6jyy - Revision history

OCA at 10:40, 27 March 2024

OCA — Wed, 27 Mar 2024 10:40:26 GMT

←Older revision		Revision as of 10:40, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6jyy' size='340' side='right'caption='[[6jyy]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6jyy' size='340' side='right'caption='[[6jyy]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jyy]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus~~ pneumoniae~~" (schroeter 1886) flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JYY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6JYY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jyy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JYY FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>thiM, BN49_3768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~573~~ "~~Bacillus pneumoniae~~" ~~(Schroeter 1886) Flugge 1886])</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]] 2Å</td></tr>
-	~~<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'~~>[~~http://en.wikipedia.org/wiki/Transferase Transferase~~]~~, with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=~~2~~.7.1.50 2.7.1.50] </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=6jyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jyy OCA], [https://pdbe.org/6jyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jyy RCSB], [https://www.ebi.ac.uk/pdbsum/6jyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jyy 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=6jyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jyy OCA], [~~http~~://pdbe.org/6jyy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jyy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jyy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jyy ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~W9BB97_KLEPN W9BB97_KLEPN]~~] Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ).[HAMAP-Rule:MF_00228]~~[SAAS:SAAS00158945]~~	+	[https://www.uniprot.org/uniprot/THIM_KLEP7 THIM_KLEP7] Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ).[HAMAP-Rule:MF_00228]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Thiamin pyrophosphate (TPP) is an essential co-factor in amino acid and carbohydrate metabolic pathways. The TPP-related vitamin B1 biosynthetic pathway is found in most bacterial, plant and lower eukaryotic processes; however, it is not present in humans. In bacterial thiamin synthesis and salvage pathways, the 5-(hydroxyethyl)-methylthiazole kinase (ThiM) is essential in the pathway forming TPP. Thus, ThiM is considered to be an attractive antibacterial drug target. Here, we determined the crystal structures of ThiM from pathogenic Klebsiella pneumoniae (KpThiM) and KpThiM in complex with its substrate 5-(hydroxyethyl)-4-methylthiazole (TZE). KpThiM, consisting of an alpha-beta-alpha domain, shows a pseudosymmetric trimeric formation. TZE molecules are located in the interface between the KpThiM subunits in the trimer and interact with Met49 and Cys200. Superimposition of the apo and TZE-complexed structures of KpThiM show that the side chains of the amino acids interacting with TZE and Mg(2+) have a rigid configuration. Comparison of the ThiM structures shows that KpThiM could, in terms of sequence and configuration, be different from other ThiM proteins, which possess different amino acids that recognize TZE and Mg(2+). The structures will provide new insight into the ThiM subfamily proteins for antibacterial drug development.	+
-		+
-	Structural insight of the 5-(Hydroxyethyl)-methylthiazole kinase ThiM involving vitamin B1 biosynthetic pathway from the Klebsiella pneumoniae.,Chen Y, Wang L, Shang F, Liu W, Lan J, Chen J, Ha NC, Quan C, Nam KH, Xu Y Biochem Biophys Res Commun. 2019 Oct 20;518(3):513-518. doi:, 10.1016/j.bbrc.2019.08.086. Epub 2019 Aug 19. PMID:31439375<ref>PMID:31439375</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6jyy" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Klebsiella pneumoniae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Transferase]]~~	+	[[Category: Chen Y]]
-	[[Category: Chen, Y]]	+	[[Category: Lan J]]
-	[[Category: Lan, J]]	+	[[Category: Liu W]]
-	[[Category: Liu, W]]	+	[[Category: Shang F]]
-	[[Category: Shang, F]]	+	[[Category: Wang L]]
-	[[Category: Wang, L]]	+	[[Category: Xu Y]]
-	[[Category: Xu, Y]]	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Klebsiella pneumonia]]~~	+
-	~~[[Category: Thim~~]]	+

OCA at 06:24, 6 May 2020

OCA — Wed, 06 May 2020 06:24:29 GMT

←Older revision		Revision as of 06:24, 6 May 2020
Line 3:		Line 3:
	<StructureSection load='6jyy' size='340' side='right'caption='[[6jyy]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6jyy' size='340' side='right'caption='[[6jyy]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jyy]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JYY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JYY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jyy]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus pneumoniae" (schroeter 1886) flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JYY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JYY FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.50 2.7.1.50] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thiM, BN49_3768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</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=6jyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jyy OCA], [http://pdbe.org/6jyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jyy RCSB], [http://www.ebi.ac.uk/pdbsum/6jyy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jyy ProSAT]</span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.50 2.7.1.50] </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=6jyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jyy OCA], [http://pdbe.org/6jyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jyy RCSB], [http://www.ebi.ac.uk/pdbsum/6jyy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jyy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/W9BB97_KLEPN W9BB97_KLEPN]] Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ).[HAMAP-Rule:MF_00228][SAAS:SAAS00158945]		[[http://www.uniprot.org/uniprot/W9BB97_KLEPN W9BB97_KLEPN]] Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ).[HAMAP-Rule:MF_00228][SAAS:SAAS00158945]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Thiamin pyrophosphate (TPP) is an essential co-factor in amino acid and carbohydrate metabolic pathways. The TPP-related vitamin B1 biosynthetic pathway is found in most bacterial, plant and lower eukaryotic processes; however, it is not present in humans. In bacterial thiamin synthesis and salvage pathways, the 5-(hydroxyethyl)-methylthiazole kinase (ThiM) is essential in the pathway forming TPP. Thus, ThiM is considered to be an attractive antibacterial drug target. Here, we determined the crystal structures of ThiM from pathogenic Klebsiella pneumoniae (KpThiM) and KpThiM in complex with its substrate 5-(hydroxyethyl)-4-methylthiazole (TZE). KpThiM, consisting of an alpha-beta-alpha domain, shows a pseudosymmetric trimeric formation. TZE molecules are located in the interface between the KpThiM subunits in the trimer and interact with Met49 and Cys200. Superimposition of the apo and TZE-complexed structures of KpThiM show that the side chains of the amino acids interacting with TZE and Mg(2+) have a rigid configuration. Comparison of the ThiM structures shows that KpThiM could, in terms of sequence and configuration, be different from other ThiM proteins, which possess different amino acids that recognize TZE and Mg(2+). The structures will provide new insight into the ThiM subfamily proteins for antibacterial drug development.
		+
		+	Structural insight of the 5-(Hydroxyethyl)-methylthiazole kinase ThiM involving vitamin B1 biosynthetic pathway from the Klebsiella pneumoniae.,Chen Y, Wang L, Shang F, Liu W, Lan J, Chen J, Ha NC, Quan C, Nam KH, Xu Y Biochem Biophys Res Commun. 2019 Oct 20;518(3):513-518. doi:, 10.1016/j.bbrc.2019.08.086. Epub 2019 Aug 19. PMID:31439375<ref>PMID:31439375</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6jyy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:54, 26 June 2019

OCA — Wed, 26 Jun 2019 06:54:30 GMT

←Older revision		Revision as of 06:54, 26 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jyy ~~is ON HOLD until Jun 24 2020~~	+	==Crystal structure of the 5-(Hydroxyethyl)-methylthiazole Kinase ThiM from Klebsiella pneumonia==
-		+	<StructureSection load='6jyy' size='340' side='right'caption='[[6jyy]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Chen~~, Y., ~~Wang, L~~., ~~Shang, F~~., ~~Lan, J~~., ~~Liu, W~~., ~~Xu, Y~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6jyy]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JYY FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of the 5-(~~Hydroxyethyl~~)-~~methylthiazole Kinase ThiM from Klebsiella pneumonia~~	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.50 2.7.1.50] </span></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=6jyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jyy OCA], [http://pdbe.org/6jyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jyy RCSB], [http://www.ebi.ac.uk/pdbsum/6jyy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jyy ProSAT]</span></td></tr>
-	[[Category: ~~Shang, F~~]]	+	</table>
-	[[Category: ~~Liu, W~~]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/W9BB97_KLEPN W9BB97_KLEPN]] Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ).[HAMAP-Rule:MF_00228][SAAS:SAAS00158945]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Transferase]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]
-	[[Category: Xu, Y]]
	[[Category: Lan, J]]		[[Category: Lan, J]]
		+	[[Category: Liu, W]]
		+	[[Category: Shang, F]]
	[[Category: Wang, L]]		[[Category: Wang, L]]
		+	[[Category: Xu, Y]]
		+	[[Category: Hydrolase]]
		+	[[Category: Klebsiella pneumonia]]
		+	[[Category: Thim]]

OCA at 04:22, 29 May 2019

OCA — Wed, 29 May 2019 04:22:40 GMT

←Older revision		Revision as of 04:22, 29 May 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6jyy is ON HOLD	+	The entry 6jyy is ON HOLD until Jun 24 2020

	Authors: Chen, Y., Wang, L., Shang, F., Lan, J., Liu, W., Xu, Y.		Authors: Chen, Y., Wang, L., Shang, F., Lan, J., Liu, W., Xu, Y.
Line 7:		Line 7:
	Description: Crystal structure of the 5-(Hydroxyethyl)-methylthiazole Kinase ThiM from Klebsiella pneumonia		Description: Crystal structure of the 5-(Hydroxyethyl)-methylthiazole Kinase ThiM from Klebsiella pneumonia
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Lan, J]]
	[[Category: Shang, F]]		[[Category: Shang, F]]
-	[[Category: Wang, L]]
	[[Category: Liu, W]]		[[Category: Liu, W]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]
	[[Category: Xu, Y]]		[[Category: Xu, Y]]
		+	[[Category: Lan, J]]
		+	[[Category: Wang, L]]

OCA: Protected "6jyy" [edit=sysop:move=sysop]

OCA — Fri, 10 May 2019 07:37:48 GMT

Protected "6jyy" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:37, 10 May 2019

OCA: New page: '''Unreleased structure''' The entry 6jyy is ON HOLD Authors: Chen, Y., Wang, L., Shang, F., Lan, J., Liu, W., Xu, Y. Description: Crystal structure of the 5-(Hydroxyethyl)-methylthiaz...

OCA — Fri, 10 May 2019 07:37:45 GMT

New page: '''Unreleased structure''' The entry 6jyy is ON HOLD Authors: Chen, Y., Wang, L., Shang, F., Lan, J., Liu, W., Xu, Y. Description: Crystal structure of the 5-(Hydroxyethyl)-methylthiaz...

New page

'''Unreleased structure'''

The entry 6jyy is ON HOLD

Authors: Chen, Y., Wang, L., Shang, F., Lan, J., Liu, W., Xu, Y.

Description: Crystal structure of the 5-(Hydroxyethyl)-methylthiazole Kinase ThiM from Klebsiella pneumonia
[[Category: Unreleased Structures]]
[[Category: Lan, J]]
[[Category: Shang, F]]
[[Category: Wang, L]]
[[Category: Liu, W]]
[[Category: Chen, Y]]
[[Category: Xu, Y]]