4xh4 - Revision history

OCA at 15:27, 8 November 2023

OCA — Wed, 08 Nov 2023 15:27:53 GMT

←Older revision		Revision as of 15:27, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xh4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XH4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xh4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XH4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</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]] 1.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</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'>[https://proteopedia.org/fgij/fg.htm?mol=4xh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xh4 OCA], [https://pdbe.org/4xh4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xh4 RCSB], [https://www.ebi.ac.uk/pdbsum/4xh4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xh4 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=4xh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xh4 OCA], [https://pdbe.org/4xh4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xh4 RCSB], [https://www.ebi.ac.uk/pdbsum/4xh4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xh4 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 09:58, 19 April 2023

OCA — Wed, 19 Apr 2023 09:58:45 GMT

←Older revision		Revision as of 09:58, 19 April 2023
Line 1:		Line 1:

	==Crystal structure of Salmonella typhimurium propionate kinase A88V mutant, in complex with AMPPNP and propionate==		==Crystal structure of Salmonella typhimurium propionate kinase A88V mutant, in complex with AMPPNP and propionate==
-	<StructureSection load='4xh4' size='340' side='right' caption='[[4xh4]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='4xh4' size='340' side='right'caption='[[4xh4]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xh4]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Salty Salty~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XH4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XH4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xh4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XH4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xh1\|4xh1]], [[4xh5\|4xh5]]</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=4xh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xh4 OCA], [https://pdbe.org/4xh4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xh4 RCSB], [https://www.ebi.ac.uk/pdbsum/4xh4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xh4 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tdcD, oxd-2, STM3242 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propionate_kinase Propionate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.15 2.7.2.15] </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=4xh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xh4 OCA], [~~http~~://pdbe.org/4xh4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xh4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xh4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xh4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TDCD_SALTY TDCD_SALTY]] Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.[HAMAP-Rule:MF_01881]	+	[https://www.uniprot.org/uniprot/TDCD_SALTY TDCD_SALTY] Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.[HAMAP-Rule:MF_01881]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Propionate kinase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Salty~~]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
-	[[Category: Chittori, S]]	+	[[Category: Chittori S]]
-	[[Category: Mathivanan, S]]	+	[[Category: Mathivanan S]]
-	[[Category: Murthy~~, A M.V~~]]	+	[[Category: Murthy AMV]]
-	[[Category: Murthy~~, M R.N~~]]	+	[[Category: Murthy MRN]]
-	[[Category: Savithri~~, H S]]~~	+	[[Category: Savithri HS]]
-	~~[[Category: Amppnp]]~~	+
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Propionate]]~~	+
-	~~[[Category: Tdcd]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 15:18, 16 November 2017

OCA — Thu, 16 Nov 2017 15:18:54 GMT

←Older revision		Revision as of 15:18, 16 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4xh4 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Salmonella typhimurium propionate kinase A88V mutant, in complex with AMPPNP and propionate==
		+	<StructureSection load='4xh4' size='340' side='right' caption='[[4xh4]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xh4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XH4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XH4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xh1\|4xh1]], [[4xh5\|4xh5]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tdcD, oxd-2, STM3242 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propionate_kinase Propionate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.15 2.7.2.15] </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=4xh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xh4 OCA], [http://pdbe.org/4xh4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xh4 RCSB], [http://www.ebi.ac.uk/pdbsum/4xh4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xh4 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TDCD_SALTY TDCD_SALTY]] Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.[HAMAP-Rule:MF_01881]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Kinases are ubiquitous enzymes that are pivotal to many biochemical processes. There are contrasting views on the phosphoryl-transfer mechanism in propionate kinase, an enzyme that reversibly transfers a phosphoryl group from propionyl phosphate to ADP in the final step of non-oxidative catabolism of L-threonine to propionate. Here, X-ray crystal structures of propionate- and nucleotide-bound Salmonella typhimurium propionate kinase are reported at 1.8-2.0 A resolution. Although the mode of nucleotide binding is comparable to those of other members of the ASKHA superfamily, propionate is bound at a distinct site deeper in the hydrophobic pocket defining the active site. The propionate carboxyl is at a distance of approximately 5 A from the gamma-phosphate of the nucleotide, supporting a direct in-line transfer mechanism. The phosphoryl-transfer reaction is likely to occur via an associative SN2-like transition state that involves a pentagonal bipyramidal structure with the axial positions occupied by the nucleophile of the substrate and the O atom between the beta- and the gamma-phosphates, respectively. The proximity of the strictly conserved His175 and Arg236 to the carboxyl group of the propionate and the gamma-phosphate of ATP suggests their involvement in catalysis. Moreover, ligand binding does not induce global domain movement as reported in some other members of the ASKHA superfamily. Instead, residues Arg86, Asp143 and Pro116-Leu117-His118 that define the active-site pocket move towards the substrate and expel water molecules from the active site. The role of Ala88, previously proposed to be the residue determining substrate specificity, was examined by determining the crystal structures of the propionate-bound Ala88 mutants A88V and A88G. Kinetic analysis and structural data are consistent with a significant role of Ala88 in substrate-specificity determination. The active-site pocket-defining residues Arg86, Asp143 and the Pro116-Leu117-His118 segment are also likely to contribute to substrate specificity.

-	~~Authors~~: Murthy~~, A.M.V.~~, Mathivanan, S., Chittori, S., Savithri, H.S., ~~Murthy, M~~.R.N.	+	Structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate-transfer mechanism.,Murthy AM, Mathivanan S, Chittori S, Savithri HS, Murthy MR Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1640-8. doi:, 10.1107/S1399004715009992. Epub 2015 Jul 28. PMID:26249345<ref>PMID:26249345</ref>

-	~~Description: Crystal structure~~ of ~~Salmonella typhimurium propionate kinase A88V mutant, in complex with AMPPNP and propionate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Murthy, M.R.N~~]]	+	<div class="pdbe-citations 4xh4" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Savithri, H.S~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Propionate kinase]]
		+	[[Category: Salty]]
	[[Category: Chittori, S]]		[[Category: Chittori, S]]
	[[Category: Mathivanan, S]]		[[Category: Mathivanan, S]]
-	[[Category: Murthy, A.M.V]]	+	[[Category: Murthy, A M.V]]
		+	[[Category: Murthy, M R.N]]
		+	[[Category: Savithri, H S]]
		+	[[Category: Amppnp]]
		+	[[Category: Kinase]]
		+	[[Category: Propionate]]
		+	[[Category: Tdcd]]
		+	[[Category: Transferase]]

OCA at 08:03, 20 August 2015

OCA — Thu, 20 Aug 2015 08:03:44 GMT

←Older revision		Revision as of 08:03, 20 August 2015
Line 5:		Line 5:
	Authors: Murthy, A.M.V., Mathivanan, S., Chittori, S., Savithri, H.S., Murthy, M.R.N.		Authors: Murthy, A.M.V., Mathivanan, S., Chittori, S., Savithri, H.S., Murthy, M.R.N.

-	Description: Crystal structure of Salmonella typhimurium propionate kinase ~~(TdcD)~~ in complex with ~~propionate and~~ AMPPNP	+	Description: Crystal structure of Salmonella typhimurium propionate kinase A88V mutant, in complex with AMPPNP and propionate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Murthy, M.R.N]]		[[Category: Murthy, M.R.N]]

OCA at 12:02, 25 February 2015

OCA — Wed, 25 Feb 2015 12:02:55 GMT

←Older revision		Revision as of 12:02, 25 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xh4 is ON HOLD until ~~sometime in the future~~	+	The entry 4xh4 is ON HOLD until Paper Publication

	Authors: Murthy, A.M.V., Mathivanan, S., Chittori, S., Savithri, H.S., Murthy, M.R.N.		Authors: Murthy, A.M.V., Mathivanan, S., Chittori, S., Savithri, H.S., Murthy, M.R.N.

OCA at 10:23, 12 February 2015

OCA — Thu, 12 Feb 2015 10:23:22 GMT

←Older revision		Revision as of 10:23, 12 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xh4 is ON HOLD	+	The entry 4xh4 is ON HOLD until sometime in the future

	Authors: Murthy, A.M.V., Mathivanan, S., Chittori, S., Savithri, H.S., Murthy, M.R.N.		Authors: Murthy, A.M.V., Mathivanan, S., Chittori, S., Savithri, H.S., Murthy, M.R.N.

OCA at 15:24, 28 January 2015

OCA — Wed, 28 Jan 2015 15:24:48 GMT

←Older revision		Revision as of 15:24, 28 January 2015
Line 3:		Line 3:
	The entry 4xh4 is ON HOLD		The entry 4xh4 is ON HOLD

-	Authors: Murthy, A.M, Mathivanan, S., Chittori, S., Savithri, H.S., Murthy, M.R.N.	+	Authors: Murthy, A.M.V., Mathivanan, S., Chittori, S., Savithri, H.S., Murthy, M.R.N.

	Description: Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with propionate and AMPPNP		Description: Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with propionate and AMPPNP
Line 10:		Line 10:
	[[Category: Savithri, H.S]]		[[Category: Savithri, H.S]]
	[[Category: Chittori, S]]		[[Category: Chittori, S]]
-	[[Category: Murthy, A.M~~, Mathivanan, S~~]]	+	[[Category: Mathivanan, S]]
		+	[[Category: Murthy, A.M.V]]

OCA: Protected "4xh4" [edit=sysop:move=sysop]

OCA — Wed, 14 Jan 2015 12:42:04 GMT

Protected "4xh4" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:42, 14 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xh4 is ON HOLD Authors: Murthy, A.M, Mathivanan, S., Chittori, S., Savithri, H.S., Murthy, M.R.N. Description: Crystal structure of Salmonella typ...

OCA — Wed, 14 Jan 2015 12:42:03 GMT

New page: '''Unreleased structure''' The entry 4xh4 is ON HOLD Authors: Murthy, A.M, Mathivanan, S., Chittori, S., Savithri, H.S., Murthy, M.R.N. Description: Crystal structure of Salmonella typ...

New page

'''Unreleased structure'''

The entry 4xh4 is ON HOLD

Authors: Murthy, A.M, Mathivanan, S., Chittori, S., Savithri, H.S., Murthy, M.R.N.

Description: Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with propionate and AMPPNP
[[Category: Unreleased Structures]]
[[Category: Murthy, M.R.N]]
[[Category: Savithri, H.S]]
[[Category: Chittori, S]]
[[Category: Murthy, A.M, Mathivanan, S]]