5vit - Revision history

OCA at 14:10, 13 March 2024

2024-03-13T14:10:43Z

←Older revision		Revision as of 14:10, 13 March 2024
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	<StructureSection load='5vit' size='340' side='right'caption='[[5vit]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5vit' size='340' side='right'caption='[[5vit]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vit]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VIT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5VIT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vit]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa], [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1] and [https://en.wikipedia.org/wiki/Pseudomonas_protegens_Pf-5 Pseudomonas protegens Pf-5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VIT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MLI:MALONATE+ION'>MLI</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]] 2.203Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5vip\|5vip]], [[5vj1\|5vj1]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[http://en.wikipedia.org/wiki/Malonyl-S-ACP:biotin-protein_carboxyltransferase Malonyl-S-ACP:biotin-protein carboxyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.3.10 2.1.3.10] </~~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=5vit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vit OCA], [https://pdbe.org/5vit PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vit RCSB], [https://www.ebi.ac.uk/pdbsum/5vit PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vit 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=5vit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vit OCA], [~~http~~://pdbe.org/5vit PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vit RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vit PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vit ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~MDCC_PSEF5 MDCC_PSEF5~~]] Subunit of malonate decarboxylase, it is an acyl carrier protein to which acetyl and malonyl thioester residues are bound via a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group and turn over during the catalytic mechanism.	+	[https://www.uniprot.org/uniprot/Q9I6T0_PSEAE Q9I6T0_PSEAE]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Pseudomonas species and other aerobic bacteria have a biotin-independent malonate decarboxylase that is crucial for their utilization of malonate as the sole carbon and energy source. The malonate decarboxylase holoenzyme contains four subunits, having an acyl-carrier protein (MdcC subunit) with a distinct prosthetic group, as well as decarboxylase (MdcD-MdcE) and acyl-carrier protein transferase (MdcA) catalytic activities. Here we report the crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer, as well as biochemical and functional studies based on the structural information. We observe a malonate molecule in the active site of MdcA and we also determine the structure of malonate decarboxylase with CoA in the active site of MdcD-MdcE. Both structures provide molecular insights into malonate decarboxylase catalysis. Mutations in the hetero-tetramer interface can abolish holoenzyme formation. Mutations in the hetero-tetramer interface and the active sites can abolish Pseudomonas aeruginosa growth in a defined medium with malonate as the sole carbon source.Some aerobic bacteria contain a biotin-independent malonate decarboxylase (MDC), which allows them to use malonate as the sole carbon source. Here, the authors present the crystal structure of a Pseudomonas MDC and give insights into its catalytic mechanism and function.	+
-		+
-	Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer.,Maderbocus R, Fields BL, Hamilton K, Luo S, Tran TH, Dietrich LEP, Tong L Nat Commun. 2017 Jul 31;8(1):160. doi: 10.1038/s41467-017-00233-z. PMID:28757619<ref>PMID:28757619</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5vit" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Malonyl-S-ACP:biotin-protein carboxyltransferase~~]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: ~~Maderbocus, R~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: ~~Tong, L]]~~	+	[[Category: Pseudomonas protegens Pf-5]]
-	~~[[Category: Acetyl~~-~~coa carboxylase~~]]	+	[[Category: Maderbocus R]]
-	[[Category: ~~Acyl carrier protein~~]]	+	[[Category: Tong L]]
-	[[Category: ~~Transferase~~]]	+

OCA at 08:37, 30 September 2020

2020-09-30T08:37:49Z

←Older revision		Revision as of 08:37, 30 September 2020
Line 1:		Line 1:

	==Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with malonate==		==Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with malonate==
-	<StructureSection load='5vit' size='340' side='right' caption='[[5vit]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5vit' size='340' side='right'caption='[[5vit]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vit]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VIT OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VIT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vit]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VIT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5VIT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vip\|5vip]], [[5vj1\|5vj1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vip\|5vip]], [[5vj1\|5vj1]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malonyl-S-ACP:biotin-protein_carboxyltransferase Malonyl-S-ACP:biotin-protein carboxyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.3.10 2.1.3.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malonyl-S-ACP:biotin-protein_carboxyltransferase Malonyl-S-ACP:biotin-protein carboxyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.3.10 2.1.3.10] </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=5vit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vit OCA], [http://pdbe.org/5vit PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vit RCSB], [http://www.ebi.ac.uk/pdbsum/5vit PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vit 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=5vit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vit OCA], [http://pdbe.org/5vit PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vit RCSB], [http://www.ebi.ac.uk/pdbsum/5vit PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vit ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Malonyl-S-ACP:biotin-protein carboxyltransferase]]		[[Category: Malonyl-S-ACP:biotin-protein carboxyltransferase]]
	[[Category: Maderbocus, R]]		[[Category: Maderbocus, R]]

OCA at 05:57, 17 August 2017

2017-08-17T05:57:05Z

←Older revision		Revision as of 05:57, 17 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vit is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with malonate==
		+	<StructureSection load='5vit' size='340' side='right' caption='[[5vit]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vit]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VIT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VIT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vip\|5vip]], [[5vj1\|5vj1]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malonyl-S-ACP:biotin-protein_carboxyltransferase Malonyl-S-ACP:biotin-protein carboxyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.3.10 2.1.3.10] </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=5vit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vit OCA], [http://pdbe.org/5vit PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vit RCSB], [http://www.ebi.ac.uk/pdbsum/5vit PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vit ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MDCC_PSEF5 MDCC_PSEF5]] Subunit of malonate decarboxylase, it is an acyl carrier protein to which acetyl and malonyl thioester residues are bound via a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group and turn over during the catalytic mechanism.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pseudomonas species and other aerobic bacteria have a biotin-independent malonate decarboxylase that is crucial for their utilization of malonate as the sole carbon and energy source. The malonate decarboxylase holoenzyme contains four subunits, having an acyl-carrier protein (MdcC subunit) with a distinct prosthetic group, as well as decarboxylase (MdcD-MdcE) and acyl-carrier protein transferase (MdcA) catalytic activities. Here we report the crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer, as well as biochemical and functional studies based on the structural information. We observe a malonate molecule in the active site of MdcA and we also determine the structure of malonate decarboxylase with CoA in the active site of MdcD-MdcE. Both structures provide molecular insights into malonate decarboxylase catalysis. Mutations in the hetero-tetramer interface can abolish holoenzyme formation. Mutations in the hetero-tetramer interface and the active sites can abolish Pseudomonas aeruginosa growth in a defined medium with malonate as the sole carbon source.Some aerobic bacteria contain a biotin-independent malonate decarboxylase (MDC), which allows them to use malonate as the sole carbon source. Here, the authors present the crystal structure of a Pseudomonas MDC and give insights into its catalytic mechanism and function.

-	~~Authors: Maderbocus~~, R., ~~Tong~~, L.	+	Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer.,Maderbocus R, Fields BL, Hamilton K, Luo S, Tran TH, Dietrich LEP, Tong L Nat Commun. 2017 Jul 31;8(1):160. doi: 10.1038/s41467-017-00233-z. PMID:28757619<ref>PMID:28757619</ref>

-	~~Description: Crystal structure of~~ a ~~Pseudomonas malonate decarboxylase hetero-tetramer in complex with malonate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Tong, L~~]]	+	<div class="pdbe-citations 5vit" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Malonyl-S-ACP:biotin-protein carboxyltransferase]]
	[[Category: Maderbocus, R]]		[[Category: Maderbocus, R]]
		+	[[Category: Tong, L]]
		+	[[Category: Acetyl-coa carboxylase]]
		+	[[Category: Acyl carrier protein]]
		+	[[Category: Transferase]]

OCA at 11:21, 4 May 2017

2017-05-04T11:21:27Z

←Older revision		Revision as of 11:21, 4 May 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5vit is ON HOLD	+	The entry 5vit is ON HOLD until Paper Publication

	Authors: Maderbocus, R., Tong, L.		Authors: Maderbocus, R., Tong, L.

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

2017-04-27T12:19:55Z

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

←Older revision

Revision as of 12:19, 27 April 2017

OCA: New page: '''Unreleased structure''' The entry 5vit is ON HOLD Authors: Maderbocus, R., Tong, L. Description: Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex...

2017-04-27T12:19:53Z

New page: '''Unreleased structure''' The entry 5vit is ON HOLD Authors: Maderbocus, R., Tong, L. Description: Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex...

New page

'''Unreleased structure'''

The entry 5vit is ON HOLD

Authors: Maderbocus, R., Tong, L.

Description: Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with malonate
[[Category: Unreleased Structures]]
[[Category: Tong, L]]
[[Category: Maderbocus, R]]