6u1j - Revision history

OCA at 07:42, 11 October 2023

2023-10-11T07:42:30Z

←Older revision		Revision as of 07:42, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6u1j' size='340' side='right'caption='[[6u1j]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6u1j' size='340' side='right'caption='[[6u1j]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u1j]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thet8 Thet8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U1J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6U1J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u1j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U1J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U1J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.2Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6u1c\|6u1c]], [[6u1d\|6u1d]], [[6u1e\|6u1e]], [[6u1f\|6u1f]], [[6u1g\|6u1g]], [[6u1h\|6u1h]], [[6u1i\|6u1i]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddl, TTHA1587 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=6u1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u1j OCA], [https://pdbe.org/6u1j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u1j RCSB], [https://www.ebi.ac.uk/pdbsum/6u1j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u1j 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/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </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=6u1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u1j OCA], [~~http~~://pdbe.org/6u1j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6u1j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6u1j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6u1j ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DDL_THET8 DDL_THET8]] Cell wall formation.[HAMAP-Rule:MF_00047]	+	[https://www.uniprot.org/uniprot/DDL_THET8 DDL_THET8] Cell wall formation.[HAMAP-Rule:MF_00047]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6u1j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6u1j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[D-alanine-D-alanine ligase 3D structures\|D-alanine-D-alanine ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: D-alanine--D-alanine ligase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet8~~]]	+	[[Category: Thermus thermophilus HB8]]
-	[[Category: Bruning~~, J B~~]]	+	[[Category: Bruning JB]]
-	[[Category: Pederick~~, J L~~]]	+	[[Category: Pederick JL]]
-	[[Category: Thompson~~, A P]]~~	+	[[Category: Thompson AP]]
-	~~[[Category: Atp binding]]~~	+
-	~~[[Category: Atp-grasp domain]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Metal binding~~]]	+

OCA at 10:43, 17 June 2020

2020-06-17T10:43:00Z

←Older revision		Revision as of 10:43, 17 June 2020
Line 1:		Line 1:

	==Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphate, D-ala-D-ala, Mg2+ and K+==		==Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphate, D-ala-D-ala, Mg2+ and K+==
-	<StructureSection load='6u1j' size='340' side='right'caption='[[6u1j]]' scene=''>	+	<StructureSection load='6u1j' size='340' side='right'caption='[[6u1j]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U1J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6U1J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u1j]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U1J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6U1J FirstGlance]. <br>
-	</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=6u1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u1j OCA], [http://pdbe.org/6u1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u1j RCSB], [http://www.ebi.ac.uk/pdbsum/6u1j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u1j ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6u1c\|6u1c]], [[6u1d\|6u1d]], [[6u1e\|6u1e]], [[6u1f\|6u1f]], [[6u1g\|6u1g]], [[6u1h\|6u1h]], [[6u1i\|6u1i]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddl, TTHA1587 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </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=6u1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u1j OCA], [http://pdbe.org/6u1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u1j RCSB], [http://www.ebi.ac.uk/pdbsum/6u1j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u1j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DDL_THET8 DDL_THET8]] Cell wall formation.[HAMAP-Rule:MF_00047]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The ATP-grasp superfamily of enzymes shares an atypical nucleotide-binding site known as the ATP-grasp fold. These enzymes are involved in many biological pathways in all domains of life. One ATP-grasp enzyme, D-alanine-D-alanine ligase (Ddl), catalyzes the ATP-dependent formation of the D-alanyl-D-alanine dipeptide essential for bacterial cell-wall biosynthesis, and is therefore an important antibiotic drug target. Ddl is activated by the monovalent cation (MVC) K(+), but despite its clinical relevance and decades of research, how this activation occurs has not been elucidated. We demonstrate here that activating MVCs bind adjacent to the active site of Ddl from Thermus thermophilus and used a combined biochemical and structural approach to characterize the MVC activation. We found that TtDdl is a Type II MVC-activated enzyme, retaining activity in the absence of MVCs. However, the efficiency of TtDdl increased ~20-fold in the presence of activating MVCs, and it was maximally activated by K(+) and Rb(+) ions. A strict dependence on ionic radius of the MVC was observed, with Li(+) and Na(+) providing little-to-no TtDdl activation. To understand the mechanism of MVC activation, we solved crystal structures of TtDdl representing distinct catalytic stages in complex with K(+), Rb(+), or Cs(+) Comparison of these structures with apo TtDdl revealed no evident conformational change on MVC binding. Of note, the identified MVC-binding site is structurally conserved within the ATP-grasp superfamily. We propose that MVCs activate Ddl by altering the charge distribution of its active site. These findings provide insight into the catalytic mechanism of ATP-grasp enzymes.
		+
		+	D-alanine-D-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations.,Pederick JL, Thompson AP, Bell SG, Bruning JB J Biol Chem. 2020 Apr 25. pii: RA120.012936. doi: 10.1074/jbc.RA120.012936. PMID:32335509<ref>PMID:32335509</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6u1j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: D-alanine--D-alanine ligase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bruning JB]]	+	[[Category: Thet8]]
-	[[Category: Pederick JL]]	+	[[Category: Bruning, J B]]
-	[[Category: Thompson AP]]	+	[[Category: Pederick, J L]]
		+	[[Category: Thompson, A P]]
		+	[[Category: Atp binding]]
		+	[[Category: Atp-grasp domain]]
		+	[[Category: Ligase]]
		+	[[Category: Metal binding]]

OCA at 06:04, 6 May 2020

2020-05-06T06:04:07Z

←Older revision		Revision as of 06:04, 6 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6u1j is ~~ON HOLD until Paper Publication~~	+	==Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphate, D-ala-D-ala, Mg2+ and K+==
-		+	<StructureSection load='6u1j' size='340' side='right'caption='[[6u1j]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U1J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6U1J FirstGlance]. <br>
-	~~Description~~:	+	</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=6u1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u1j OCA], [http://pdbe.org/6u1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u1j RCSB], [http://www.ebi.ac.uk/pdbsum/6u1j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u1j ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bruning JB]]
		+	[[Category: Pederick JL]]
		+	[[Category: Thompson AP]]

OCA at 05:06, 29 April 2020

2020-04-29T05:06:59Z

←Older revision		Revision as of 05:06, 29 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6u1j is ON HOLD	+	The entry 6u1j is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 04:10, 22 April 2020

2020-04-22T04:10:12Z

←Older revision		Revision as of 04:10, 22 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6u1j is ON HOLD ~~until Paper Publication~~	+	The entry 6u1j is ON HOLD

	Authors:		Authors:

OCA at 08:06, 2 October 2019

2019-10-02T08:06:26Z

←Older revision		Revision as of 08:06, 2 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6u1j is ON HOLD	+	The entry 6u1j is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6u1j" [edit=sysop:move=sysop]

2019-08-21T04:31:55Z

Protected "6u1j" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:31, 21 August 2019

OCA: New page: '''Unreleased structure''' The entry 6u1j is ON HOLD Authors: Description: Category: Unreleased Structures

2019-08-21T04:31:54Z

New page: '''Unreleased structure''' The entry 6u1j is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6u1j is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]