5n3u - Revision history

OCA at 07:26, 1 May 2024

2024-05-01T07:26:54Z

←Older revision		Revision as of 07:26, 1 May 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/CPCE_NOSS1 CPCE_NOSS1] Required for the chromophorylation of the CpcA gene product.		[https://www.uniprot.org/uniprot/CPCE_NOSS1 CPCE_NOSS1] Required for the chromophorylation of the CpcA gene product.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The light-harvesting phycobilisome in cyanobacteria and red algae requires the lyase-catalyzed chromophorylation of phycobiliproteins. There are three functionally distinct lyase families known. The heterodimeric E/F type is specific for attaching bilins covalently to alpha-subunits of phycocyanins and phycoerythrins. Unlike other lyases, the lyase also has chromophore-detaching activity. A subclass of the E/F-type lyases is, furthermore, capable of chemically modifying the chromophore. Although these enzymes were characterized >25 y ago, their structures remained unknown. We determined the crystal structure of the heterodimer of CpcE/F from Nostoc sp. PCC7120 at 1.89-A resolution. Both subunits are twisted, crescent-shaped alpha-solenoid structures. CpcE has 15 and CpcF 10 helices. The inner (concave) layer of CpcE (helices h2, 4, 6, 8, 10, 12, and 14) and the outer (convex) layer of CpcF (h16, 18, 20, 22, and 24) form a cavity into which the phycocyanobilin chromophore can be modeled. This location of the chromophore is supported by mutations at the interface between the subunits and within the cavity. The structure of a structurally related, isomerizing lyase, PecE/F, that converts phycocyanobilin into phycoviolobilin, was modeled using the CpcE/F structure as template. A H87C88 motif critical for the isomerase activity of PecE/F is located at the loop between h20 and h21, supporting the proposal that the nucleophilic addition of Cys-88 to C10 of phycocyanobilin induces the isomerization of phycocyanobilin into phycoviolobilin. Also, the structure of NblB, involved in phycobilisome degradation could be modeled using CpcE as template. Combined with CpcF, NblB shows a low chromophore-detaching activity.
-
-	Structures and enzymatic mechanisms of phycobiliprotein lyases CpcE/F and PecE/F.,Zhao C, Hoppner A, Xu QZ, Gartner W, Scheer H, Zhou M, Zhao KH Proc Natl Acad Sci U S A. 2017 Nov 27. pii: 1715495114. doi:, 10.1073/pnas.1715495114. PMID:29180420<ref>PMID:29180420</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5n3u" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:00, 8 November 2023

2023-11-08T18:00:59Z

←Older revision		Revision as of 18:00, 8 November 2023
Line 1:		Line 1:

	==The structure of the complex of CpcE and CpcF of phycocyanin lyase from Nostoc sp. PCC7120==		==The structure of the complex of CpcE and CpcF of phycocyanin lyase from Nostoc sp. PCC7120==
-	<StructureSection load='5n3u' size='340' side='right' caption='[[5n3u]], [[Resolution\|resolution]] 1.89Å' scene=''>	+	<StructureSection load='5n3u' size='340' side='right'caption='[[5n3u]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n3u]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Anabaena_7120 Anabaena~~ 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N3U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5N3U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n3u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Nostoc_sp._PCC_7120_=_FACHB-418 Nostoc sp. PCC 7120 = FACHB-418]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5N3U FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~cpcE~~, ~~alr0532 (~~[~~http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=103690 Anabaena 7120~~]~~), cpcF, alr0533 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=103690 Anabaena 7120])~~</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]] 1.89Å</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=5n3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n3u OCA], [~~http~~://pdbe.org/5n3u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5n3u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5n3u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5n3u 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=5n3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n3u OCA], [https://pdbe.org/5n3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5n3u RCSB], [https://www.ebi.ac.uk/pdbsum/5n3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5n3u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CPCE_NOSS1 CPCE_NOSS1~~]] Required for the chromophorylation of the CpcA gene product. [[http://www.uniprot.org/uniprot/CPCF_NOSS1 CPCF_NOSS1]~~] Required for the chromophorylation of the CpcA gene product.	+	[https://www.uniprot.org/uniprot/CPCE_NOSS1 CPCE_NOSS1] Required for the chromophorylation of the CpcA gene product.
	<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: ~~Anabaena~~ 7120]]	+	[[Category: Large Structures]]
-	[[Category: Gaertner, W]]	+	[[Category: Nostoc sp. PCC 7120 = FACHB-418]]
-	[[Category: Hoeppner, A]]	+	[[Category: Gaertner W]]
-	[[Category: Scheer, H]]	+	[[Category: Hoeppner A]]
-	[[Category: Xu, Q Z]]	+	[[Category: Scheer H]]
-	[[Category: Zhao, C]]	+	[[Category: Xu Q-Z]]
-	[[Category: Zhao, K H]]	+	[[Category: Zhao C]]
-	~~[[Category: Chromophorylation]]~~	+	[[Category: Zhao K-H]]
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Phycobilisome]]~~	+
-	~~[[Category: Phycocyanin~~]]	+

OCA at 07:28, 13 December 2017

2017-12-13T07:28:23Z

←Older revision		Revision as of 07:28, 13 December 2017
Line 3:		Line 3:
	<StructureSection load='5n3u' size='340' side='right' caption='[[5n3u]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='5n3u' size='340' side='right' caption='[[5n3u]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n3u]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N3U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n3u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Anabaena_7120 Anabaena 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N3U FirstGlance]. <br>
-	</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=5n3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n3u OCA], [http://pdbe.org/5n3u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n3u RCSB], [http://www.ebi.ac.uk/pdbsum/5n3u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n3u ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cpcE, alr0532 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=103690 Anabaena 7120]), cpcF, alr0533 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=103690 Anabaena 7120])</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=5n3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n3u OCA], [http://pdbe.org/5n3u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n3u RCSB], [http://www.ebi.ac.uk/pdbsum/5n3u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n3u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CPCE_NOSS1 CPCE_NOSS1]] Required for the chromophorylation of the CpcA gene product. [[http://www.uniprot.org/uniprot/CPCF_NOSS1 CPCF_NOSS1]] Required for the chromophorylation of the CpcA gene product.		[[http://www.uniprot.org/uniprot/CPCE_NOSS1 CPCE_NOSS1]] Required for the chromophorylation of the CpcA gene product. [[http://www.uniprot.org/uniprot/CPCF_NOSS1 CPCF_NOSS1]] Required for the chromophorylation of the CpcA gene product.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The light-harvesting phycobilisome in cyanobacteria and red algae requires the lyase-catalyzed chromophorylation of phycobiliproteins. There are three functionally distinct lyase families known. The heterodimeric E/F type is specific for attaching bilins covalently to alpha-subunits of phycocyanins and phycoerythrins. Unlike other lyases, the lyase also has chromophore-detaching activity. A subclass of the E/F-type lyases is, furthermore, capable of chemically modifying the chromophore. Although these enzymes were characterized >25 y ago, their structures remained unknown. We determined the crystal structure of the heterodimer of CpcE/F from Nostoc sp. PCC7120 at 1.89-A resolution. Both subunits are twisted, crescent-shaped alpha-solenoid structures. CpcE has 15 and CpcF 10 helices. The inner (concave) layer of CpcE (helices h2, 4, 6, 8, 10, 12, and 14) and the outer (convex) layer of CpcF (h16, 18, 20, 22, and 24) form a cavity into which the phycocyanobilin chromophore can be modeled. This location of the chromophore is supported by mutations at the interface between the subunits and within the cavity. The structure of a structurally related, isomerizing lyase, PecE/F, that converts phycocyanobilin into phycoviolobilin, was modeled using the CpcE/F structure as template. A H87C88 motif critical for the isomerase activity of PecE/F is located at the loop between h20 and h21, supporting the proposal that the nucleophilic addition of Cys-88 to C10 of phycocyanobilin induces the isomerization of phycocyanobilin into phycoviolobilin. Also, the structure of NblB, involved in phycobilisome degradation could be modeled using CpcE as template. Combined with CpcF, NblB shows a low chromophore-detaching activity.
		+
		+	Structures and enzymatic mechanisms of phycobiliprotein lyases CpcE/F and PecE/F.,Zhao C, Hoppner A, Xu QZ, Gartner W, Scheer H, Zhou M, Zhao KH Proc Natl Acad Sci U S A. 2017 Nov 27. pii: 1715495114. doi:, 10.1073/pnas.1715495114. PMID:29180420<ref>PMID:29180420</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5n3u" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Anabaena 7120]]
	[[Category: Gaertner, W]]		[[Category: Gaertner, W]]
	[[Category: Hoeppner, A]]		[[Category: Hoeppner, A]]

OCA at 07:09, 6 December 2017

2017-12-06T07:09:59Z

←Older revision		Revision as of 07:09, 6 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5n3u ~~is ON HOLD until Paper Publication~~	+	==The structure of the complex of CpcE and CpcF of phycocyanin lyase from Nostoc sp. PCC7120==
-		+	<StructureSection load='5n3u' size='340' side='right' caption='[[5n3u]], [[Resolution\|resolution]] 1.89Å' scene=''>
-	~~Authors~~: ~~Hoeppner, A~~.~~, Zhao, C~~.~~, Xu, Q~~.-Z., ~~Gaertner~~, W., ~~Scheer~~, H., ~~Zhao, K~~.-H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5n3u]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N3U FirstGlance]. <br>
-	~~Description~~: ~~The structure~~ of the ~~complex~~ of ~~CpcE and CpcF of phycocyanin lyase from Nostoc sp~~. ~~PCC7120~~	+	</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=5n3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n3u OCA], [http://pdbe.org/5n3u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n3u RCSB], [http://www.ebi.ac.uk/pdbsum/5n3u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n3u ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Zhao~~, ~~K.-~~H]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CPCE_NOSS1 CPCE_NOSS1]] Required for the chromophorylation of the CpcA gene product. [[http://www.uniprot.org/uniprot/CPCF_NOSS1 CPCF_NOSS1]] Required for the chromophorylation of the CpcA gene product.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gaertner, W]]
		+	[[Category: Hoeppner, A]]
		+	[[Category: Scheer, H]]
		+	[[Category: Xu, Q Z]]
	[[Category: Zhao, C]]		[[Category: Zhao, C]]
-	[[Category: Xu, ~~Q.-Z~~]]	+	[[Category: Zhao, K H]]
-	[[Category: ~~Scheer, H~~]]	+	[[Category: Chromophorylation]]
-	[[Category: ~~Hoeppner, A~~]]	+	[[Category: Lyase]]
-	[[Category: ~~Gaertner, W~~]]	+	[[Category: Phycobilisome]]
		+	[[Category: Phycocyanin]]

OCA: Protected "5n3u" [edit=sysop:move=sysop]

2017-03-09T12:01:01Z

Protected "5n3u" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:01, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5n3u is ON HOLD until Paper Publication Authors: Hoeppner, A., Zhao, C., Xu, Q.-Z., Gaertner, W., Scheer, H., Zhao, K.-H. Description: The structur...

2017-03-09T12:01:00Z

New page: '''Unreleased structure''' The entry 5n3u is ON HOLD until Paper Publication Authors: Hoeppner, A., Zhao, C., Xu, Q.-Z., Gaertner, W., Scheer, H., Zhao, K.-H. Description: The structur...

New page

'''Unreleased structure'''

The entry 5n3u is ON HOLD until Paper Publication

Authors: Hoeppner, A., Zhao, C., Xu, Q.-Z., Gaertner, W., Scheer, H., Zhao, K.-H.

Description: The structure of the complex of CpcE and CpcF of phycocyanin lyase from Nostoc sp. PCC7120
[[Category: Unreleased Structures]]
[[Category: Zhao, K.-H]]
[[Category: Zhao, C]]
[[Category: Xu, Q.-Z]]
[[Category: Scheer, H]]
[[Category: Hoeppner, A]]
[[Category: Gaertner, W]]