5z2f - Revision history

OCA at 10:26, 27 March 2024

2024-03-27T10:26:29Z

←Older revision		Revision as of 10:26, 27 March 2024
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	<StructureSection load='5z2f' size='340' side='right'caption='[[5z2f]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5z2f' size='340' side='right'caption='[[5z2f]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z2f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z2F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Z2F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z2f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenisporosarcina_sp._TG-14 Paenisporosarcina sp. TG-14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z2F FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</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]] 2.1Å</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=5z2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2f OCA], [~~http~~://pdbe.org/5z2f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z2f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z2f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2f ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</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=5z2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2f OCA], [https://pdbe.org/5z2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z2f RCSB], [https://www.ebi.ac.uk/pdbsum/5z2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2f ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A3B6UER2_9BACL A0A3B6UER2_9BACL] Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate.[HAMAP-Rule:MF_00102]
-	~~Dihydrodipicolinate reductase (DHDPR) is a key enzyme in the diaminopimelate- and lysine-synthesis pathways that reduces DHDP to tetrahydrodipicolinate~~. ~~Although DHDPR uses both NADPH and NADH as a cofactor, the structural basis for cofactor specificity and preference remains unclear~~. ~~Here, we report that Paenisporosarcina sp. TG-14 PaDHDPR has a strong preference for NADPH over NADH, as determined by isothermal titration calorimetry and enzymatic activity assays. We determined~~ the ~~crystal structures~~ of PaDHDPR alone, with its competitive inhibitor (dipicolinate), and the ternary complex of the enzyme with dipicolinate and NADPH, with results showing that only the ternary complex had a fully closed conformation and suggesting that binding of both substrate and nucleotide cofactor is required for enzymatic activity. Moreover, NADPH binding induced local conformational changes in the N-~~terminal long loop (residues 34~~-59) of PaDHDPR, as the His35 and Lys36 residues in this loop interacted with the 2'-phosphate group of NADPH, possibly accounting for the strong preference of PaDHDPR for NADPH. Mutation of these residues revealed reduced NADPH binding and enzymatic activity, confirming their importance in NADPH binding. These findings provide insight into the mechanism of action and cofactor selectivity of this important bacterial enzyme.	+
-		+
-	~~Crystal structure of dihydrodipicolinate reductase~~ (~~PaDHDPR~~) ~~from Paenisporosarcina sp~~. TG-14: structural basis for NADPH preference as a cofactor.,Lee CW, Park SH, Lee SG, Park HH, Kim HJ, Park H, Park H, Lee JH Sci Rep. 2018 May 21;8(1):7936. doi: 10.1038/s41598-018-26291-x. PMID:29786696<ref>PMID:29786696</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5z2f" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lee, C W~~]]	+	[[Category: Paenisporosarcina sp. TG-14]]
-	[[Category: Lee~~, J H~~]]	+	[[Category: Lee CW]]
-	[[Category: ~~Park, S~~]]	+	[[Category: Lee JH]]
-	[[Category: ~~Dihydrodipicolinate reductase]]~~	+	[[Category: Park S]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Paenisporosarcina sp. tg-14~~]]	+

OCA at 21:13, 28 October 2020

2020-10-28T21:13:33Z

←Older revision		Revision as of 21:13, 28 October 2020
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	==NADPH/PDA bound Dihydrodipicolinate reductase from Paenisporosarcina sp. TG-14==		==NADPH/PDA bound Dihydrodipicolinate reductase from Paenisporosarcina sp. TG-14==
-	<StructureSection load='5z2f' size='340' side='right' caption='[[5z2f]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5z2f' size='340' side='right'caption='[[5z2f]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z2f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z2F OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z2F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z2f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z2F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Z2F FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</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=5z2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2f OCA], [http://pdbe.org/5z2f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z2f RCSB], [http://www.ebi.ac.uk/pdbsum/5z2f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2f 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=5z2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2f OCA], [http://pdbe.org/5z2f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z2f RCSB], [http://www.ebi.ac.uk/pdbsum/5z2f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2f ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lee, C W]]		[[Category: Lee, C W]]
	[[Category: Lee, J H]]		[[Category: Lee, J H]]

OCA at 05:32, 27 June 2018

2018-06-27T05:32:10Z

←Older revision		Revision as of 05:32, 27 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5z2f is ~~ON HOLD until Paper~~ Publication	+	==NADPH/PDA bound Dihydrodipicolinate reductase from Paenisporosarcina sp. TG-14==
		+	<StructureSection load='5z2f' size='340' side='right' caption='[[5z2f]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5z2f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z2F FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</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=5z2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2f OCA], [http://pdbe.org/5z2f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z2f RCSB], [http://www.ebi.ac.uk/pdbsum/5z2f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2f ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dihydrodipicolinate reductase (DHDPR) is a key enzyme in the diaminopimelate- and lysine-synthesis pathways that reduces DHDP to tetrahydrodipicolinate. Although DHDPR uses both NADPH and NADH as a cofactor, the structural basis for cofactor specificity and preference remains unclear. Here, we report that Paenisporosarcina sp. TG-14 PaDHDPR has a strong preference for NADPH over NADH, as determined by isothermal titration calorimetry and enzymatic activity assays. We determined the crystal structures of PaDHDPR alone, with its competitive inhibitor (dipicolinate), and the ternary complex of the enzyme with dipicolinate and NADPH, with results showing that only the ternary complex had a fully closed conformation and suggesting that binding of both substrate and nucleotide cofactor is required for enzymatic activity. Moreover, NADPH binding induced local conformational changes in the N-terminal long loop (residues 34-59) of PaDHDPR, as the His35 and Lys36 residues in this loop interacted with the 2'-phosphate group of NADPH, possibly accounting for the strong preference of PaDHDPR for NADPH. Mutation of these residues revealed reduced NADPH binding and enzymatic activity, confirming their importance in NADPH binding. These findings provide insight into the mechanism of action and cofactor selectivity of this important bacterial enzyme.

-	~~Authors~~: Lee, ~~J.H.~~, Lee, ~~C.W.~~, Park, S.	+	Crystal structure of dihydrodipicolinate reductase (PaDHDPR) from Paenisporosarcina sp. TG-14: structural basis for NADPH preference as a cofactor.,Lee CW, Park SH, Lee SG, Park HH, Kim HJ, Park H, Park H, Lee JH Sci Rep. 2018 May 21;8(1):7936. doi: 10.1038/s41598-018-26291-x. PMID:29786696<ref>PMID:29786696</ref>

-	~~Description: NADPH~~/~~PDA bound Dihydrodipicolinate reductase from Paenisporosarcina sp~~. TG-14	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5z2f" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lee, C W]]
		+	[[Category: Lee, J H]]
	[[Category: Park, S]]		[[Category: Park, S]]
-	[[Category: ~~Lee, J.H~~]]	+	[[Category: Dihydrodipicolinate reductase]]
-	[[Category: ~~Lee, C~~.W]]	+	[[Category: Oxidoreductase]]
		+	[[Category: Paenisporosarcina sp. tg-14]]

OCA at 04:38, 31 January 2018

2018-01-31T04:38:09Z

←Older revision		Revision as of 04:38, 31 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z2f is ON HOLD	+	The entry 5z2f is ON HOLD until Paper Publication

	Authors: Lee, J.H., Lee, C.W., Park, S.		Authors: Lee, J.H., Lee, C.W., Park, S.
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	Description: NADPH/PDA bound Dihydrodipicolinate reductase from Paenisporosarcina sp. TG-14		Description: NADPH/PDA bound Dihydrodipicolinate reductase from Paenisporosarcina sp. TG-14
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Lee, J.H]]
	[[Category: Park, S]]		[[Category: Park, S]]
		+	[[Category: Lee, J.H]]
	[[Category: Lee, C.W]]		[[Category: Lee, C.W]]

OCA: Protected "5z2f" [edit=sysop:move=sysop]

2018-01-10T07:05:10Z

Protected "5z2f" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:05, 10 January 2018

OCA: New page: '''Unreleased structure''' The entry 5z2f is ON HOLD Authors: Lee, J.H., Lee, C.W., Park, S. Description: NADPH/PDA bound Dihydrodipicolinate reductase from Paenisporosarcina sp. TG-14...

2018-01-10T07:05:08Z

New page: '''Unreleased structure''' The entry 5z2f is ON HOLD Authors: Lee, J.H., Lee, C.W., Park, S. Description: NADPH/PDA bound Dihydrodipicolinate reductase from Paenisporosarcina sp. TG-14...

New page

'''Unreleased structure'''

The entry 5z2f is ON HOLD

Authors: Lee, J.H., Lee, C.W., Park, S.

Description: NADPH/PDA bound Dihydrodipicolinate reductase from Paenisporosarcina sp. TG-14
[[Category: Unreleased Structures]]
[[Category: Lee, J.H]]
[[Category: Park, S]]
[[Category: Lee, C.W]]