5ugv - Revision history

OCA at 13:27, 4 October 2023

OCA — Wed, 04 Oct 2023 13:27:20 GMT

←Older revision		Revision as of 13:27, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5ugv' size='340' side='right'caption='[[5ugv]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='5ugv' size='340' side='right'caption='[[5ugv]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ugv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Mycta Mycta~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UGV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ugv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Ra Mycobacterium tuberculosis H37Ra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UGV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NAD:NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE'>NAD</scene>~~, ~~<scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 2.25Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~dapB, MRA_2798 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=419947 MYCTA])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_reductase 4-hydroxy-tetrahydrodipicolinate reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.1.8 1.17.1.8] </~~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=5ugv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ugv OCA], [https://pdbe.org/5ugv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ugv RCSB], [https://www.ebi.ac.uk/pdbsum/5ugv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ugv 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=5ugv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ugv OCA], [https://pdbe.org/5ugv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ugv RCSB], [https://www.ebi.ac.uk/pdbsum/5ugv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ugv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~DAPB_MYCTA DAPB_MYCTA]~~] Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate.~~[HAMAP~~-~~Rule~~:~~MF_00102]~~	+	[https://www.uniprot.org/uniprot/DAPB_MYCTU DAPB_MYCTU] Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate (Probable). Can use both NADH and NADPH as a reductant, with NADH being 6-fold as effective as NADPH.<ref>PMID:12962488</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 4-hydroxy-tetrahydrodipicolinate reductase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mycta~~]]	+	[[Category: Mycobacterium tuberculosis H37Ra]]
-	[[Category: Chruszcz, M]]	+	[[Category: Chruszcz M]]
-	[[Category: Mank, N]]	+	[[Category: Mank N]]
-	[[Category: Pote~~, S P]]~~	+	[[Category: Pote SP]]
-	~~[[Category: Dapb]]~~	+
-	~~[[Category: Lysine biosynthesis]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 03:40, 2 July 2021

OCA — Fri, 02 Jul 2021 03:40:03 GMT

←Older revision		Revision as of 03:40, 2 July 2021
Line 3:		Line 3:
	<StructureSection load='5ugv' size='340' side='right'caption='[[5ugv]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='5ugv' size='340' side='right'caption='[[5ugv]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ugv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5UGV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ugv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycta Mycta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UGV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_reductase 4-hydroxy-tetrahydrodipicolinate reductase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.1.8 1.17.1.8] </span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapB, MRA_2798 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</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=5ugv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ugv OCA], [~~http~~://pdbe.org/5ugv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ugv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ugv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ugv ProSAT]</span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_reductase 4-hydroxy-tetrahydrodipicolinate reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.1.8 1.17.1.8] </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=5ugv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ugv OCA], [https://pdbe.org/5ugv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ugv RCSB], [https://www.ebi.ac.uk/pdbsum/5ugv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ugv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DAPB_MYCTA DAPB_MYCTA]] Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate.[HAMAP-Rule:MF_00102]	+	[[https://www.uniprot.org/uniprot/DAPB_MYCTA DAPB_MYCTA]] Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate.[HAMAP-Rule:MF_00102]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: The products of the lysine biosynthesis pathway, meso-diaminopimelate and lysine, are essential for bacterial survival. This paper focuses on the structural and mechanistic characterization of 4-hydroxy-tetrahydrodipicolinate reductase (DapB), which is one of the enzymes from the lysine biosynthesis pathway. DapB catalyzes the conversion of (2S, 4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate (HTPA) to 2,3,4,5-tetrahydrodipicolinate in an NADH/NADPH dependent reaction. Genes coding for DapBs were identified as essential for many pathogenic bacteria, and therefore DapB is an interesting new target for the development of antibiotics. METHODS: We have combined experimental and computational approaches to provide novel insights into mechanism of the DapB catalyzed reaction. RESULTS: Structures of DapBs originating from Mycobacterium tuberculosis and Vibrio vulnificus in complexes with NAD(+), NADP(+), as well as with inhibitors, were determined and described. The structures determined by us, as well as currently available structures of DapBs from other bacterial species, were compared and used to elucidate a mechanism of reaction catalyzed by this group of enzymes. Several different computational methods were used to provide a detailed description of a plausible reaction mechanism. CONCLUSIONS: This is the first report presenting the detailed mechanism of reaction catalyzed by DapB. GENERAL SIGNIFICANCE: Structural data in combination with information on the reaction mechanism provide a background for development of DapB inhibitors, including transition-state analogues.
		+
		+	Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.,Pote S, Kachhap S, Mank NJ, Daneshian L, Klapper V, Pye S, Arnette AK, Shimizu LS, Borowski T, Chruszcz M Biochim Biophys Acta Gen Subj. 2021 Jan;1865(1):129750. doi:, 10.1016/j.bbagen.2020.129750. Epub 2020 Sep 24. PMID:32980502<ref>PMID:32980502</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ugv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: 4-hydroxy-tetrahydrodipicolinate reductase]]		[[Category: 4-hydroxy-tetrahydrodipicolinate reductase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Mycta]]
	[[Category: Chruszcz, M]]		[[Category: Chruszcz, M]]
	[[Category: Mank, N]]		[[Category: Mank, N]]

OCA at 12:36, 23 September 2020

OCA — Wed, 23 Sep 2020 12:36:15 GMT

←Older revision		Revision as of 12:36, 23 September 2020
Line 1:		Line 1:

	==DapB from Mycobacterium tuberculosis==		==DapB from Mycobacterium tuberculosis==
-	<StructureSection load='5ugv' size='340' side='right' caption='[[5ugv]], [[Resolution\|resolution]] 2.25Å' scene=''>	+	<StructureSection load='5ugv' size='340' side='right'caption='[[5ugv]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ugv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGV OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UGV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ugv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5UGV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_reductase 4-hydroxy-tetrahydrodipicolinate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.1.8 1.17.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_reductase 4-hydroxy-tetrahydrodipicolinate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.1.8 1.17.1.8] </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=5ugv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ugv OCA], [http://pdbe.org/5ugv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ugv RCSB], [http://www.ebi.ac.uk/pdbsum/5ugv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ugv 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=5ugv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ugv OCA], [http://pdbe.org/5ugv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ugv RCSB], [http://www.ebi.ac.uk/pdbsum/5ugv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ugv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 13:
	</StructureSection>		</StructureSection>
	[[Category: 4-hydroxy-tetrahydrodipicolinate reductase]]		[[Category: 4-hydroxy-tetrahydrodipicolinate reductase]]
		+	[[Category: Large Structures]]
	[[Category: Chruszcz, M]]		[[Category: Chruszcz, M]]
	[[Category: Mank, N]]		[[Category: Mank, N]]

OCA at 06:52, 17 January 2018

OCA — Wed, 17 Jan 2018 06:52:02 GMT

←Older revision		Revision as of 06:52, 17 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ugv is ~~ON HOLD until Paper Publication~~	+	==DapB from Mycobacterium tuberculosis==
-		+	<StructureSection load='5ugv' size='340' side='right' caption='[[5ugv]], [[Resolution\|resolution]] 2.25Å' scene=''>
-	~~Authors~~: ~~Pote~~, S.P., ~~Mank~~, N., ~~Chruszcz~~, M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ugv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UGV FirstGlance]. <br>
-	~~Description: DapB from Mycobacterium tuberculosis~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_reductase 4-hydroxy-tetrahydrodipicolinate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.1.8 1.17.1.8] </span></td></tr>
-	[[Category: ~~Pote, S.P~~]]	+	<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=5ugv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ugv OCA], [http://pdbe.org/5ugv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ugv RCSB], [http://www.ebi.ac.uk/pdbsum/5ugv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ugv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DAPB_MYCTA DAPB_MYCTA]] Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate.[HAMAP-Rule:MF_00102]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 4-hydroxy-tetrahydrodipicolinate reductase]]
	[[Category: Chruszcz, M]]		[[Category: Chruszcz, M]]
	[[Category: Mank, N]]		[[Category: Mank, N]]
		+	[[Category: Pote, S P]]
		+	[[Category: Dapb]]
		+	[[Category: Lysine biosynthesis]]
		+	[[Category: Oxidoreductase]]

OCA at 14:27, 9 March 2017

OCA — Thu, 09 Mar 2017 14:27:54 GMT

←Older revision		Revision as of 14:27, 9 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Pote, S.P., Mank, N., Chruszcz, M.		Authors: Pote, S.P., Mank, N., Chruszcz, M.

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

OCA — Wed, 18 Jan 2017 14:58:56 GMT

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

←Older revision

Revision as of 14:58, 18 January 2017

OCA: New page: '''Unreleased structure''' The entry 5ugv is ON HOLD Authors: Pote, S.P., Mank, N., Chruszcz, M. Description: DapB from Mycobacterium tuberculosis Category: Unreleased Structures [...

OCA — Wed, 18 Jan 2017 14:58:55 GMT

New page: '''Unreleased structure''' The entry 5ugv is ON HOLD Authors: Pote, S.P., Mank, N., Chruszcz, M. Description: DapB from Mycobacterium tuberculosis Category: Unreleased Structures [...

New page

'''Unreleased structure'''

The entry 5ugv is ON HOLD

Authors: Pote, S.P., Mank, N., Chruszcz, M.

Description: DapB from Mycobacterium tuberculosis
[[Category: Unreleased Structures]]
[[Category: Pote, S.P]]
[[Category: Chruszcz, M]]
[[Category: Mank, N]]