5wlw - Revision history

OCA at 14:16, 4 October 2023

2023-10-04T14:16:47Z

←Older revision		Revision as of 14:16, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5wlw' size='340' side='right'caption='[[5wlw]], [[Resolution\|resolution]] 3.32Å' scene=''>		<StructureSection load='5wlw' size='340' side='right'caption='[[5wlw]], [[Resolution\|resolution]] 3.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wlw]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5WLW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wlw]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_S88 Escherichia coli S88] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WLW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8Q1:S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]+dodecanethioate'>8Q1</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.317Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wgb\|5wgb]], [[5wkp\|5wkp]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8Q1:S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]+dodecanethioate'>8Q1</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cysteine_desulfurase Cysteine desulfurase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.8.1.7 2.8.1.7] </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=5wlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wlw OCA], [https://pdbe.org/5wlw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wlw RCSB], [https://www.ebi.ac.uk/pdbsum/5wlw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wlw 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=5wlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wlw OCA], [~~http~~://pdbe.org/5wlw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wlw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wlw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wlw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/ISCU_HUMAN ISCU_HUMAN]] Hereditary myopathy with lactic acidosis due to ISCU deficiency. The disease is caused by mutations affecting the gene represented in this entry. [[http://www.uniprot.org/uniprot/NFS1_HUMAN NFS1_HUMAN]] Severe neonatal lactic acidosis due to NFS1-ISD11 complex deficiency. [[http://www.uniprot.org/uniprot/LYRM4_HUMAN LYRM4_HUMAN]] Severe neonatal lactic acidosis due to NFS1-ISD11 complex deficiency. The disease is caused by mutations affecting the gene represented in this entry.	+	[https://www.uniprot.org/uniprot/ISCU_HUMAN ISCU_HUMAN] Hereditary myopathy with lactic acidosis due to ISCU deficiency. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ISCU_HUMAN ISCU_HUMAN]] Scaffold protein for the de novo synthesis of iron-sulfur (Fe-S) clusters within mitochondria, which is required for maturation of both mitochondrial and cytoplasmic [2Fe-2S] and [4Fe-4S] proteins (PubMed:11060020). First, a [2Fe-2S] cluster is transiently assembled on the scaffold protein ISCU. In a second step, the cluster is released from ISCU, transferred to a glutaredoxin GLRX5, followed by the formation of mitochondrial [2Fe-2S] proteins, the synthesis of [4Fe-4S] clusters and their target-specific insertion into the recipient apoproteins. Cluster assembly on ISCU depends on the function of the cysteine desulfurase complex NFS1-LYRM4/ISD11, which serves as the sulfur donor for cluster synthesis, the iron-binding protein frataxin as the putative iron donor, and the electron transfer chain comprised of ferredoxin reductase and ferredoxin, which receive their electrons from NADH (By similarity).[UniProtKB:Q03020]<ref>PMID:11060020</ref> [[http://www.uniprot.org/uniprot/NFS1_HUMAN NFS1_HUMAN]] Catalyzes the removal of elemental sulfur from cysteine to produce alanine. It supplies the inorganic sulfur for iron-sulfur (Fe-S) clusters. May be involved in the biosynthesis of molybdenum cofactor.<ref>PMID:18650437</ref> [[http://www.uniprot.org/uniprot/ACP_ECO45 ACP_ECO45]] Carrier of the growing fatty acid chain in fatty acid biosynthesis.[HAMAP-Rule:MF_01217] [[http://www.uniprot.org/uniprot/LYRM4_HUMAN LYRM4_HUMAN]] Required for nuclear and mitochondrial iron-sulfur protein biosynthesis.<ref>PMID:17331979</ref> <ref>PMID:19454487</ref>	+	[https://www.uniprot.org/uniprot/ISCU_HUMAN ISCU_HUMAN] Scaffold protein for the de novo synthesis of iron-sulfur (Fe-S) clusters within mitochondria, which is required for maturation of both mitochondrial and cytoplasmic [2Fe-2S] and [4Fe-4S] proteins (PubMed:11060020). First, a [2Fe-2S] cluster is transiently assembled on the scaffold protein ISCU. In a second step, the cluster is released from ISCU, transferred to a glutaredoxin GLRX5, followed by the formation of mitochondrial [2Fe-2S] proteins, the synthesis of [4Fe-4S] clusters and their target-specific insertion into the recipient apoproteins. Cluster assembly on ISCU depends on the function of the cysteine desulfurase complex NFS1-LYRM4/ISD11, which serves as the sulfur donor for cluster synthesis, the iron-binding protein frataxin as the putative iron donor, and the electron transfer chain comprised of ferredoxin reductase and ferredoxin, which receive their electrons from NADH (By similarity).[UniProtKB:Q03020]<ref>PMID:11060020</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 30:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cysteine desulfurase~~]]	+	[[Category: Escherichia coli S88]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boniecki~~, M T~~]]	+	[[Category: Boniecki MT]]
-	[[Category: Cygler, M]]	+	[[Category: Cygler M]]
-	~~[[Category: Transferase~~]]	+

OCA at 08:53, 30 September 2020

2020-09-30T08:53:52Z

←Older revision		Revision as of 08:53, 30 September 2020
Line 1:		Line 1:

	==Crystal Structure of the Human Mitochondrial Cysteine Desulfurase with active Cysteine Loop within ISCU1 active site, coordinating Zn ion. Complexed with human ISD11 and E. coli ACP1 at 3.3A.==		==Crystal Structure of the Human Mitochondrial Cysteine Desulfurase with active Cysteine Loop within ISCU1 active site, coordinating Zn ion. Complexed with human ISD11 and E. coli ACP1 at 3.3A.==
-	<StructureSection load='5wlw' size='340' side='right' caption='[[5wlw]], [[Resolution\|resolution]] 3.32Å' scene=''>	+	<StructureSection load='5wlw' size='340' side='right'caption='[[5wlw]], [[Resolution\|resolution]] 3.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wlw]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLW OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WLW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wlw]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5WLW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8Q1:S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]+dodecanethioate'>8Q1</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8Q1:S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]+dodecanethioate'>8Q1</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wgb\|5wgb]], [[5wkp\|5wkp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wgb\|5wgb]], [[5wkp\|5wkp]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cysteine_desulfurase Cysteine desulfurase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.8.1.7 2.8.1.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cysteine_desulfurase Cysteine desulfurase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.8.1.7 2.8.1.7] </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=5wlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wlw OCA], [http://pdbe.org/5wlw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wlw RCSB], [http://www.ebi.ac.uk/pdbsum/5wlw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wlw 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=5wlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wlw OCA], [http://pdbe.org/5wlw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wlw RCSB], [http://www.ebi.ac.uk/pdbsum/5wlw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wlw ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 22:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 5wlw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5wlw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Acyl carrier protein 3D structures\|Acyl carrier protein 3D structures]]
		+	*[[Cysteine desulfurase 3D structures\|Cysteine desulfurase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Cysteine desulfurase]]		[[Category: Cysteine desulfurase]]
		+	[[Category: Large Structures]]
	[[Category: Boniecki, M T]]		[[Category: Boniecki, M T]]
	[[Category: Cygler, M]]		[[Category: Cygler, M]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 07:36, 15 November 2017

2017-11-15T07:36:22Z

←Older revision		Revision as of 07:36, 15 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The entry ~~5wlw~~ is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal Structure of the Human Mitochondrial Cysteine Desulfurase with active Cysteine Loop within ISCU1 active site, coordinating Zn ion. Complexed with human ISD11 and E. coli ACP1 at 3.3A.==
		+	<StructureSection load='5wlw' size='340' side='right' caption='[[5wlw]], [[Resolution\|resolution]] 3.32Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5wlw]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WLW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8Q1:S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]+dodecanethioate'>8Q1</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wgb\|5wgb]], [[5wkp\|5wkp]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cysteine_desulfurase Cysteine desulfurase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.8.1.7 2.8.1.7] </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=5wlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wlw OCA], [http://pdbe.org/5wlw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wlw RCSB], [http://www.ebi.ac.uk/pdbsum/5wlw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wlw ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/ISCU_HUMAN ISCU_HUMAN]] Hereditary myopathy with lactic acidosis due to ISCU deficiency. The disease is caused by mutations affecting the gene represented in this entry. [[http://www.uniprot.org/uniprot/NFS1_HUMAN NFS1_HUMAN]] Severe neonatal lactic acidosis due to NFS1-ISD11 complex deficiency. [[http://www.uniprot.org/uniprot/LYRM4_HUMAN LYRM4_HUMAN]] Severe neonatal lactic acidosis due to NFS1-ISD11 complex deficiency. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ISCU_HUMAN ISCU_HUMAN]] Scaffold protein for the de novo synthesis of iron-sulfur (Fe-S) clusters within mitochondria, which is required for maturation of both mitochondrial and cytoplasmic [2Fe-2S] and [4Fe-4S] proteins (PubMed:11060020). First, a [2Fe-2S] cluster is transiently assembled on the scaffold protein ISCU. In a second step, the cluster is released from ISCU, transferred to a glutaredoxin GLRX5, followed by the formation of mitochondrial [2Fe-2S] proteins, the synthesis of [4Fe-4S] clusters and their target-specific insertion into the recipient apoproteins. Cluster assembly on ISCU depends on the function of the cysteine desulfurase complex NFS1-LYRM4/ISD11, which serves as the sulfur donor for cluster synthesis, the iron-binding protein frataxin as the putative iron donor, and the electron transfer chain comprised of ferredoxin reductase and ferredoxin, which receive their electrons from NADH (By similarity).[UniProtKB:Q03020]<ref>PMID:11060020</ref> [[http://www.uniprot.org/uniprot/NFS1_HUMAN NFS1_HUMAN]] Catalyzes the removal of elemental sulfur from cysteine to produce alanine. It supplies the inorganic sulfur for iron-sulfur (Fe-S) clusters. May be involved in the biosynthesis of molybdenum cofactor.<ref>PMID:18650437</ref> [[http://www.uniprot.org/uniprot/ACP_ECO45 ACP_ECO45]] Carrier of the growing fatty acid chain in fatty acid biosynthesis.[HAMAP-Rule:MF_01217] [[http://www.uniprot.org/uniprot/LYRM4_HUMAN LYRM4_HUMAN]] Required for nuclear and mitochondrial iron-sulfur protein biosynthesis.<ref>PMID:17331979</ref> <ref>PMID:19454487</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Iron-sulfur (Fe/S) clusters are essential protein cofactors crucial for many cellular functions including DNA maintenance, protein translation, and energy conversion. De novo Fe/S cluster synthesis occurs on the mitochondrial scaffold protein ISCU and requires cysteine desulfurase NFS1, ferredoxin, frataxin, and the small factors ISD11 and ACP (acyl carrier protein). Both the mechanism of Fe/S cluster synthesis and function of ISD11-ACP are poorly understood. Here, we present crystal structures of three different NFS1-ISD11-ACP complexes with and without ISCU, and we use SAXS analyses to define the 3D architecture of the complete mitochondrial Fe/S cluster biosynthetic complex. Our structural and biochemical studies provide mechanistic insights into Fe/S cluster synthesis at the catalytic center defined by the active-site Cys of NFS1 and conserved Cys, Asp, and His residues of ISCU. We assign specific regulatory rather than catalytic roles to ISD11-ACP that link Fe/S cluster synthesis with mitochondrial lipid synthesis and cellular energy status.

-	~~Authors:~~ Boniecki, ~~M.T.~~, ~~Cygler~~, M.	+	Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex.,Boniecki MT, Freibert SA, Muhlenhoff U, Lill R, Cygler M Nat Commun. 2017 Nov 3;8(1):1287. doi: 10.1038/s41467-017-01497-1. PMID:29097656<ref>PMID:29097656</ref>

-	~~Description: Crystal Structure~~ of the ~~Human Mitochondrial Cysteine Desulfurase with active Cysteine Loop within ISCU1 active site, coordinating Zn ion~~. ~~Complexed with human ISD11 and E~~. ~~coli ACP1 at 3.3A~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5wlw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cysteine desulfurase]]
		+	[[Category: Boniecki, M T]]
	[[Category: Cygler, M]]		[[Category: Cygler, M]]
-	[[Category: ~~Boniecki, M.T~~]]	+	[[Category: Transferase]]

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

2017-09-27T14:58:09Z

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

←Older revision

Revision as of 14:58, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5wlw is ON HOLD until Paper Publication Authors: Boniecki, M.T., Cygler, M. Description: Crystal Structure of the Human Mitochondrial Cysteine Desu...

2017-09-27T14:58:07Z

New page: '''Unreleased structure''' The entry 5wlw is ON HOLD until Paper Publication Authors: Boniecki, M.T., Cygler, M. Description: Crystal Structure of the Human Mitochondrial Cysteine Desu...

New page

'''Unreleased structure'''

The entry 5wlw is ON HOLD until Paper Publication

Authors: Boniecki, M.T., Cygler, M.

Description: Crystal Structure of the Human Mitochondrial Cysteine Desulfurase with active Cysteine Loop within ISCU1 active site, coordinating Zn ion. Complexed with human ISD11 and E. coli ACP1 at 3.3A.
[[Category: Unreleased Structures]]
[[Category: Cygler, M]]
[[Category: Boniecki, M.T]]