6o0b: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 6o0b is ~~ON HOLD until Paper~~ Publication

==Structural and Mechanistic Insights into CO2 Activation by Nitrogenase Iron Protein==

== Structural highlights ==

<table><tr><td colspan='2'>[[6o0b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Azovd Azovd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O0B FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>

<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nifH, Avin_01380 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=322710 AZOVD])</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=6o0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o0b OCA], [http://pdbe.org/6o0b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o0b RCSB], [http://www.ebi.ac.uk/pdbsum/6o0b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o0b ProSAT]</span></td></tr>

</table>

== Function ==

[[http://www.uniprot.org/uniprot/C1DGZ6_AZOVD C1DGZ6_AZOVD]] The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein and the molybdenum-iron protein.[HAMAP-Rule:MF_00533]

== Publication Abstract from PubMed ==

The Fe protein of nitrogenase catalyzes the ambient reduction of CO2 when its cluster is present in the all-ferrous, [Fe4 S4 ](0) oxidation state. Here, we report a combined structural and theoretical study that probes the unique reactivity of the all-ferrous Fe protein toward CO2 . Structural comparisons of the Azotobacter vinelandii Fe protein in the [Fe4 S4 ](0) and [Fe4 S4 ](+) states point to a possible asymmetric functionality of a highly conserved Arg pair in CO2 binding and reduction. Density functional theory (DFT) calculations provide further support for the asymmetric coordination of O by the "proximal" Arg and binding of C to a unique Fe atom of the all-ferrous cluster, followed by donation of protons by the proximate guanidinium group of Arg that eventually results in the scission of a C-O bond. These results provide important mechanistic and structural insights into CO2 activation by a surface-exposed, scaffold-held [Fe4 S4 ] cluster.

~~Authors~~:

Structural and Mechanistic Insights into CO2 Activation by Nitrogenase Iron Protein.,Rettberg LA, Stiebritz MT, Kang W, Lee CC, Ribbe MW, Hu Y Chemistry. 2019 Oct 11;25(57):13078-13082. doi: 10.1002/chem.201903387. Epub 2019, Sep 4. PMID:31402524<ref>PMID:31402524</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Azovd]]

[[Category: Large Structures]]

[[Category: Nitrogenase]]

[[Category: Hu, Y]]

[[Category: Kang, W]]

[[Category: Lee, C C]]

[[Category: Rettberg, L A]]

[[Category: Ribbe, M W]]

[[Category: Stiebritz, M T]]

[[Category: Iron protein]]

[[Category: Iron-sulfur cluster]]

[[Category: Oxidoreductase]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6o0b is ON HOLD  until Paper Publication
+==Structural and Mechanistic Insights into CO2 Activation by Nitrogenase Iron Protein==
+<StructureSection load='6o0b' size='340' side='right'caption='[[6o0b]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6o0b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Azovd Azovd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O0B FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nifH, Avin_01380 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=322710 AZOVD])</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=6o0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o0b OCA], [http://pdbe.org/6o0b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o0b RCSB], [http://www.ebi.ac.uk/pdbsum/6o0b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o0b ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/C1DGZ6_AZOVD C1DGZ6_AZOVD]] The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein and the molybdenum-iron protein.[HAMAP-Rule:MF_00533]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The Fe protein of nitrogenase catalyzes the ambient reduction of CO2 when its cluster is present in the all-ferrous, [Fe4 S4 ](0) oxidation state. Here, we report a combined structural and theoretical study that probes the unique reactivity of the all-ferrous Fe protein toward CO2 . Structural comparisons of the Azotobacter vinelandii Fe protein in the [Fe4 S4 ](0) and [Fe4 S4 ](+) states point to a possible asymmetric functionality of a highly conserved Arg pair in CO2 binding and reduction. Density functional theory (DFT) calculations provide further support for the asymmetric coordination of O by the "proximal" Arg and binding of C to a unique Fe atom of the all-ferrous cluster, followed by donation of protons by the proximate guanidinium group of Arg that eventually results in the scission of a C-O bond. These results provide important mechanistic and structural insights into CO2 activation by a surface-exposed, scaffold-held [Fe4 S4 ] cluster.
-Authors:
+Structural and Mechanistic Insights into CO2 Activation by Nitrogenase Iron Protein.,Rettberg LA, Stiebritz MT, Kang W, Lee CC, Ribbe MW, Hu Y Chemistry. 2019 Oct 11;25(57):13078-13082. doi: 10.1002/chem.201903387. Epub 2019, Sep 4. PMID:31402524<ref>PMID:31402524</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6o0b" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Azovd]]
+[[Category: Large Structures]]
+[[Category: Nitrogenase]]
+[[Category: Hu, Y]]
+[[Category: Kang, W]]
+[[Category: Lee, C C]]
+[[Category: Rettberg, L A]]
+[[Category: Ribbe, M W]]
+[[Category: Stiebritz, M T]]
+[[Category: Iron protein]]
+[[Category: Iron-sulfur cluster]]
+[[Category: Oxidoreductase]]