6vza - Revision history

OCA at 08:22, 11 October 2023

OCA — Wed, 11 Oct 2023 08:22:45 GMT

←Older revision		Revision as of 08:22, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6vza' size='340' side='right'caption='[[6vza]], [[Resolution\|resolution]] 1.47Å' scene=''>		<StructureSection load='6vza' size='340' side='right'caption='[[6vza]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vza]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Streptomyces_sp.~~_nrrl_f~~-5053 Streptomyces sp. ~~nrrl f~~-5053]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VZA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VZA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vza]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._NRRL_F-5053 Streptomyces sp. NRRL F-5053]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VZA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VZA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=QRP:(3S,8AS)-3-(1H-INDOL-3-YLMETHYL)HEXAHYDROPYRROLO[1,2-A]PYRAZINE-1,4-DIONE'>QRP</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]] 1.47Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6vza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vza OCA], [~~http~~://pdbe.org/6vza PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vza RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vza PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vza ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=QRP:(3S,8AS)-3-(1H-INDOL-3-YLMETHYL)HEXAHYDROPYRROLO[1,2-A]PYRAZINE-1,4-DIONE'>QRP</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=6vza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vza OCA], [https://pdbe.org/6vza PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vza RCSB], [https://www.ebi.ac.uk/pdbsum/6vza PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vza ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Streptomyces sp. ~~nrrl f~~-5053]]	+	[[Category: Streptomyces sp. NRRL F-5053]]
-	[[Category: Jia, X]]	+	[[Category: Jia X]]
-	[[Category: Kobe, B]]	+	[[Category: Kobe B]]
-	[[Category: Luo, Z]]	+	[[Category: Luo Z]]
-	[[Category: Qu, X]]	+	[[Category: Qu X]]
-	[[Category: Sun, C]]	+	[[Category: Sun C]]
-	~~[[Category: Biosynthetic protein]]~~	+
-	~~[[Category: Cyclodipeptide]]~~	+
-	~~[[Category: Cytochrome p450]]~~	+
-	~~[[Category: F5053]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Pyrroloindoline alkaloid]]~~	+
-	~~[[Category: Radical mediated reaction]]~~	+
-	~~[[Category: Regio-selecitivty]]~~	+
-	~~[[Category: Stereo-selectivity]]~~	+
-	~~[[Category: Streptomyce~~]]	+

OCA at 10:53, 24 December 2020

OCA — Thu, 24 Dec 2020 10:53:59 GMT

←Older revision		Revision as of 10:53, 24 December 2020
Line 1:		Line 1:

	==Crystal structure of cytochrome P450 NasF5053 Q65I-A86G mutant variant from Streptomyces sp. NRRL F-5053 in the cyclo-L-Trp-L-Pro-bound state==		==Crystal structure of cytochrome P450 NasF5053 Q65I-A86G mutant variant from Streptomyces sp. NRRL F-5053 in the cyclo-L-Trp-L-Pro-bound state==
-	<StructureSection load='6vza' size='340' side='right'caption='[[6vza]]' scene=''>	+	<StructureSection load='6vza' size='340' side='right'caption='[[6vza]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VZA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VZA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vza]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp._nrrl_f-5053 Streptomyces sp. nrrl f-5053]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VZA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VZA FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vza OCA], [http://pdbe.org/6vza PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vza RCSB], [http://www.ebi.ac.uk/pdbsum/6vza PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vza ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=QRP:(3S,8AS)-3-(1H-INDOL-3-YLMETHYL)HEXAHYDROPYRROLO[1,2-A]PYRAZINE-1,4-DIONE'>QRP</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vza OCA], [http://pdbe.org/6vza PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vza RCSB], [http://www.ebi.ac.uk/pdbsum/6vza PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vza ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial heterodimeric tryptophan-containing diketopiperazines (HTDKPs) are a growing family of bioactive natural products. They are challenging to prepare by chemical routes due to the polycyclic and densely functionalized backbone. Through functional characterization and investigation, we herein identify a family of three related HTDKP-forming cytochrome P450s (NasbB, NasS1868 and NasF5053) and reveal four critical residues (Qln65, Ala86, Ser284 and Val288) that control their regio- and stereo-selectivity to generate diverse dimeric DKP frameworks. Engineering these residues can alter the specificities of the enzymes to produce diverse frameworks. Determining the crystal structures (1.70-1.47 A) of NasF5053 (ligand-free and substrate-bound NasF5053 and its Q65I-A86G and S284A-V288A mutants) and molecular dynamics simulation finally elucidate the specificity-conferring mechanism of these residues. Our results provide a clear molecular and mechanistic basis into this family of HTDKP-forming P450s, laying a solid foundation for rapid access to the molecular diversity of HTDKP frameworks through rational engineering of the P450s.
		+
		+	Molecular basis of regio- and stereo-specificity in biosynthesis of bacterial heterodimeric diketopiperazines.,Sun C, Luo Z, Zhang W, Tian W, Peng H, Lin Z, Deng Z, Kobe B, Jia X, Qu X Nat Commun. 2020 Dec 7;11(1):6251. doi: 10.1038/s41467-020-20022-5. PMID:33288748<ref>PMID:33288748</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6vza" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jia X]]	+	[[Category: Streptomyces sp. nrrl f-5053]]
-	[[Category: Kobe B]]	+	[[Category: Jia, X]]
-	[[Category: Luo Z]]	+	[[Category: Kobe, B]]
-	[[Category: Qu X]]	+	[[Category: Luo, Z]]
-	[[Category: Sun C]]	+	[[Category: Qu, X]]
		+	[[Category: Sun, C]]
		+	[[Category: Biosynthetic protein]]
		+	[[Category: Cyclodipeptide]]
		+	[[Category: Cytochrome p450]]
		+	[[Category: F5053]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Pyrroloindoline alkaloid]]
		+	[[Category: Radical mediated reaction]]
		+	[[Category: Regio-selecitivty]]
		+	[[Category: Stereo-selectivity]]
		+	[[Category: Streptomyce]]

OCA at 07:59, 11 November 2020

OCA — Wed, 11 Nov 2020 07:59:25 GMT

←Older revision		Revision as of 07:59, 11 November 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6vza is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of cytochrome P450 NasF5053 Q65I-A86G mutant variant from Streptomyces sp. NRRL F-5053 in the cyclo-L-Trp-L-Pro-bound state==
-		+	<StructureSection load='6vza' size='340' side='right'caption='[[6vza]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VZA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VZA FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vza OCA], [http://pdbe.org/6vza PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vza RCSB], [http://www.ebi.ac.uk/pdbsum/6vza PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vza ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Jia X]]
		+	[[Category: Kobe B]]
		+	[[Category: Luo Z]]
		+	[[Category: Qu X]]
		+	[[Category: Sun C]]

OCA at 07:24, 1 April 2020

OCA — Wed, 01 Apr 2020 07:24:38 GMT

←Older revision		Revision as of 07:24, 1 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6vza is ON HOLD	+	The entry 6vza is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6vza" [edit=sysop:move=sysop]

OCA — Wed, 04 Mar 2020 05:41:42 GMT

Protected "6vza" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:41, 4 March 2020

OCA: New page: '''Unreleased structure''' The entry 6vza is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 04 Mar 2020 05:41:41 GMT

New page: '''Unreleased structure''' The entry 6vza is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6vza is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]