain to tyrosine resulted in strongly reduced activity. However, the activity of this S23Y mutant could be completely restored by addition of the intact MbtH-like protein CloY from another organism. This suggests that the interface found in the structure of SlgN1 is the genuine interface between MbtH-like proteins and adenylating enzymes.
-
-	Structural Basis of the Interaction of MbtH-Like Proteins, Putative Regulators of Non-Ribosomal Peptide Biosynthesis, with Adenylating Enzymes.,Herbst DA, Boll B, Zocher G, Stehle T, Heide L J Biol Chem. 2012 Nov 28. PMID:23192349<ref>PMID:23192349</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4gr4" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:11, 26 October 2022

OCA — Wed, 26 Oct 2022 07:11:55 GMT

←Older revision		Revision as of 07:11, 26 October 2022
Line 1:		Line 1:

	==Crystal structure of SlgN1deltaAsub==		==Crystal structure of SlgN1deltaAsub==
-	<StructureSection load='4gr4' size='340' side='right' caption='[[4gr4]], [[Resolution\|resolution]] 2.44Å' scene=''>	+	<StructureSection load='4gr4' size='340' side='right'caption='[[4gr4]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gr4]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~As_4.1412 As 4.1412~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GR4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4GR4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gr4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lydicus Streptomyces lydicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GR4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gr5\|4gr5]]</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=4gr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gr4 OCA], [https://pdbe.org/4gr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gr4 RCSB], [https://www.ebi.ac.uk/pdbsum/4gr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gr4 ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slgN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=47763 AS 4.1412])~~</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=4gr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gr4 OCA], [~~http~~://pdbe.org/4gr4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4gr4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4gr4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4gr4 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D1GLU5_9ACTN D1GLU5_9ACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~As 4 1412~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Herbst, D A~~]]	+	[[Category: Streptomyces lydicus]]
-	[[Category: ~~Stehle, T~~]]	+	[[Category: Herbst DA]]
-	[[Category: ~~Zocher, G~~]]	+	[[Category: Stehle T]]
-	[[Category: ~~Adenylation domain]]~~	+	[[Category: Zocher G]]
-	~~[[Category: Atp binding]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Mbth-like domain]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 19:58, 15 December 2016

OCA — Thu, 15 Dec 2016 19:58:06 GMT

←Older revision		Revision as of 19:58, 15 December 2016
Line 1:		Line 1:
		+
	==Crystal structure of SlgN1deltaAsub==		==Crystal structure of SlgN1deltaAsub==
	<StructureSection load='4gr4' size='340' side='right' caption='[[4gr4]], [[Resolution\|resolution]] 2.44Å' scene=''>		<StructureSection load='4gr4' size='340' side='right' caption='[[4gr4]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gr4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_lydicus Streptomyces lydicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GR4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gr4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1412 As 4.1412]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GR4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gr5\|4gr5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gr5\|4gr5]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slgN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=47763 ~~Streptomyces lydicus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slgN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=47763 AS 4.1412])</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=4gr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gr4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gr4 RCSB], [http://www.ebi.ac.uk/pdbsum/4gr4 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=4gr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gr4 OCA], [http://pdbe.org/4gr4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gr4 RCSB], [http://www.ebi.ac.uk/pdbsum/4gr4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gr4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4gr4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Streptomyces lydicus~~]]	+	[[Category: As 4 1412]]
	[[Category: Herbst, D A]]		[[Category: Herbst, D A]]
	[[Category: Stehle, T]]		[[Category: Stehle, T]]

OCA at 09:30, 10 December 2014

OCA — Wed, 10 Dec 2014 09:30:52 GMT

←Older revision		Revision as of 09:30, 10 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4gr4.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of SlgN1deltaAsub==
		+	<StructureSection load='4gr4' size='340' side='right' caption='[[4gr4]], [[Resolution\|resolution]] 2.44Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4gr4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_lydicus Streptomyces lydicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GR4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gr5\|4gr5]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slgN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=47763 Streptomyces lydicus])</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=4gr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gr4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gr4 RCSB], [http://www.ebi.ac.uk/pdbsum/4gr4 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The biosynthesis of non-ribosomally formed peptides (NRPs), which include important antibiotics such as vancomycin, requires the activation of amino acids through adenylate formation. The biosynthetic gene clusters of NRPs frequently contain genes for small, so-called MbtH-like proteins. Recently it was discovered that these MbtH-like proteins are required for some of the adenylation reactions in NRP biosynthesis, but the mechanism of their interaction with the adenylating enzymes has remained unknown. In this study, we determined the structure of SlgN1, a 3-methylaspartate adenylating enzyme involved in the biosynthesis of the hybrid polyketide/NRP antibiotic streptolydigin. SlgN1 contains an MbtH-like domain at its N-terminus, and our analysis defines the parameters required for an interaction between MbtH-like domains and an adenylating enzyme. Highly conserved tryptophan residues of the MbtH-like domain critically contribute to this interaction. W25 and W35 form a cleft on the surface of the MbtH-like domain, which accommodates the alanine side chain of A433 of the adenylating domain. Mutation of A433 to glutamate abolished the activity of SlgN1. Mutation of S23 of the MbtH-like domain to tyrosine resulted in strongly reduced activity. However, the activity of this S23Y mutant could be completely restored by addition of the intact MbtH-like protein CloY from another organism. This suggests that the interface found in the structure of SlgN1 is the genuine interface between MbtH-like proteins and adenylating enzymes.

-	~~{{STRUCTURE_4gr4\| PDB=4gr4 \| SCENE= }}~~	+	Structural Basis of the Interaction of MbtH-Like Proteins, Putative Regulators of Non-Ribosomal Peptide Biosynthesis, with Adenylating Enzymes.,Herbst DA, Boll B, Zocher G, Stehle T, Heide L J Biol Chem. 2012 Nov 28. PMID:23192349<ref>PMID:23192349</ref>

-	~~===Crystal structure~~ of ~~SlgN1deltaAsub===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_23192349}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[4gr4]] is a 4 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Streptomyces_lydicus Streptomyces lydicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GR4 OCA].~~	+	</StructureSection>
	[[Category: Streptomyces lydicus]]		[[Category: Streptomyces lydicus]]
-	[[Category: Herbst, D A.]]	+	[[Category: Herbst, D A]]
-	[[Category: Stehle, T.]]	+	[[Category: Stehle, T]]
-	[[Category: Zocher, G.]]	+	[[Category: Zocher, G]]
	[[Category: Adenylation domain]]		[[Category: Adenylation domain]]
	[[Category: Atp binding]]		[[Category: Atp binding]]

OCA at 21:18, 12 December 2012

OCA — Wed, 12 Dec 2012 21:18:50 GMT

←Older revision		Revision as of 21:18, 12 December 2012
Line 1:		Line 1:
-	[[Image:4gr4.~~jpg~~\|left\|200px]]	+	[[Image:4gr4.png\|left\|200px]]

	{{STRUCTURE_4gr4\| PDB=4gr4 \| SCENE= }}		{{STRUCTURE_4gr4\| PDB=4gr4 \| SCENE= }}
Line 5:		Line 5:
	===Crystal structure of SlgN1deltaAsub===		===Crystal structure of SlgN1deltaAsub===

		+	{{ABSTRACT_PUBMED_23192349}}

	==About this Structure==		==About this Structure==

OCA at 14:39, 28 November 2012

OCA — Wed, 28 Nov 2012 14:39:35 GMT

←Older revision		Revision as of 14:39, 28 November 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4gr4.jpg\|left\|200px]]

-	~~The entry~~ 4gr4 ~~is ON HOLD~~	+	{{STRUCTURE_4gr4\| PDB=4gr4 \| SCENE= }}

-	~~Authors: Herbst, D.A., Zocher, G., Stehle, T.~~	+	===Crystal structure of SlgN1deltaAsub===

-	~~Description: Crystal~~ structure ~~of SlgN1deltaAsub~~	+
		+	==About this Structure==
		+	[[4gr4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_lydicus Streptomyces lydicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GR4 OCA].
		+	[[Category: Streptomyces lydicus]]
		+	[[Category: Herbst, D A.]]
		+	[[Category: Stehle, T.]]
		+	[[Category: Zocher, G.]]
		+	[[Category: Adenylation domain]]
		+	[[Category: Atp binding]]
		+	[[Category: Ligase]]
		+	[[Category: Mbth-like domain]]
		+	[[Category: Rossmann fold]]

OCA at 06:12, 14 November 2012

OCA — Wed, 14 Nov 2012 06:12:44 GMT

←Older revision		Revision as of 06:12, 14 November 2012
Line 5:		Line 5:
	Authors: Herbst, D.A., Zocher, G., Stehle, T.		Authors: Herbst, D.A., Zocher, G., Stehle, T.

-	Description: Crystal structure of ~~a non-ribosomal peptide synthetase~~	+	Description: Crystal structure of SlgN1deltaAsub

OCA at 04:52, 12 September 2012

OCA — Wed, 12 Sep 2012 04:52:49 GMT

←Older revision		Revision as of 04:52, 12 September 2012
Line 5:		Line 5:
	Authors: Herbst, D.A., Zocher, G., Stehle, T.		Authors: Herbst, D.A., Zocher, G., Stehle, T.

-	Description: Crystal structure of	+	Description: Crystal structure of a non-ribosomal peptide synthetase

OCA: Protected "4gr4" [edit=sysop:move=sysop]

OCA — Wed, 05 Sep 2012 04:56:32 GMT

Protected "4gr4" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:56, 5 September 2012

OCA: New page: '''Unreleased structure''' The entry 4gr4 is ON HOLD Authors: Herbst, D.A., Zocher, G., Stehle, T. Description: Crystal structure of

OCA — Wed, 05 Sep 2012 04:56:31 GMT

New page: '''Unreleased structure''' The entry 4gr4 is ON HOLD Authors: Herbst, D.A., Zocher, G., Stehle, T. Description: Crystal structure of

New page

'''Unreleased structure'''

The entry 4gr4 is ON HOLD

Authors: Herbst, D.A., Zocher, G., Stehle, T.

Description: Crystal structure of