1m1y - Revision history

OCA at 07:38, 14 February 2024

OCA — Wed, 14 Feb 2024 07:38:45 GMT

←Older revision		Revision as of 07:38, 14 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m1y]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M1Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m1y]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M1Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CFM:FE-MO-S+CLUSTER'>CFM</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 3.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1n2c\|1n2c]], [[3min\|3min]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CFM:FE-MO-S+CLUSTER'>CFM</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </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=1m1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1y OCA], [https://pdbe.org/1m1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m1y RCSB], [https://www.ebi.ac.uk/pdbsum/1m1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m1y 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=1m1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1y OCA], [https://pdbe.org/1m1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m1y RCSB], [https://www.ebi.ac.uk/pdbsum/1m1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m1y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	~~[[https://www.uniprot.org/uniprot/NIFD_AZOVI NIFD_AZOVI]] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation. [~~[https://www.uniprot.org/uniprot/NIFH1_AZOVI NIFH1_AZOVI]] The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein (component 2) and a component 1 which is either a molybdenum-iron protein, a vanadium-iron, or an iron-iron protein.[HAMAP-Rule:MF_00533] ~~[[https://www.uniprot.org/uniprot/NIFK_AZOVI NIFK_AZOVI]] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.~~	+	[https://www.uniprot.org/uniprot/NIFH1_AZOVI NIFH1_AZOVI] The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein (component 2) and a component 1 which is either a molybdenum-iron protein, a vanadium-iron, or an iron-iron protein.[HAMAP-Rule:MF_00533]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m1y ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m1y ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The transient formation of a complex between the component Fe- and MoFe-proteins of nitrogenase represents a central event in the substrate reduction mechanism of this enzyme. Previously, we have isolated an N-[3-(dimethylamino)propyl]-N'-ethylcarbodiimide (EDC) cross-linked complex of these proteins stabilized by a covalent isopeptide linkage between Glu 112 and Lys beta400 of the Fe-protein and MoFe-protein, respectively [Willing, A., et al. (1989) J. Biol. Chem. 264, 8499-8503; Willing, A., and Howard, J. B. (1990) J. Biol. Chem. 265, 6596-6599]. We report here the biochemical and structural characterization of the cross-linked complex to assess the mechanistic relevance of this species. Glycinamide inhibits the cross-linking reaction, and is found to be specifically incorporated into Glu 112 of the Fe-protein, without detectable modification of either of the neighboring residues (Glu 110 and Glu 111). This modified protein is still competent for substrate reduction, demonstrating that formation of the cross-linked complex is responsible for the enzymatic inactivation, and not the EDC reaction or the modification of the Fe-protein. Crystallographic analysis of the EDC-cross-linked complex at 3.2 A resolution confirms the site of the isopeptide linkage. The nature of the protein surfaces around the cross-linking site suggests there is a strong electrostatic component to the formation of the complex, although the interface area between the component proteins is small. The binding footprints between proteins in the cross-linked complex are adjacent, but with little overlap, to those observed in the complex of the nitrogenase proteins stabilized by ADP-AlF(4)(-). The results of these studies suggest that EDC cross-linking traps a nucleotide-independent precomplex of the nitrogenase proteins driven by complementary electrostatic interactions that subsequently rearranges in a nucleotide-dependent fashion to the electron transfer competent state observed in the ADP-AlF(4)(-) structure.
-
-	Biochemical and structural characterization of the cross-linked complex of nitrogenase: comparison to the ADP-AlF4(-)-stabilized structure.,Schmid B, Einsle O, Chiu HJ, Willing A, Yoshida M, Howard JB, Rees DC Biochemistry. 2002 Dec 31;41(52):15557-65. PMID:12501184<ref>PMID:12501184</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1m1y" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Nitrogenase 3D structures\|Nitrogenase 3D structures]]		*[[Nitrogenase 3D structures\|Nitrogenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Nitrogenase]]~~	+	[[Category: Chiu HJ]]
-	[[Category: Chiu~~, H J~~]]	+	[[Category: Einsle O]]
-	[[Category: Einsle, O]]	+	[[Category: Howard JB]]
-	[[Category: Howard~~, J B~~]]	+	[[Category: Rees DC]]
-	[[Category: Rees~~, D C~~]]	+	[[Category: Schmid B]]
-	[[Category: Schmid, B]]	+	[[Category: Willing A]]
-	[[Category: Willing, A]]	+	[[Category: Yoshida M]]
-	[[Category: Yoshida, M]]	+
-	~~[[Category: Chemical crosslink]]~~	+
-	~~[[Category: Nitrogen fixation]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Protein interaction~~]]	+

OCA at 09:01, 21 July 2021

OCA — Wed, 21 Jul 2021 09:01:27 GMT

←Older revision		Revision as of 09:01, 21 July 2021
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	<StructureSection load='1m1y' size='340' side='right'caption='[[1m1y]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='1m1y' size='340' side='right'caption='[[1m1y]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m1y]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M1Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1M1Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m1y]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M1Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CFM:FE-MO-S+CLUSTER'>CFM</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CFM:FE-MO-S+CLUSTER'>CFM</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n2c\|1n2c]], [[3min\|3min]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1n2c\|1n2c]], [[3min\|3min]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </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=1m1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1y OCA], [~~http~~://pdbe.org/1m1y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1m1y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1m1y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1m1y 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=1m1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1y OCA], [https://pdbe.org/1m1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m1y RCSB], [https://www.ebi.ac.uk/pdbsum/1m1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m1y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NIFD_AZOVI NIFD_AZOVI]] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation. [[~~http~~://www.uniprot.org/uniprot/NIFH1_AZOVI NIFH1_AZOVI]] The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein (component 2) and a component 1 which is either a molybdenum-iron protein, a vanadium-iron, or an iron-iron protein.[HAMAP-Rule:MF_00533] [[~~http~~://www.uniprot.org/uniprot/NIFK_AZOVI NIFK_AZOVI]] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.	+	[[https://www.uniprot.org/uniprot/NIFD_AZOVI NIFD_AZOVI]] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation. [[https://www.uniprot.org/uniprot/NIFH1_AZOVI NIFH1_AZOVI]] The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein (component 2) and a component 1 which is either a molybdenum-iron protein, a vanadium-iron, or an iron-iron protein.[HAMAP-Rule:MF_00533] [[https://www.uniprot.org/uniprot/NIFK_AZOVI NIFK_AZOVI]] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 12:08, 13 November 2019

OCA — Wed, 13 Nov 2019 12:08:43 GMT

←Older revision		Revision as of 12:08, 13 November 2019
Line 1:		Line 1:

	==Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein==		==Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein==
-	<StructureSection load='1m1y' size='340' side='right' caption='[[1m1y]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='1m1y' size='340' side='right'caption='[[1m1y]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m1y]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M1Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m1y]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M1Y FirstGlance]. <br>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1m1y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m1y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrogenase 3D structures\|Nitrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
		+	[[Category: Large Structures]]
	[[Category: Nitrogenase]]		[[Category: Nitrogenase]]
	[[Category: Chiu, H J]]		[[Category: Chiu, H J]]

OCA at 07:45, 31 January 2018

OCA — Wed, 31 Jan 2018 07:45:25 GMT

←Older revision		Revision as of 07:45, 31 January 2018
Line 1:		Line 1:
		+
	==Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein==		==Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein==
	<StructureSection load='1m1y' size='340' side='right' caption='[[1m1y]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='1m1y' size='340' side='right' caption='[[1m1y]], [[Resolution\|resolution]] 3.20Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n2c\|1n2c]], [[3min\|3min]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n2c\|1n2c]], [[3min\|3min]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </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=1m1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1y OCA], [http://pdbe.org/1m1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m1y RCSB], [http://www.ebi.ac.uk/pdbsum/1m1y 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=1m1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1y OCA], [http://pdbe.org/1m1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m1y RCSB], [http://www.ebi.ac.uk/pdbsum/1m1y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m1y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m1/1m1y_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m1/1m1y_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1m1y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m1y" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Nitrogenase\|Nitrogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:27, 7 February 2016

OCA — Sun, 07 Feb 2016 14:27:42 GMT

←Older revision		Revision as of 14:27, 7 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m1y ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:22, 10 September 2015

OCA — Thu, 10 Sep 2015 02:22:48 GMT

←Older revision		Revision as of 02:22, 10 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n2c\|1n2c]], [[3min\|3min]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n2c\|1n2c]], [[3min\|3min]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </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=1m1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m1y RCSB], [http://www.ebi.ac.uk/pdbsum/1m1y 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=1m1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1y OCA], [http://pdbe.org/1m1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m1y RCSB], [http://www.ebi.ac.uk/pdbsum/1m1y PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1m1y" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 15:55, 24 December 2014

OCA — Wed, 24 Dec 2014 15:55:53 GMT

←Older revision		Revision as of 15:55, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m1y]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M1Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m1y]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M1Y FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CFM:FE-MO-S+CLUSTER'>CFM</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CFM:FE-MO-S+CLUSTER'>CFM</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n2c\|1n2c]], [[3min\|3min]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n2c\|1n2c]], [[3min\|3min]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m1y RCSB], [http://www.ebi.ac.uk/pdbsum/1m1y 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=1m1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m1y RCSB], [http://www.ebi.ac.uk/pdbsum/1m1y PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NIFD_AZOVI NIFD_AZOVI]] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation. [[http://www.uniprot.org/uniprot/NIFH1_AZOVI NIFH1_AZOVI]] The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein (component 2) and a component 1 which is either a molybdenum-iron protein, a vanadium-iron, or an iron-iron protein.[HAMAP-Rule:MF_00533] [[http://www.uniprot.org/uniprot/NIFK_AZOVI NIFK_AZOVI]] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
	[[Category: Nitrogenase]]		[[Category: Nitrogenase]]
-	[[Category: Chiu, H J.]]	+	[[Category: Chiu, H J]]
-	[[Category: Einsle, O.]]	+	[[Category: Einsle, O]]
-	[[Category: Howard, J B.]]	+	[[Category: Howard, J B]]
-	[[Category: Rees, D C.]]	+	[[Category: Rees, D C]]
-	[[Category: Schmid, B.]]	+	[[Category: Schmid, B]]
-	[[Category: Willing, A.]]	+	[[Category: Willing, A]]
-	[[Category: Yoshida, M.]]	+	[[Category: Yoshida, M]]
	[[Category: Chemical crosslink]]		[[Category: Chemical crosslink]]
	[[Category: Nitrogen fixation]]		[[Category: Nitrogen fixation]]
-	[[Category: Nitrogenase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Protein interaction]]		[[Category: Protein interaction]]

OCA at 16:36, 28 September 2014

OCA — Sun, 28 Sep 2014 16:36:49 GMT

←Older revision		Revision as of 16:36, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1m1y.~~png~~\|~~left~~\|200px]]	+	==Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein==
		+	<StructureSection load='1m1y' size='340' side='right' caption='[[1m1y]], [[Resolution\|resolution]] 3.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1m1y]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M1Y FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CFM:FE-MO-S+CLUSTER'>CFM</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n2c\|1n2c]], [[3min\|3min]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m1y RCSB], [http://www.ebi.ac.uk/pdbsum/1m1y PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m1/1m1y_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The transient formation of a complex between the component Fe- and MoFe-proteins of nitrogenase represents a central event in the substrate reduction mechanism of this enzyme. Previously, we have isolated an N-[3-(dimethylamino)propyl]-N'-ethylcarbodiimide (EDC) cross-linked complex of these proteins stabilized by a covalent isopeptide linkage between Glu 112 and Lys beta400 of the Fe-protein and MoFe-protein, respectively [Willing, A., et al. (1989) J. Biol. Chem. 264, 8499-8503; Willing, A., and Howard, J. B. (1990) J. Biol. Chem. 265, 6596-6599]. We report here the biochemical and structural characterization of the cross-linked complex to assess the mechanistic relevance of this species. Glycinamide inhibits the cross-linking reaction, and is found to be specifically incorporated into Glu 112 of the Fe-protein, without detectable modification of either of the neighboring residues (Glu 110 and Glu 111). This modified protein is still competent for substrate reduction, demonstrating that formation of the cross-linked complex is responsible for the enzymatic inactivation, and not the EDC reaction or the modification of the Fe-protein. Crystallographic analysis of the EDC-cross-linked complex at 3.2 A resolution confirms the site of the isopeptide linkage. The nature of the protein surfaces around the cross-linking site suggests there is a strong electrostatic component to the formation of the complex, although the interface area between the component proteins is small. The binding footprints between proteins in the cross-linked complex are adjacent, but with little overlap, to those observed in the complex of the nitrogenase proteins stabilized by ADP-AlF(4)(-). The results of these studies suggest that EDC cross-linking traps a nucleotide-independent precomplex of the nitrogenase proteins driven by complementary electrostatic interactions that subsequently rearranges in a nucleotide-dependent fashion to the electron transfer competent state observed in the ADP-AlF(4)(-) structure.

-	~~{{STRUCTURE_1m1y\| PDB=1m1y \| SCENE= }}~~	+	Biochemical and structural characterization of the cross-linked complex of nitrogenase: comparison to the ADP-AlF4(-)-stabilized structure.,Schmid B, Einsle O, Chiu HJ, Willing A, Yoshida M, Howard JB, Rees DC Biochemistry. 2002 Dec 31;41(52):15557-65. PMID:12501184<ref>PMID:12501184</ref>

-	~~===Chemical Crosslink~~ of ~~Nitrogenase MoFe Protein and Fe Protein===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12501184}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1m1y]] is a 16 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1M1Y OCA].~~	+

	==See Also==		==See Also==
	*[[Nitrogenase\|Nitrogenase]]		*[[Nitrogenase\|Nitrogenase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012501184<~~/~~ref~~><~~ref group="xtra">PMID:020400946</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
	[[Category: Nitrogenase]]		[[Category: Nitrogenase]]

OCA at 06:55, 20 October 2012

OCA — Sat, 20 Oct 2012 06:55:32 GMT

←Older revision		Revision as of 06:55, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1m1y]] is a 16 chain structure ~~of [[Nitrogenase]]~~ with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M1Y OCA].	+	[[1m1y]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M1Y OCA].

	==See Also==		==See Also==

OCA: Protected "1m1y" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 14:45:50 GMT

Protected "1m1y" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:45, 25 July 2012