5npu - Revision history

OCA at 13:20, 15 November 2023

OCA — Wed, 15 Nov 2023 13:20:46 GMT

←Older revision		Revision as of 13:20, 15 November 2023
Line 3:		Line 3:
	<StructureSection load='5npu' size='340' side='right'caption='[[5npu]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='5npu' size='340' side='right'caption='[[5npu]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5npu]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NPU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5NPU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5npu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NPU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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]] 3.5Å</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=5npu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5npu OCA], [~~http~~://pdbe.org/5npu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5npu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5npu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5npu ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></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=5npu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5npu OCA], [https://pdbe.org/5npu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5npu RCSB], [https://www.ebi.ac.uk/pdbsum/5npu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5npu ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5npu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5npu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pyruvate decarboxylase\|Pyruvate decarboxylase]]
	== References ==		== References ==
	<references/>		<references/>
Line 21:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Andrews~~, E S.V~~]]	+	[[Category: Andrews ESV]]
-	[[Category: Arcus~~, V L~~]]	+	[[Category: Arcus VL]]
-	[[Category: Buddrus, L]]	+	[[Category: Buddrus L]]
-	[[Category: Crennell~~, S J~~]]	+	[[Category: Crennell SJ]]
-	[[Category: Danson~~, M J~~]]	+	[[Category: Danson MJ]]
-	[[Category: Leak~~, D J]]~~	+	[[Category: Leak DJ]]
-	~~[[Category: Ancestral sequence reconstruction]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Pyruvate decarboxylase~~]]	+

OCA at 10:52, 9 September 2020

OCA — Wed, 09 Sep 2020 10:52:50 GMT

←Older revision		Revision as of 10:52, 9 September 2020
Line 1:		Line 1:

	==Inferred ancestral pyruvate decarboxylase==		==Inferred ancestral pyruvate decarboxylase==
-	<StructureSection load='5npu' size='340' side='right' caption='[[5npu]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='5npu' size='340' side='right'caption='[[5npu]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5npu]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NPU OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NPU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5npu]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NPU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5NPU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></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=5npu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5npu OCA], [http://pdbe.org/5npu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5npu RCSB], [http://www.ebi.ac.uk/pdbsum/5npu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5npu 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=5npu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5npu OCA], [http://pdbe.org/5npu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5npu RCSB], [http://www.ebi.ac.uk/pdbsum/5npu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5npu ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Andrews, E S.V]]		[[Category: Andrews, E S.V]]

OCA at 20:44, 2 December 2018

OCA — Sun, 02 Dec 2018 20:44:06 GMT

←Older revision		Revision as of 20:44, 2 December 2018
Line 3:		Line 3:
	<StructureSection load='5npu' size='340' side='right' caption='[[5npu]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='5npu' size='340' side='right' caption='[[5npu]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5npu]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NPU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5npu]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NPU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></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=5npu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5npu OCA], [http://pdbe.org/5npu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5npu RCSB], [http://www.ebi.ac.uk/pdbsum/5npu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5npu 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=5npu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5npu OCA], [http://pdbe.org/5npu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5npu RCSB], [http://www.ebi.ac.uk/pdbsum/5npu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5npu ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Synthetic construct sequences]]
	[[Category: Andrews, E S.V]]		[[Category: Andrews, E S.V]]
	[[Category: Arcus, V L]]		[[Category: Arcus, V L]]

OCA at 06:27, 18 April 2018

OCA — Wed, 18 Apr 2018 06:27:08 GMT

←Older revision		Revision as of 06:27, 18 April 2018
Line 7:		Line 7:
	<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=5npu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5npu OCA], [http://pdbe.org/5npu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5npu RCSB], [http://www.ebi.ac.uk/pdbsum/5npu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5npu 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=5npu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5npu OCA], [http://pdbe.org/5npu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5npu RCSB], [http://www.ebi.ac.uk/pdbsum/5npu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5npu ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a key enzyme in homofermentative metabolism where ethanol is the major product. PDCs are thiamine pyrophosphate- and Mg(2+) ion-dependent enzymes that catalyse the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. As this enzyme class is rare in bacteria, current knowledge of bacterial PDCs is extremely limited. One approach to further the understanding of bacterial PDCs is to exploit the diversity provided by evolution. Ancestral sequence reconstruction (ASR) is a method of computational molecular evolution to infer extinct ancestral protein sequences, which can then be synthesized and experimentally characterized. Through ASR a novel PDC was generated, designated ANC27, that shares only 78% amino-acid sequence identity with its closest extant homologue (Komagataeibacter medellinensis PDC, GenBank accession No. WP_014105323.1), yet is fully functional. Crystals of this PDC diffracted to 3.5 A resolution. The data were merged in space group P3221, with unit-cell parameters a = b = 108.33, c = 322.65 A, and contained two dimers (two tetramer halves) in the asymmetric unit. The structure was solved by molecular replacement using PDB entry 2wvg as a model, and the final R values were Rwork = 0.246 (0.3671 in the highest resolution bin) and Rfree = 0.319 (0.4482 in the highest resolution bin). Comparison with extant bacterial PDCs supports the previously observed correlation between decreased tetramer interface area (and number of interactions) and decreased thermostability.
		+
		+	Crystal structure of an inferred ancestral bacterial pyruvate decarboxylase.,Buddrus L, Andrews ESV, Leak DJ, Danson MJ, Arcus VL, Crennell SJ Acta Crystallogr F Struct Biol Commun. 2018 Mar 1;74(Pt 3):179-186. doi:, 10.1107/S2053230X18002819. Epub 2018 Feb 26. PMID:29497023<ref>PMID:29497023</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5npu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 04:58, 8 March 2018

OCA — Thu, 08 Mar 2018 04:58:45 GMT

←Older revision		Revision as of 04:58, 8 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5npu ~~is ON HOLD until Paper Publication~~	+	==Inferred ancestral pyruvate decarboxylase==
-		+	<StructureSection load='5npu' size='340' side='right' caption='[[5npu]], [[Resolution\|resolution]] 3.50Å' scene=''>
-	~~Authors~~: ~~Buddrus, L~~.~~, Crennell, S~~.~~, Leak, D~~.J.~~, Danson, M~~.J.~~, Andrews, E~~.S.~~V., Arcus, V.L~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5npu]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NPU FirstGlance]. <br>
-	~~Description: INFERRED ANCESTRAL PYRUVATE DECARBOXYLASE~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5npu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5npu OCA], [http://pdbe.org/5npu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5npu RCSB], [http://www.ebi.ac.uk/pdbsum/5npu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5npu ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Danson~~, M.J]]	+	</table>
-	[~~[Category~~: ~~Crennell~~, S]]	+	__TOC__
-	[[Category: ~~Arcus~~, V.L]]	+	</StructureSection>
-	[[Category: ~~Andrews~~, ~~E.S.~~V]]	+	[[Category: Andrews, E S.V]]
		+	[[Category: Arcus, V L]]
	[[Category: Buddrus, L]]		[[Category: Buddrus, L]]
-	[[Category: Leak, D.J]]	+	[[Category: Crennell, S J]]
		+	[[Category: Danson, M J]]
		+	[[Category: Leak, D J]]
		+	[[Category: Ancestral sequence reconstruction]]
		+	[[Category: Lyase]]
		+	[[Category: Pyruvate decarboxylase]]

OCA at 11:38, 27 September 2017

OCA — Wed, 27 Sep 2017 11:38:55 GMT

←Older revision		Revision as of 11:38, 27 September 2017
Line 3:		Line 3:
	The entry 5npu is ON HOLD until Paper Publication		The entry 5npu is ON HOLD until Paper Publication

-	Authors: ~~BUDDRUS~~, L., ~~CRENNELL~~, S., ~~LEAK~~, D.J., ~~DANSON~~, M.J., ~~ANDREWS~~, E.S.V., ~~ARCUS~~, V.L.	+	Authors: Buddrus, L., Crennell, S., Leak, D.J., Danson, M.J., Andrews, E.S.V., Arcus, V.L.

	Description: INFERRED ANCESTRAL PYRUVATE DECARBOXYLASE		Description: INFERRED ANCESTRAL PYRUVATE DECARBOXYLASE

OCA at 09:13, 10 May 2017

OCA — Wed, 10 May 2017 09:13:22 GMT

←Older revision		Revision as of 09:13, 10 May 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: BUDDRUS, L., CRENNELL, S., LEAK, D.J., DANSON, M.J., ANDREWS, E.S.V., ARCUS, V.L.		Authors: BUDDRUS, L., CRENNELL, S., LEAK, D.J., DANSON, M.J., ANDREWS, E.S.V., ARCUS, V.L.

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

OCA — Thu, 27 Apr 2017 10:45:59 GMT

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

←Older revision

Revision as of 10:45, 27 April 2017

OCA: New page: '''Unreleased structure''' The entry 5npu is ON HOLD Authors: BUDDRUS, L., CRENNELL, S., LEAK, D.J., DANSON, M.J., ANDREWS, E.S.V., ARCUS, V.L. Description: INFERRED ANCESTRAL PYRUVATE...

OCA — Thu, 27 Apr 2017 10:45:57 GMT

New page: '''Unreleased structure''' The entry 5npu is ON HOLD Authors: BUDDRUS, L., CRENNELL, S., LEAK, D.J., DANSON, M.J., ANDREWS, E.S.V., ARCUS, V.L. Description: INFERRED ANCESTRAL PYRUVATE...

New page

'''Unreleased structure'''

The entry 5npu is ON HOLD

Authors: BUDDRUS, L., CRENNELL, S., LEAK, D.J., DANSON, M.J., ANDREWS, E.S.V., ARCUS, V.L.

Description: INFERRED ANCESTRAL PYRUVATE DECARBOXYLASE
[[Category: Unreleased Structures]]
[[Category: Danson, M.J]]
[[Category: Crennell, S]]
[[Category: Arcus, V.L]]
[[Category: Andrews, E.S.V]]
[[Category: Buddrus, L]]
[[Category: Leak, D.J]]