6j27 - Revision history

OCA at 09:58, 22 November 2023

OCA — Wed, 22 Nov 2023 09:58:44 GMT

←Older revision		Revision as of 09:58, 22 November 2023
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	<StructureSection load='6j27' size='340' side='right'caption='[[6j27]], [[Resolution\|resolution]] 1.66Å' scene=''>		<StructureSection load='6j27' size='340' side='right'caption='[[6j27]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6j27]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thet2 Thet2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J27 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6J27 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6j27]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J27 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J27 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=N4P:N,N-bis(3-aminopropyl)butane-1,4-diamine'>N4P</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.66Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bpsA, TT_C0171 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=N4P:N,N-bis(3-aminopropyl)butane-1,4-diamine'>N4P</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.128 2.5.1.128] </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=6j27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j27 OCA], [https://pdbe.org/6j27 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j27 RCSB], [https://www.ebi.ac.uk/pdbsum/6j27 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j27 ProSAT]</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=6j27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j27 OCA], [~~http~~://pdbe.org/6j27 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6j27 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6j27 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6j27 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/Q72L89_THET2 Q72L89_THET2]] Involved in the biosynthesis of branched-chain polyamines, which support the growth of thermophiles under high-temperature conditions. Catalyzes the sequential condensation of spermidine with the aminopropyl groups of decarboxylated S-adenosylmethionines to produce N(4)-bis(aminopropyl)spermidine via N(4)-aminopropylspermidine.[HAMAP-Rule:MF_01947]	+	[https://www.uniprot.org/uniprot/Q72L89_THET2 Q72L89_THET2] Involved in the biosynthesis of branched-chain polyamines, which support the growth of thermophiles under high-temperature conditions. Catalyzes the sequential condensation of spermidine with the aminopropyl groups of decarboxylated S-adenosylmethionines to produce N(4)-bis(aminopropyl)spermidine via N(4)-aminopropylspermidine.[HAMAP-Rule:MF_01947]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6j27" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6j27" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Spermidine synthase 3D structures\|Spermidine synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet2]]~~	+	[[Category: Thermus thermophilus HB27]]
-	~~[[Category: Transferase~~]]	+	[[Category: Fujita J]]
-	[[Category: Fujita, J]]	+	[[Category: Inoue T]]
-	[[Category: Inoue, T]]	+	[[Category: Mizohata E]]
-	[[Category: Mizohata, E]]	+	[[Category: Toyoda M]]
-	[[Category: Toyoda, M]]	+
-	~~[[Category: Branched polyamine]]~~	+
-	~~[[Category: Polyamine biosynthesis]]~~	+
-	~~[[Category: Spermidine~~]]	+

OCA at 07:55, 23 October 2019

OCA — Wed, 23 Oct 2019 07:55:21 GMT

←Older revision		Revision as of 07:55, 23 October 2019
Line 3:		Line 3:
	<StructureSection load='6j27' size='340' side='right'caption='[[6j27]], [[Resolution\|resolution]] 1.66Å' scene=''>		<StructureSection load='6j27' size='340' side='right'caption='[[6j27]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6j27]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J27 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J27 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6j27]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J27 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J27 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=N4P:N,N-bis(3-aminopropyl)butane-1,4-diamine'>N4P</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=N4P:N,N-bis(3-aminopropyl)butane-1,4-diamine'>N4P</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bpsA, TT_C0171 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.128 2.5.1.128] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.128 2.5.1.128] </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=6j27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j27 OCA], [http://pdbe.org/6j27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j27 RCSB], [http://www.ebi.ac.uk/pdbsum/6j27 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j27 ProSAT]</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=6j27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j27 OCA], [http://pdbe.org/6j27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j27 RCSB], [http://www.ebi.ac.uk/pdbsum/6j27 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j27 ProSAT]</span></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Thet2]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Fujita, J]]		[[Category: Fujita, J]]

OCA at 06:51, 26 June 2019

OCA — Wed, 26 Jun 2019 06:51:39 GMT

←Older revision		Revision as of 06:51, 26 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6j27 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the branched-chain polyamine synthase from Thermus thermophilus (Tth-BpsA) in complex with N4-aminopropylspermidine and 5'-methylthioadenosine==
		+	<StructureSection load='6j27' size='340' side='right'caption='[[6j27]], [[Resolution\|resolution]] 1.66Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6j27]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J27 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J27 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=N4P:N,N-bis(3-aminopropyl)butane-1,4-diamine'>N4P</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.128 2.5.1.128] </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=6j27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j27 OCA], [http://pdbe.org/6j27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j27 RCSB], [http://www.ebi.ac.uk/pdbsum/6j27 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j27 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q72L89_THET2 Q72L89_THET2]] Involved in the biosynthesis of branched-chain polyamines, which support the growth of thermophiles under high-temperature conditions. Catalyzes the sequential condensation of spermidine with the aminopropyl groups of decarboxylated S-adenosylmethionines to produce N(4)-bis(aminopropyl)spermidine via N(4)-aminopropylspermidine.[HAMAP-Rule:MF_01947]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Branched-chain polyamine synthase (BpsA) catalyzes sequential aminopropyl transfer from the donor, decarboxylated S-adenosylmethionine (dcSAM), to the acceptor, linear-chain polyamine, resulting in the production of a quaternary-branched polyamine via tertiary branched polyamine intermediates. Here, we analyzed the catalytic properties and X-ray crystal structure of Tth-BpsA from Thermus thermophilus and compared them with those of Tk-BpsA from Thermococcus kodakarensis, which revealed differences in acceptor substrate specificity and C-terminal structure between these two enzymes. To investigate the role of the C-terminal flexible region in acceptor recognition, a region (QDEEATTY) in Tth-BpsA was replaced with that in Tk-BpsA (YDDEESSTT) to create chimeric Tth-BpsA C9, which showed a severe reduction in catalytic efficiency toward N(4) -aminopropylnorspermidine, but not toward N(4) -aminopropylspermidine, mimicking Tk-BpsA substrate specificity. Tth-BpsA C9 Tyr(346) and Thr(354) contributed to discrimination between tertiary branched-chain polyamine substrates, suggesting that the C-terminal region of BpsA recognizes acceptor substrates. Liquid chromatography-tandem mass spectrometry analysis on a Tk-BpsA reaction mixture with dcSAM revealed two aminopropyl groups bound to two of five aspartate/glutamate residues (Glu(339) , Asp(342) , Asp(343) , Glu(344) , and Glu(345) ) in the C-terminal flexible region. Mutating each of these five amino acid residues to asparagine/glutamine resulted in a slight decrease in activity. The quadruple mutant D342N/D343N/E344Q/E345Q exhibited a severe reduction in catalytic efficiency, suggesting that these aspartate/glutamate residues function to receive aminopropyl chains. In addition, the X-ray crystal structure of the Tk-BpsA ternary complex bound to N(4) -bis(aminopropyl)spermidine revealed that Asp(126) and Glu(259) interacted with the aminopropyl moiety in N(4) -aminopropylspermidine.

-	~~Authors: Mizohata, E~~., ~~Toyoda~~, M., ~~Fujita~~, J., ~~Inoue~~, T.	+	The C-terminal flexible region of branched-chain polyamine synthase facilitates substrate specificity and catalysis.,Hidese R, Toyoda M, Yoshino KI, Fukuda W, Wihardja GA, Kimura S, Fujita J, Niitsu M, Oshima T, Imanaka T, Mizohata E, Fujiwara S FEBS J. 2019 Jun 4. doi: 10.1111/febs.14949. PMID:31162806<ref>PMID:31162806</ref>

-	~~Description: Crystal structure~~ of the ~~branched~~-~~chain polyamine synthase from Thermus thermophilus (Tth~~-~~BpsA) in complex with N4-aminopropylspermidine and 5'-methylthioadenosine~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Mizohata, E]]~~	+	<div class="pdbe-citations 6j27" style="background-color:#fffaf0;"></div>
-	~~[[Category: Inoue, T~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Transferase]]
	[[Category: Fujita, J]]		[[Category: Fujita, J]]
		+	[[Category: Inoue, T]]
		+	[[Category: Mizohata, E]]
	[[Category: Toyoda, M]]		[[Category: Toyoda, M]]
		+	[[Category: Branched polyamine]]
		+	[[Category: Polyamine biosynthesis]]
		+	[[Category: Spermidine]]

OCA at 09:57, 13 March 2019

OCA — Wed, 13 Mar 2019 09:57:22 GMT

←Older revision		Revision as of 09:57, 13 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6j27 is ON HOLD	+	The entry 6j27 is ON HOLD until Paper Publication

	Authors: Mizohata, E., Toyoda, M., Fujita, J., Inoue, T.		Authors: Mizohata, E., Toyoda, M., Fujita, J., Inoue, T.

OCA: Protected "6j27" [edit=sysop:move=sysop]

OCA — Wed, 09 Jan 2019 04:56:41 GMT

Protected "6j27" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:56, 9 January 2019

OCA: New page: '''Unreleased structure''' The entry 6j27 is ON HOLD Authors: Mizohata, E., Toyoda, M., Fujita, J., Inoue, T. Description: Crystal structure of the branched-chain polyamine synthase fr...

OCA — Wed, 09 Jan 2019 04:56:39 GMT

New page: '''Unreleased structure''' The entry 6j27 is ON HOLD Authors: Mizohata, E., Toyoda, M., Fujita, J., Inoue, T. Description: Crystal structure of the branched-chain polyamine synthase fr...

New page

'''Unreleased structure'''

The entry 6j27 is ON HOLD

Authors: Mizohata, E., Toyoda, M., Fujita, J., Inoue, T.

Description: Crystal structure of the branched-chain polyamine synthase from Thermus thermophilus (Tth-BpsA) in complex with N4-aminopropylspermidine and 5'-methylthioadenosine
[[Category: Unreleased Structures]]
[[Category: Mizohata, E]]
[[Category: Inoue, T]]
[[Category: Fujita, J]]
[[Category: Toyoda, M]]