5xnf - Revision history

OCA at 08:06, 22 November 2023

OCA — Wed, 22 Nov 2023 08:06:50 GMT

←Older revision		Revision as of 08:06, 22 November 2023
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	<StructureSection load='5xnf' size='340' side='right'caption='[[5xnf]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5xnf' size='340' side='right'caption='[[5xnf]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xnf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XNF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xnf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XNF FirstGlance]. <br>
-	</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9Å</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='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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5xnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xnf OCA], [~~http~~://pdbe.org/5xnf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xnf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xnf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xnf 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=5xnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xnf OCA], [https://pdbe.org/5xnf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xnf RCSB], [https://www.ebi.ac.uk/pdbsum/5xnf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xnf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BPSA_THEKO BPSA_THEKO]] 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. Can also use spermine to produce N(4)-aminopropylspermine.<ref>PMID:24610711</ref>	+	[https://www.uniprot.org/uniprot/BPSA_THEKO BPSA_THEKO] 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. Can also use spermine to produce N(4)-aminopropylspermine.<ref>PMID:24610711</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Transferase~~]]	+	[[Category: Thermococcus kodakarensis KOD1]]
-	[[Category: Fujita, J]]	+	[[Category: Fujita J]]
-	[[Category: Inoue, T]]	+	[[Category: Inoue T]]
-	[[Category: Mizohata, E]]	+	[[Category: Mizohata E]]
-	[[Category: Tse~~, K M]]~~	+	[[Category: Tse KM]]
-	~~[[Category: Polyamine biosynthesis~~]]	+

OCA at 06:55, 14 October 2020

OCA — Wed, 14 Oct 2020 06:55:22 GMT

←Older revision		Revision as of 06:55, 14 October 2020
Line 1:		Line 1:

	==Crystal structure of the branched-chain polyamine synthase (BpsA) from Thermococcus kodakarensis==		==Crystal structure of the branched-chain polyamine synthase (BpsA) from Thermococcus kodakarensis==
-	<StructureSection load='5xnf' size='340' side='right' caption='[[5xnf]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5xnf' size='340' side='right'caption='[[5xnf]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xnf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XNF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xnf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XNF 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='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=5xnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xnf OCA], [http://pdbe.org/5xnf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xnf RCSB], [http://www.ebi.ac.uk/pdbsum/5xnf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xnf ProSAT]</span></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=5xnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xnf OCA], [http://pdbe.org/5xnf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xnf RCSB], [http://www.ebi.ac.uk/pdbsum/5xnf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xnf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5xnf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xnf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Spermidine synthase 3D structures\|Spermidine synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Fujita, J]]		[[Category: Fujita, J]]

OCA at 16:07, 15 August 2018

OCA — Wed, 15 Aug 2018 16:07:07 GMT

←Older revision		Revision as of 16:07, 15 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xnf is ~~ON HOLD~~	+	==Crystal structure of the branched-chain polyamine synthase (BpsA) from Thermococcus kodakarensis==
		+	<StructureSection load='5xnf' size='340' side='right' caption='[[5xnf]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xnf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XNF 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5xnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xnf OCA], [http://pdbe.org/5xnf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xnf RCSB], [http://www.ebi.ac.uk/pdbsum/5xnf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xnf ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BPSA_THEKO BPSA_THEKO]] 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. Can also use spermine to produce N(4)-aminopropylspermine.<ref>PMID:24610711</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Branched-chain polyamines are found exclusively in thermophilic bacteria and Euryarchaeota and play essential roles in survival at high temperatures. In the present study, kinetic analyses of a branched-chain polyamine synthase from the hyperthermophilic archaeon Thermococcus kodakarensis (Tk-BpsA) were conducted, showing that N4 -bis(aminopropyl)spermidine was produced by sequential additions of decarboxylated S-adenosylmethionine (dcSAM) aminopropyl groups to spermidine, through bifunctional catalytic action. Tk-BpsA catalyzed the aminopropylation of the linear-chain polyamines spermidine, spermine, norspermidine, and the tertiary-branched polyamines N4 -aminopropylspermidine and N4 -aminopropylnorspermidine, but not of short-chain diamines, putrescine, and cadaverine, suggesting that Tk-BpsA does not catalyze the aminopropylation of primary amino groups of diamines. X-ray structural analyses of Tk-BpsA in the presence or absence of the substrates spermidine and dcSAM revealed that a large, negatively charged cavity is responsible for the binding of branched-chain substrates. The binding is different from that in the active site of linear polyamine spermidine/spermine synthases, and loop-closures occur upon the binding of spermidine. Based on structural analyses, further kinetic studies were carried out for various mutants, revealing that Asp159, positioned between the reactive secondary amino group of the substrate polyamine and a sulfur atom of the product 5'-methylthioadenosine and in a Gly-Asp-Asp-Asp motif, functions as a catalytic center, with reactions proceeding via a ping-pong mechanism. Our study provides a novel aminopropyltransfer reaction mechanism, distinct from the SN 2 displacement mechanism found in other known linear spermidine/spermine synthases. DATABASE: Atomic coordinates and structure factors have been deposited in the Protein Data Bank with PDB codes 5XNF for apo-Tk-BpsA, 5XNH for the binary complex, and 5XNC for the ternary complex.

-	~~Authors: Mizohata, E~~., Tse, ~~K.M.~~, ~~Fujita~~, J., ~~Inoue~~, T.	+	Active site geometry of a novel aminopropyltransferase for biosynthesis of hyperthermophile-specific branched-chain polyamine.,Hidese R, Tse KM, Kimura S, Mizohata E, Fujita J, Horai Y, Umezawa N, Higuchi T, Niitsu M, Oshima T, Imanaka T, Inoue T, Fujiwara S FEBS J. 2017 Sep 7. doi: 10.1111/febs.14262. PMID:28881427<ref>PMID:28881427</ref>

-	~~Description: Crystal structure~~ of the ~~branched~~-~~chain polyamine synthase (BpsA) from Thermococcus kodakarensis~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Tse~~, ~~K.M~~]]	+	<div class="pdbe-citations 5xnf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Transferase]]
		+	[[Category: Fujita, J]]
	[[Category: Inoue, T]]		[[Category: Inoue, T]]
	[[Category: Mizohata, E]]		[[Category: Mizohata, E]]
-	[[Category: ~~Fujita~~, J]]	+	[[Category: Tse, K M]]
		+	[[Category: Polyamine biosynthesis]]

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

OCA — Wed, 27 Sep 2017 15:35:44 GMT

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

←Older revision

Revision as of 15:35, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xnf is ON HOLD Authors: Mizohata, E., Tse, K.M., Fujita, J., Inoue, T. Description: Crystal structure of the branched-chain polyamine synthase (Bp...

OCA — Wed, 27 Sep 2017 15:35:43 GMT

New page: '''Unreleased structure''' The entry 5xnf is ON HOLD Authors: Mizohata, E., Tse, K.M., Fujita, J., Inoue, T. Description: Crystal structure of the branched-chain polyamine synthase (Bp...

New page

'''Unreleased structure'''

The entry 5xnf is ON HOLD

Authors: Mizohata, E., Tse, K.M., Fujita, J., Inoue, T.

Description: Crystal structure of the branched-chain polyamine synthase (BpsA) from Thermococcus kodakarensis
[[Category: Unreleased Structures]]
[[Category: Tse, K.M]]
[[Category: Inoue, T]]
[[Category: Mizohata, E]]
[[Category: Fujita, J]]