4yl5 - Revision history

OCA at 19:25, 29 May 2024

2024-05-29T19:25:09Z

←Older revision		Revision as of 19:25, 29 May 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A0J9X285_ACIBA A0A0J9X285_ACIBA]		[https://www.uniprot.org/uniprot/A0A0J9X285_ACIBA A0A0J9X285_ACIBA]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Thiamin and its phosphate derivatives are ubiquitous molecules involved as essential cofactors in many cellular processes. The de novo biosynthesis of thiamin employs the parallel synthesis of 4-methyl-5-(2-hydroxyethyl)thiazole (THZ-P) and 4-amino-2-methyl-5(diphosphooxymethyl) pyrimidine (HMP) pyrophosphate (HMP-PP), which are coupled to generate thiamin phosphate. Most organisms that can biosynthesize thiamin employ a kinase (HMPK or ThiD) to generate HMP-PP. In nearly all cases, this enzyme is bifunctional and can also salvage free HMP, producing HMP-P, the monophosphate precursor of HMP-PP. Here we present high-resolution crystal structures of an HMPK from Acinetobacter baumannii (AbHMPK), both unliganded and with pyridoxal 5-phosphate (PLP) noncovalently bound. Despite the similarity between HMPK and pyridoxal kinase enzymes, our kinetics analysis indicates that AbHMPK accepts HMP exclusively as a substrate and cannot turn over pyridoxal, pyridoxamine, or pyridoxine nor does it display phosphatase activity. PLP does, however, act as a weak inhibitor of AbHMPK with an IC(50) of 768 muM. Surprisingly, unlike other HMPKs, AbHMPK catalyzes only the phosphorylation of HMP and does not generate the diphosphate HMP-PP. This suggests that an additional kinase is present in A. baumannii, or an alternative mechanism is in operation to complete the biosynthesis of thiamin.
		+
		+	Characterization of an Acinetobacter baumannii Monofunctional Phosphomethylpyrimidine Kinase That Is Inhibited by Pyridoxal Phosphate.,De Vitto H, Belfon KKJ, Sharma N, Toay S, Abendroth J, Dranow DM, Lukacs CM, Choi R, Udell HS, Willis S, Barrera G, Beyer O, Li TD, Hicks KA, Torelli AT, French JB Biochemistry. 2024 Feb 2. doi: 10.1021/acs.biochem.3c00640. PMID:38306231<ref>PMID:38306231</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4yl5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Acinetobacter baumannii IS-123]]		[[Category: Acinetobacter baumannii IS-123]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 08:02, 27 September 2023

2023-09-27T08:02:00Z

←Older revision		Revision as of 08:02, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yl5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii_IS-123 Acinetobacter baumannii IS-123]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YL5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YL5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yl5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii_IS-123 Acinetobacter baumannii IS-123]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YL5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YL5 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></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]] 1.7Å</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></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=4yl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yl5 OCA], [https://pdbe.org/4yl5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yl5 RCSB], [https://www.ebi.ac.uk/pdbsum/4yl5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yl5 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=4yl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yl5 OCA], [https://pdbe.org/4yl5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yl5 RCSB], [https://www.ebi.ac.uk/pdbsum/4yl5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yl5 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:17, 3 May 2023

2023-05-03T08:17:32Z

←Older revision		Revision as of 08:17, 3 May 2023
Line 1:		Line 1:

	==Structure of a putative phosphomethylpyrimidine kinase from Acinetobacter baumannii==		==Structure of a putative phosphomethylpyrimidine kinase from Acinetobacter baumannii==
-	<StructureSection load='4yl5' size='340' side='right' caption='[[4yl5]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='4yl5' size='340' side='right'caption='[[4yl5]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yl5]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Acinetobacter_baumannii_is~~-123 Acinetobacter baumannii is-123]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YL5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YL5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yl5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii_IS-123 Acinetobacter baumannii IS-123]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YL5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YL5 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>~~</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></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ACINIS123_0279 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=903899 Acinetobacter baumannii IS-123])</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=4yl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yl5 OCA], [https://pdbe.org/4yl5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yl5 RCSB], [https://www.ebi.ac.uk/pdbsum/4yl5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yl5 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=4yl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yl5 OCA], [~~http~~://pdbe.org/4yl5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4yl5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4yl5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4yl5 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0J9X285_ACIBA A0A0J9X285_ACIBA]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Acinetobacter baumannii is-123]]	+	[[Category: Acinetobacter baumannii IS-123]]
-	[[Category: ~~Structural genomic]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Putative phosphomethylpyrimidine kinase]]~~	+
-	~~[[Category: Ssgcid]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:40, 22 November 2017

2017-11-22T09:40:12Z

←Older revision		Revision as of 09:40, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4yl5' size='340' side='right' caption='[[4yl5]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4yl5' size='340' side='right' caption='[[4yl5]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yl5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YL5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YL5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yl5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baumannii_is-123 Acinetobacter baumannii is-123]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YL5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YL5 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></td></tr>		</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></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ACINIS123_0279 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=903899 Acinetobacter baumannii IS-123])</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=4yl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yl5 OCA], [http://pdbe.org/4yl5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yl5 RCSB], [http://www.ebi.ac.uk/pdbsum/4yl5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yl5 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=4yl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yl5 OCA], [http://pdbe.org/4yl5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yl5 RCSB], [http://www.ebi.ac.uk/pdbsum/4yl5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yl5 ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Acinetobacter baumannii is-123]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Putative phosphomethylpyrimidine kinase]]		[[Category: Putative phosphomethylpyrimidine kinase]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 10:00, 10 March 2017

2017-03-10T10:00:48Z

←Older revision		Revision as of 10:00, 10 March 2017
Line 1:		Line 1:
		+
	==Structure of a putative phosphomethylpyrimidine kinase from Acinetobacter baumannii==		==Structure of a putative phosphomethylpyrimidine kinase from Acinetobacter baumannii==
	<StructureSection load='4yl5' size='340' side='right' caption='[[4yl5]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4yl5' size='340' side='right' caption='[[4yl5]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4yl5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YL5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YL5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yl5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YL5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YL5 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></td></tr>		</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></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=4yl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yl5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yl5 RCSB], [http://www.ebi.ac.uk/pdbsum/4yl5 PDBsum]</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=4yl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yl5 OCA], [http://pdbe.org/4yl5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yl5 RCSB], [http://www.ebi.ac.uk/pdbsum/4yl5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yl5 ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 13:23, 1 April 2015

2015-04-01T13:23:09Z

←Older revision		Revision as of 13:23, 1 April 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Structure of a putative phosphomethylpyrimidine kinase from Acinetobacter baumannii==
-		+	<StructureSection load='4yl5' size='340' side='right' caption='[[4yl5]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~The entry~~ 4yl5 is ~~ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4yl5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YL5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YL5 FirstGlance]. <br>
-	~~Authors~~: ~~Seattle Structural Genomics Center for Infectious Disease (SSGCID)~~	+	</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></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=4yl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yl5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yl5 RCSB], [http://www.ebi.ac.uk/pdbsum/4yl5 PDBsum]</span></td></tr>
-	~~Description~~: ~~Structure of a putative~~ phosphomethylpyrimidine kinase ~~from Acinetobacter baumannii~~	+	</table>
-	[[Category: ~~Unreleased Structures~~]]	+	__TOC__
-	[[Category: ~~Seattle Structural Genomics Center For Infectious Disease (Ssgcid)~~]]	+	</StructureSection>
		+	[[Category: Structural genomic]]
		+	[[Category: Putative phosphomethylpyrimidine kinase]]
		+	[[Category: Ssgcid]]
		+	[[Category: Transferase]]

OCA: Protected "4yl5" [edit=sysop:move=sysop]

2015-03-11T10:47:10Z

Protected "4yl5" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:47, 11 March 2015

OCA: New page: '''Unreleased structure''' The entry 4yl5 is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Description: Structure of a putative phosphomethylpyrim...

2015-03-11T10:47:09Z

New page: '''Unreleased structure''' The entry 4yl5 is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Description: Structure of a putative phosphomethylpyrim...

New page

'''Unreleased structure'''

The entry 4yl5 is ON HOLD

Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Description: Structure of a putative phosphomethylpyrimidine kinase from Acinetobacter baumannii
[[Category: Unreleased Structures]]
[[Category: Seattle Structural Genomics Center For Infectious Disease (Ssgcid)]]