5xnc - Revision history

OCA at 10:19, 27 March 2024

2024-03-27T10:19:21Z

←Older revision		Revision as of 10:19, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5xnc' size='340' side='right'caption='[[5xnc]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='5xnc' size='340' side='right'caption='[[5xnc]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xnc]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XNC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xnc]] is a 7 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=5XNC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XNC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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~~></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]] 1.84Å</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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></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=5xnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xnc OCA], [~~http~~://pdbe.org/5xnc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xnc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xnc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xnc 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=5xnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xnc OCA], [https://pdbe.org/5xnc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xnc RCSB], [https://www.ebi.ac.uk/pdbsum/5xnc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xnc 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;">~~	+
-	~~== 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.	+
-		+
-	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>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5xnc" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 27:		Line 18:
	</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: Branched polyamine]]~~	+
-	~~[[Category: N4-aminopropylspermidine]]~~	+
-	~~[[Category: Polyamine biosynthesis]]~~	+
-	~~[[Category: Spermidine~~]]	+

OCA at 06:55, 14 October 2020

2020-10-14T06:55:14Z

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

	==Crystal structure of the branched-chain polyamine synthase (BpsA) in complex with N4-aminopropylspermidine and 5-methylthioadenosine==		==Crystal structure of the branched-chain polyamine synthase (BpsA) in complex with N4-aminopropylspermidine and 5-methylthioadenosine==
-	<StructureSection load='5xnc' size='340' side='right' caption='[[5xnc]], [[Resolution\|resolution]] 1.84Å' scene=''>	+	<StructureSection load='5xnc' size='340' side='right'caption='[[5xnc]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xnc]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNC OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XNC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xnc]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XNC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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></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=5xnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xnc OCA], [http://pdbe.org/5xnc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xnc RCSB], [http://www.ebi.ac.uk/pdbsum/5xnc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xnc 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=5xnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xnc OCA], [http://pdbe.org/5xnc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xnc RCSB], [http://www.ebi.ac.uk/pdbsum/5xnc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xnc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5xnc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xnc" 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

2018-08-15T16:07:08Z

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

-	~~The entry~~ 5xnc is ~~ON HOLD~~	+	==Crystal structure of the branched-chain polyamine synthase (BpsA) in complex with N4-aminopropylspermidine and 5-methylthioadenosine==
		+	<StructureSection load='5xnc' size='340' side='right' caption='[[5xnc]], [[Resolution\|resolution]] 1.84Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xnc]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XNC FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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></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=5xnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xnc OCA], [http://pdbe.org/5xnc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xnc RCSB], [http://www.ebi.ac.uk/pdbsum/5xnc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xnc 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~~:	+	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~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5xnc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Transferase]]
		+	[[Category: Fujita, J]]
		+	[[Category: Inoue, T]]
		+	[[Category: Mizohata, E]]
		+	[[Category: Tse, K M]]
		+	[[Category: Branched polyamine]]
		+	[[Category: N4-aminopropylspermidine]]
		+	[[Category: Polyamine biosynthesis]]
		+	[[Category: Spermidine]]

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

2017-09-27T15:35:35Z

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

←Older revision

Revision as of 15:35, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xnc is ON HOLD Authors: Description: Category: Unreleased Structures

2017-09-27T15:35:34Z

New page: '''Unreleased structure''' The entry 5xnc is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xnc is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]