3vz1 - Revision history

OCA at 12:42, 8 November 2023

2023-11-08T12:42:44Z

←Older revision		Revision as of 12:42, 8 November 2023
Line 3:		Line 3:
	<StructureSection load='3vz1' size='340' side='right'caption='[[3vz1]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3vz1' size='340' side='right'caption='[[3vz1]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vz1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Agmenellum_quadruplicatum Agmenellum quadruplicatum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VZ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vz1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_sp._PCC_7002 Synechococcus sp. PCC 7002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VZ1 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[3vz0\|3vz0]], [[3vz2\|3vz2]], [[3vz3\|3vz3]]</div></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]] 2.1Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">SYNPCC7002_A2771 ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=32049 Agmenellum quadruplicatum])~~</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=3vz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vz1 OCA], [https://pdbe.org/3vz1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vz1 RCSB], [https://www.ebi.ac.uk/pdbsum/3vz1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vz1 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=3vz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vz1 OCA], [https://pdbe.org/3vz1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vz1 RCSB], [https://www.ebi.ac.uk/pdbsum/3vz1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vz1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B1XMM6_SYNP2 B1XMM6_SYNP2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Agmenellum quadruplicatum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Wei, D~~]]	+	[[Category: Synechococcus sp. PCC 7002]]
-	[[Category: ~~Yin, B~~]]	+	[[Category: Wei D]]
-	[[Category: ~~Yuan, Y A~~]]	+	[[Category: Yin B]]
-	[[Category: Yuan~~, Z~~]]	+	[[Category: Yuan YA]]
-	[[Category: ~~Cofactor preference]]~~	+	[[Category: Yuan Z]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Substrate selection~~]]	+

OCA at 19:11, 27 July 2022

2022-07-27T19:11:18Z

←Older revision		Revision as of 19:11, 27 July 2022
Line 1:		Line 1:

	==Structural insights into substrate and cofactor selelction by sp2771==		==Structural insights into substrate and cofactor selelction by sp2771==
-	<StructureSection load='3vz1' size='340' side='right' caption='[[3vz1]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3vz1' size='340' side='right'caption='[[3vz1]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vz1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Agmenellum_quadruplicatum Agmenellum quadruplicatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VZ1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VZ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vz1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agmenellum_quadruplicatum Agmenellum quadruplicatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VZ1 FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vz0\|3vz0]], [[3vz2\|3vz2]], [[3vz3\|3vz3]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vz0\|3vz0]], [[3vz2\|3vz2]], [[3vz3\|3vz3]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SYNPCC7002_A2771 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=32049 Agmenellum quadruplicatum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SYNPCC7002_A2771 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=32049 Agmenellum quadruplicatum])</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=3vz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vz1 OCA], [~~http~~://pdbe.org/3vz1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vz1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vz1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vz1 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=3vz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vz1 OCA], [https://pdbe.org/3vz1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vz1 RCSB], [https://www.ebi.ac.uk/pdbsum/3vz1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vz1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Agmenellum quadruplicatum]]		[[Category: Agmenellum quadruplicatum]]
		+	[[Category: Large Structures]]
	[[Category: Wei, D]]		[[Category: Wei, D]]
	[[Category: Yin, B]]		[[Category: Yin, B]]

OCA at 10:56, 11 August 2016

2016-08-11T10:56:06Z

←Older revision		Revision as of 10:56, 11 August 2016
Line 1:		Line 1:
		+
	==Structural insights into substrate and cofactor selelction by sp2771==		==Structural insights into substrate and cofactor selelction by sp2771==
	<StructureSection load='3vz1' size='340' side='right' caption='[[3vz1]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3vz1' size='340' side='right' caption='[[3vz1]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vz1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Synechococcus_sp._pcc_7002 Synechococcus sp. pcc 7002~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VZ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VZ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vz1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Agmenellum_quadruplicatum Agmenellum quadruplicatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VZ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VZ1 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vz0\|3vz0]], [[3vz2\|3vz2]], [[3vz3\|3vz3]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vz0\|3vz0]], [[3vz2\|3vz2]], [[3vz3\|3vz3]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SYNPCC7002_A2771 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=32049 ~~Synechococcus sp. PCC 7002~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SYNPCC7002_A2771 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=32049 Agmenellum quadruplicatum])</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=3vz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vz1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vz1 RCSB], [http://www.ebi.ac.uk/pdbsum/3vz1 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=3vz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vz1 OCA], [http://pdbe.org/3vz1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vz1 RCSB], [http://www.ebi.ac.uk/pdbsum/3vz1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vz1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 3vz1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 22:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Synechococcus sp. pcc 7002~~]]	+	[[Category: Agmenellum quadruplicatum]]
	[[Category: Wei, D]]		[[Category: Wei, D]]
	[[Category: Yin, B]]		[[Category: Yin, B]]

OCA at 09:28, 4 January 2015

2015-01-04T09:28:11Z

←Older revision		Revision as of 09:28, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3vz1\| PDB=3vz1 \| SCENE= }}~~	+	==Structural insights into substrate and cofactor selelction by sp2771==
-	===Structural insights into substrate and cofactor selelction by sp2771===	+	<StructureSection load='3vz1' size='340' side='right' caption='[[3vz1]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23500184}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3vz1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synechococcus_sp._pcc_7002 Synechococcus sp. pcc 7002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VZ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VZ1 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vz0\|3vz0]], [[3vz2\|3vz2]], [[3vz3\|3vz3]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SYNPCC7002_A2771 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=32049 Synechococcus sp. PCC 7002])</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=3vz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vz1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vz1 RCSB], [http://www.ebi.ac.uk/pdbsum/3vz1 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aldehyde dehydrogenase (ALDH) catalyzes the oxidation of aldehydes to carboxylic acids. Cyanobacterium Synechococcus contains one ALDH enzyme (Sp2771), together with a novel 2-oxoglutarate decarboxylase, to complete a non-canonical tricarboxylic acid cycle. However, the molecular mechanisms for substrate selection and cofactor preference by Sp2771 are largely unknown. Here, we report crystal structures of wild type Sp2771, Sp2771 S419A mutant and ternary structure of Sp2771 C262A mutant in complex with NADP(+) and SSA, as well as binary structure of Gluconobacter oxydans aldehyde dehydrogenase (Gox0499) in complex with PEG. Structural comparison of Sp2771 with Gox0499, coupled with mutational analysis, demonstrates that Ser157 residue in Sp2771 and corresponding Pro159 residue in Gox0499 play critical structural roles in determining NADP(+) and NAD(+) preference for Sp2771 and Gox0499, respectively, whereas size and distribution of hydrophobic residues along the substrate binding funnel determine substrate selection. Hence, our work has provided insightful structural information into cofactor and substrate selection by ALDH.

-	~~==About this Structure==~~	+	Structural basis for cofactor and substrate selection by cyanobacterium succinic semialdehyde dehydrogenase.,Yuan Z, Yin B, Wei D, Yuan YR J Struct Biol. 2013 May;182(2):125-35. doi: 10.1016/j.jsb.2013.03.001. Epub 2013 , Mar 13. PMID:23500184<ref>PMID:23500184</ref>
-	~~[[3vz1]] is a~~ 2 ~~chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org~~/~~wiki/Synechococcus_sp~~.~~_pcc_7002 Synechococcus sp~~. ~~pcc 7002]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3VZ1 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:023500184</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Succinate-semialdehyde dehydrogenase\|Succinate-semialdehyde dehydrogenase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Synechococcus sp. pcc 7002]]		[[Category: Synechococcus sp. pcc 7002]]
-	[[Category: Wei, D.]]	+	[[Category: Wei, D]]
-	[[Category: Yin, B.]]	+	[[Category: Yin, B]]
-	[[Category: Yuan, Y A.]]	+	[[Category: Yuan, Y A]]
-	[[Category: Yuan, Z.]]	+	[[Category: Yuan, Z]]
	[[Category: Cofactor preference]]		[[Category: Cofactor preference]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Substrate selection]]		[[Category: Substrate selection]]

OCA at 15:38, 10 July 2013

2013-07-10T15:38:44Z

←Older revision		Revision as of 15:38, 10 July 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_3vz1\| PDB=3vz1 \| SCENE= }}
		+	===Structural insights into substrate and cofactor selelction by sp2771===
		+	{{ABSTRACT_PUBMED_23500184}}

-	~~The entry~~ 3vz1 is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[3vz1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synechococcus_sp._pcc_7002 Synechococcus sp. pcc 7002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VZ1 OCA].

-	~~Authors~~: ~~Yuan, Y.A~~., ~~Yuan, Z~~., Yin, B., ~~Wei~~, D.	+	==Reference==
-		+	<ref group="xtra">PMID:023500184</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Structural insights into substrate and cofactor selelction by sp2771~~	+	[[Category: Synechococcus sp. pcc 7002]]
		+	[[Category: Wei, D.]]
		+	[[Category: Yin, B.]]
		+	[[Category: Yuan, Y A.]]
		+	[[Category: Yuan, Z.]]
		+	[[Category: Cofactor preference]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Substrate selection]]

OCA at 14:03, 27 February 2013

2013-02-27T14:03:55Z

←Older revision		Revision as of 14:03, 27 February 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3vz1 is ON HOLD	+	The entry 3vz1 is ON HOLD until Paper Publication

	Authors: Yuan, Y.A., Yuan, Z., Yin, B., Wei, D.		Authors: Yuan, Y.A., Yuan, Z., Yin, B., Wei, D.

	Description: Structural insights into substrate and cofactor selelction by sp2771		Description: Structural insights into substrate and cofactor selelction by sp2771

OCA at 06:55, 24 October 2012

2012-10-24T06:55:42Z

←Older revision		Revision as of 06:55, 24 October 2012
Line 3:		Line 3:
	The entry 3vz1 is ON HOLD		The entry 3vz1 is ON HOLD

-	Authors: Yuan, Y. A., Yuan, Z, Yin, B, Wei, D	+	Authors: Yuan, Y.A., Yuan, Z., Yin, B., Wei, D.

	Description: Structural insights into substrate and cofactor selelction by sp2771		Description: Structural insights into substrate and cofactor selelction by sp2771

OCA: Protected "3vz1" [edit=sysop:move=sysop]

2012-10-17T06:21:02Z

Protected "3vz1" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:21, 17 October 2012

OCA: New page: '''Unreleased structure''' The entry 3vz1 is ON HOLD Authors: Yuan, Y. A., Yuan, Z, Yin, B, Wei, D Description: Structural insights into substrate and cofactor selelction by sp2771

2012-10-17T06:21:00Z

New page: '''Unreleased structure''' The entry 3vz1 is ON HOLD Authors: Yuan, Y. A., Yuan, Z, Yin, B, Wei, D Description: Structural insights into substrate and cofactor selelction by sp2771

New page

'''Unreleased structure'''

The entry 3vz1 is ON HOLD

Authors: Yuan, Y. A., Yuan, Z, Yin, B, Wei, D

Description: Structural insights into substrate and cofactor selelction by sp2771