6n4m

From Proteopedia

(Difference between revisions)

Current revision

IDS-oxidized ADP-bound form of the nitrogenase Fe-protein from A. vinelandii

Structural highlights

6n4m is a 1 chain structure with sequence from Azotobacter vinelandii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.58Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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]

Publication Abstract from PubMed

The nitrogenase iron protein (Fe-protein) serves as the electron donor for biological nitrogen fixation. Understanding how the Fe-protein controls electron transfer to the active site is critical in addressing the mechanism of substrate reduction. The Fe-protein contains an unusual [4Fe:4S] iron-sulphur cluster that is stable in three oxidation states: 2+, 1+ and 0. Here, we combine structural and spectroscopic techniques, including spatially resolved anomalous dispersion refinement (SpReAD), to report oxidation assignments for individual irons in the cluster for each overall state. Additionally, we report the 1.13-A resolution structure for the Fe-protein with bound ADP, the highest resolution Fe-protein structure presently determined. In the dithionite-reduced [4Fe:4S]1+ state, the SpReAD analysis supports the oxidation state assignment of a delocalized Fe2.5+ pair and a reduced Fe2+ pair. Our work identifies the Fe2.5+ pair as coordinated by the solvent exposed Cys97, while the Fe2+ pair faces the protein interior and is coordinated by Cys132. It is proposed that binding of ATP to the Fe-protein promotes an internal redox rearrangement such that the solvent-exposed Fe becomes reduced, thereby facilitating electron transfer to the nitrogenase molybdenum iron-protein. The SpReAD analysis supports a uniform oxidation state assignment of Fe2+ for all irons in the titanium citrate-reduced [4Fe:4S]0 state, while all irons in the IDS oxidized [4Fe:4S]2+ state are assigned to the valence delocalized Fe2.5+ state.

Site-specific oxidation state assignments of the irons in the [4Fe:4S]2+/1+/0 states of the nitrogenase Fe-protein.,Wenke BB, Spatzal T, Rees DC Angew Chem Int Ed Engl. 2019 Jan 30. doi: 10.1002/anie.201813966. PMID:30698901^[1]

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

References

↑ Wenke BB, Spatzal T, Rees DC. Site-specific oxidation state assignments of the irons in the [4Fe:4S]2+/1+/0 states of the nitrogenase Fe-protein. Angew Chem Int Ed Engl. 2019 Jan 30. doi: 10.1002/anie.201813966. PMID:30698901 doi:http://dx.doi.org/10.1002/anie.201813966

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6n4m"

Categories: Azotobacter vinelandii | Large Structures | Rees DC | Spatzal T | Wenke BB

@@ Line 1: / Line 1: @@
 ==IDS-oxidized ADP-bound form of the nitrogenase Fe-protein from A. vinelandii==
-<StructureSection load='6n4m' size='340' side='right' caption='[[6n4m]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
+<StructureSection load='6n4m' size='340' side='right'caption='[[6n4m]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6n4m]] is a 1 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=6N4M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N4M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6n4m]] is a 1 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=6N4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N4M FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.58&#8491;</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='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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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=6n4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n4m OCA], [http://pdbe.org/6n4m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n4m RCSB], [http://www.ebi.ac.uk/pdbsum/6n4m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n4m 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=6n4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n4m OCA], [https://pdbe.org/6n4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n4m RCSB], [https://www.ebi.ac.uk/pdbsum/6n4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n4m ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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]
+[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]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 6n4m" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Nitrogenase 3D structures|Nitrogenase 3D structures]]
 == References ==
 <references/>
@@ Line 24: / Line 27: @@
 </StructureSection>
 [[Category: Azotobacter vinelandii]]
-[[Category: Nitrogenase]]
+[[Category: Large Structures]]
-[[Category: Rees, D C]]
+[[Category: Rees DC]]
-[[Category: Spatzal, T]]
+[[Category: Spatzal T]]
-[[Category: Wenke, B B]]
+[[Category: Wenke BB]]
-[[Category: Iron sulfur cluster]]
-[[Category: Oxidoreductase]]

6n4m

From Proteopedia

Current revision

IDS-oxidized ADP-bound form of the nitrogenase Fe-protein from A. vinelandii

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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