4xyl - Revision history

OCA at 10:51, 10 January 2024

OCA — Wed, 10 Jan 2024 10:51:26 GMT

←Older revision		Revision as of 10:51, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xyl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Korarchaeum_cryptofilum_OPF8 Candidatus Korarchaeum cryptofilum OPF8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XYL FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xyl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Korarchaeum_cryptofilum_OPF8 Candidatus Korarchaeum cryptofilum OPF8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XYL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</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]] 1.95Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</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=4xyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyl OCA], [https://pdbe.org/4xyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xyl RCSB], [https://www.ebi.ac.uk/pdbsum/4xyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xyl 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=4xyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyl OCA], [https://pdbe.org/4xyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xyl RCSB], [https://www.ebi.ac.uk/pdbsum/4xyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xyl ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:58, 26 April 2023

OCA — Wed, 26 Apr 2023 17:58:42 GMT

←Older revision		Revision as of 17:58, 26 April 2023
Line 1:		Line 1:

	==Ca. Korarchaeum cryptofilum ACD1 in complex with coenzyme A==		==Ca. Korarchaeum cryptofilum ACD1 in complex with coenzyme A==
-	<StructureSection load='4xyl' size='340' side='right' caption='[[4xyl]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='4xyl' size='340' side='right'caption='[[4xyl]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xyl]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Candidatus_korarchaeum_cryptofilum_opf8~~ Candidatus ~~korarchaeum~~ cryptofilum ~~opf8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XYL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xyl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Korarchaeum_cryptofilum_OPF8 Candidatus Korarchaeum cryptofilum OPF8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XYL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xym\|4xym]], [[4xz3\|4xz3]], [[4y8v\|4y8v]], [[4yak\|4yak]], [[4yaj\|4yaj]], [[4yb8\|4yb8]], [[4ybz\|4ybz]], [[5hbr\|5hbr]]</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=4xyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyl OCA], [https://pdbe.org/4xyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xyl RCSB], [https://www.ebi.ac.uk/pdbsum/4xyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xyl ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Kcr_0198 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=374847 Candidatus Korarchaeum cryptofilum OPF8]), Kcr_0115 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=374847 Candidatus Korarchaeum cryptofilum OPF8])</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=4xyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyl OCA], [~~http~~://pdbe.org/4xyl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xyl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xyl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xyl ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B1L3C9_KORCO B1L3C9_KORCO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Acetyl-CoA synthetase\|Acetyl-CoA synthetase]]	+	*[[Acetyl-CoA synthetase 3D structures\|Acetyl-CoA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Candidatus ~~korarchaeum~~ cryptofilum ~~opf8~~]]	+	[[Category: Candidatus Korarchaeum cryptofilum OPF8]]
-	[[Category: ~~Scheidig, A J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Weisse, R H.J~~]]	+	[[Category: Scheidig AJ]]
-	[[Category: ~~Acd]]~~	+	[[Category: Weisse RH-J]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Dinucleotide forming acetyl~~-~~coa synthetase]]~~	+
-	~~[[Category: Ligase~~]]	+

OCA at 05:58, 8 March 2018

OCA — Thu, 08 Mar 2018 05:58:46 GMT

←Older revision		Revision as of 05:58, 8 March 2018
Line 1:		Line 1:
		+
	==Ca. Korarchaeum cryptofilum ACD1 in complex with coenzyme A==		==Ca. Korarchaeum cryptofilum ACD1 in complex with coenzyme A==
	<StructureSection load='4xyl' size='340' side='right' caption='[[4xyl]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='4xyl' size='340' side='right' caption='[[4xyl]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xyl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XYL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xyl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Candidatus_korarchaeum_cryptofilum_opf8 Candidatus korarchaeum cryptofilum opf8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XYL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xym\|4xym]], [[4xz3\|4xz3]], [[4y8v\|4y8v]], [[4yak\|4yak]], [[4yaj\|4yaj]], [[4yb8\|4yb8]], [[4ybz\|4ybz]], [[5hbr\|5hbr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xym\|4xym]], [[4xz3\|4xz3]], [[4y8v\|4y8v]], [[4yak\|4yak]], [[4yaj\|4yaj]], [[4yb8\|4yb8]], [[4ybz\|4ybz]], [[5hbr\|5hbr]]</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=4xyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyl OCA], [http://pdbe.org/4xyl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xyl RCSB], [http://www.ebi.ac.uk/pdbsum/4xyl PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Kcr_0198 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=374847 Candidatus Korarchaeum cryptofilum OPF8]), Kcr_0115 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=374847 Candidatus Korarchaeum cryptofilum OPF8])</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=4xyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyl OCA], [http://pdbe.org/4xyl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xyl RCSB], [http://www.ebi.ac.uk/pdbsum/4xyl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xyl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4xyl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4xyl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Acetyl-CoA synthetase\|Acetyl-CoA synthetase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Candidatus korarchaeum cryptofilum opf8]]
	[[Category: Scheidig, A J]]		[[Category: Scheidig, A J]]
	[[Category: Weisse, R H.J]]		[[Category: Weisse, R H.J]]

OCA at 07:41, 3 February 2016

OCA — Wed, 03 Feb 2016 07:41:03 GMT

←Older revision		Revision as of 07:41, 3 February 2016
Line 7:		Line 7:
	<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=4xyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyl OCA], [http://pdbe.org/4xyl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xyl RCSB], [http://www.ebi.ac.uk/pdbsum/4xyl 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=4xyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyl OCA], [http://pdbe.org/4xyl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xyl RCSB], [http://www.ebi.ac.uk/pdbsum/4xyl PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The NDP-forming acyl-CoA synthetases (ACDs) catalyze the conversion of various CoA thioesters to the corresponding acids, conserving their chemical energy in form of ATP. The ACDs are the major energy-conserving enzymes in sugar and peptide fermentation of hyperthermophilic archaea. They are considered to be primordial enzymes of ATP synthesis in the early evolution of life. We present the first crystal structures, to our knowledge, of an ACD from the hyperthermophilic archaeon Candidatus Korachaeum cryptofilum. These structures reveal a unique arrangement of the ACD subunits alpha and beta within an alpha2beta2-heterotetrameric complex. This arrangement significantly differs from other members of the superfamily. To transmit an activated phosphoryl moiety from the Ac-CoA binding site (within the alpha subunit) to the NDP-binding site (within the beta subunit), a distance of 51 A has to be bridged. This transmission requires a larger rearrangement within the protein complex involving a 21-aa-long phosphohistidine-containing segment of the alpha subunit. Spatial restraints of the interaction of this segment with the beta subunit explain the necessity for a second highly conserved His residue within the beta subunit. The data support the proposed four-step reaction mechanism of ACDs, coupling acyl-CoA thioesters with ATP synthesis. Furthermore, the determined crystal structure of the complex with bound Ac-CoA allows first insight, to our knowledge, into the determinants for acyl-CoA substrate specificity. The composition and size of loops protruding into the binding pocket of acyl-CoA are determined by the individual arrangement of the characteristic subdomains.
		+
		+	Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer.,Weisse RH, Faust A, Schmidt M, Schonheit P, Scheidig AJ Proc Natl Acad Sci U S A. 2016 Jan 19. pii: 201518614. PMID:26787904<ref>PMID:26787904</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4xyl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 02:30, 28 January 2016

OCA — Thu, 28 Jan 2016 02:30:55 GMT

←Older revision		Revision as of 02:30, 28 January 2016
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Ca. Korarchaeum cryptofilum ACD1 in complex with coenzyme A==
-		+	<StructureSection load='4xyl' size='340' side='right' caption='[[4xyl]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~The entry~~ 4xyl is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4xyl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XYL FirstGlance]. <br>
-	~~Authors~~: ~~Weisse, R~~.H.-J.~~, Scheidig, A~~.J.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xym\|4xym]], [[4xz3\|4xz3]], [[4y8v\|4y8v]], [[4yak\|4yak]], [[4yaj\|4yaj]], [[4yb8\|4yb8]], [[4ybz\|4ybz]], [[5hbr\|5hbr]]</td></tr>
-	~~Description~~:	+	<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=4xyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyl OCA], [http://pdbe.org/4xyl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xyl RCSB], [http://www.ebi.ac.uk/pdbsum/4xyl PDBsum]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: Scheidig, A.J]]	+	__TOC__
-	[[Category: Weisse, R.H.-J]]	+	</StructureSection>
		+	[[Category: Scheidig, A J]]
		+	[[Category: Weisse, R H.J]]
		+	[[Category: Acd]]
		+	[[Category: Complex]]
		+	[[Category: Dinucleotide forming acetyl-coa synthetase]]
		+	[[Category: Ligase]]

OCA at 09:44, 30 September 2015

OCA — Wed, 30 Sep 2015 09:44:01 GMT

←Older revision		Revision as of 09:44, 30 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xyl is ON HOLD	+	The entry 4xyl is ON HOLD until Paper Publication

	Authors: Weisse, R.H.-J., Scheidig, A.J.		Authors: Weisse, R.H.-J., Scheidig, A.J.

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

OCA — Thu, 12 Feb 2015 10:52:21 GMT

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

←Older revision

Revision as of 10:52, 12 February 2015

OCA: New page: '''Unreleased structure''' The entry 4xyl is ON HOLD Authors: Weisse, R.H.-J., Scheidig, A.J. Description: Category: Unreleased Structures Category: Scheidig, A.J [[Category: ...

OCA — Thu, 12 Feb 2015 10:52:20 GMT

New page: '''Unreleased structure''' The entry 4xyl is ON HOLD Authors: Weisse, R.H.-J., Scheidig, A.J. Description: Category: Unreleased Structures Category: Scheidig, A.J [[Category: ...

New page

'''Unreleased structure'''

The entry 4xyl is ON HOLD

Authors: Weisse, R.H.-J., Scheidig, A.J.

Description:
[[Category: Unreleased Structures]]
[[Category: Scheidig, A.J]]
[[Category: Weisse, R.H.-J]]