8d4i - Revision history

OCA at 17:24, 18 October 2023

2023-10-18T17:24:38Z

←Older revision		Revision as of 17:24, 18 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8d4i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8D4I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8D4I FirstGlance]. <br>		<table><tr><td colspan='2'>[[8d4i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8D4I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8D4I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</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]] 1.32Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</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=8d4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8d4i OCA], [https://pdbe.org/8d4i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8d4i RCSB], [https://www.ebi.ac.uk/pdbsum/8d4i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8d4i 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=8d4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8d4i OCA], [https://pdbe.org/8d4i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8d4i RCSB], [https://www.ebi.ac.uk/pdbsum/8d4i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8d4i ProSAT]</span></td></tr>
	</table>		</table>

OCA at 20:15, 16 November 2022

2022-11-16T20:15:58Z

←Older revision		Revision as of 20:15, 16 November 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 8d4i is ~~ON HOLD until Paper~~ Publication	+	==Structure of Y430F D-ornithine/D-lysine decarboxylase complex with putrescine==
		+	<StructureSection load='8d4i' size='340' side='right'caption='[[8d4i]], [[Resolution\|resolution]] 1.32Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8d4i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8D4I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8D4I FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</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=8d4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8d4i OCA], [https://pdbe.org/8d4i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8d4i RCSB], [https://www.ebi.ac.uk/pdbsum/8d4i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8d4i ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DOKDC_SALTY DOKDC_SALTY] Catalyzes the decarboxylation of D-ornithine and D-lysine (PubMed:29024617, PubMed:30699288). Ornithine is likely the physiological substrate (PubMed:29024617). Has no detectable diaminopimelate decarboxylase activity in vitro (PubMed:29024617).<ref>PMID:29024617</ref> <ref>PMID:30699288</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tyrosine-430 of d-ornithine/d-lysine decarboxylase (DOKDC) is located in the active site, and was suggested to be responsible for the D-stereospecificity of the enzyme. We have prepared the Y430F mutant form of Salmonella enterica serovar typhimurium DOKDC and evaluated its catalytic activity with D- and l-lysine and ornithine. The kinetic results show that the Y430F mutant has measurable decarboxylase activity with both D- and l-lysine and ornithine, which wild type DOKDC does not. Spectroscopic experiments show that these amino acids bind to form external aldimine complexes with the pyridoxal-5'-phosphate with lambdamax = 425 nm. In addition, we have obtained crystal structures of Y430F DOKDC bound to HEPES, putrescine, d-ornithine, d-lysine, and d-arginine. The d-amino acids bind in the crystals to form equilibrium mixtures of gem-diamine and external aldimine complexes. Furthermore, the crystal structures reveal an unexpected allosteric product activator site for putrescine located on the 2-fold axis between the two active sites. Putrescine binds by donating hydrogen bonds from the ammonium groups to Asp-361 and Gln-358 in the specificity helix of both chains. Addition of 0.1-1 mM putrescine eliminates the lag in steady state kinetics and abolishes the sigmoid kinetics. The catalytic loop was modeled with AlphaFold2, and the model shows that Glu-181 can form additional hydrogen bonds with the bound putrescine, likely stabilizing the catalytic closed conformation.

-	~~Authors: Phillips, R.S~~., Nguyen Hoang~~, K~~.N.	+	The Y430F mutant of Salmonella d-ornithine/d-lysine decarboxylase has altered stereospecificity and a putrescine allosteric activation site.,Phillips RS, Nguyen Hoang KN Arch Biochem Biophys. 2022 Nov 30;731:109429. doi: 10.1016/j.abb.2022.109429., Epub 2022 Oct 18. PMID:36265649<ref>PMID:36265649</ref>

-	~~Description: Structure~~ of ~~Y430F D-ornithine~~/D-~~lysine decarboxylase complex with putrescine~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Phillips, R~~.S]]	+	<div class="pdbe-citations 8d4i" style="background-color:#fffaf0;"></div>
-	[[Category: Nguyen Hoang~~, K.N~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
		+	[[Category: Nguyen Hoang KN]]
		+	[[Category: Phillips RS]]

OCA at 06:27, 29 June 2022

2022-06-29T06:27:19Z

←Older revision		Revision as of 06:27, 29 June 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8d4i is ON HOLD	+	The entry 8d4i is ON HOLD until Paper Publication

	Authors: Phillips, R.S., Nguyen Hoang, K.N.		Authors: Phillips, R.S., Nguyen Hoang, K.N.

OCA: Protected "8d4i" [edit=sysop:move=sysop]

2022-06-08T04:36:53Z

Protected "8d4i" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:36, 8 June 2022

OCA: New page: '''Unreleased structure''' The entry 8d4i is ON HOLD Authors: Phillips, R.S., Nguyen Hoang, K.N. Description: Structure of Y430F D-ornithine/D-lysine decarboxylase complex with putresc...

2022-06-08T04:36:52Z

New page: '''Unreleased structure''' The entry 8d4i is ON HOLD Authors: Phillips, R.S., Nguyen Hoang, K.N. Description: Structure of Y430F D-ornithine/D-lysine decarboxylase complex with putresc...

New page

'''Unreleased structure'''

The entry 8d4i is ON HOLD

Authors: Phillips, R.S., Nguyen Hoang, K.N.

Description: Structure of Y430F D-ornithine/D-lysine decarboxylase complex with putrescine
[[Category: Unreleased Structures]]
[[Category: Phillips, R.S]]
[[Category: Nguyen Hoang, K.N]]