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New page: left|200px<br /><applet load="1rw4" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rw4, resolution 2.5Å" /> '''Nitrogenase Fe protei...
 
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[[Image:1rw4.jpg|left|200px]]<br /><applet load="1rw4" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1rw4, resolution 2.5&Aring;" />
'''Nitrogenase Fe protein l127 deletion variant'''<br />


==Overview==
==Nitrogenase Fe protein l127 deletion variant==
The crystal structure of a nitrogenase Fe protein single site deletion, variant reveals a distinctly new conformation of the Fe protein and, indicates that, upon binding of MgATP, the Fe protein undergoes a dramatic, conformational change that is largely manifested in the rigid-body, reorientation of the homodimeric Fe protein subunits with respect to one, another. The observed conformational state allows the rationalization of a, model of structurally and chemically complementary interactions that occur, upon initial complex formation with the MoFe protein component that are, distinct from the protein-protein interactions that have been, characterized previously for stabilized nitrogenase complexes. The, crystallographic results, in combination with complementary UV-visible, absorption, EPR, and resonance Raman spectroscopic data, indicate that the, [4Fe-4S] cluster of both the Fe protein deletion variant and the native Fe, protein in the presence of MgATP can reversibly cycle between a regular, cubane-type [4Fe-4S] cluster in the reduced state and a cleaved form, involving two [2Fe-2S] fragments in the oxidized state. Resonance Raman, studies indicate that this novel cluster conversion is induced by, glycerol, and the crystallographic data suggest that glycerol is bound as, a bridging bidentate ligand to both [2Fe-2S] cluster fragments in the, oxidized state.
<StructureSection load='1rw4' size='340' side='right'caption='[[1rw4]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1rw4]] 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=1RW4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RW4 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=1rw4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rw4 OCA], [https://pdbe.org/1rw4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rw4 RCSB], [https://www.ebi.ac.uk/pdbsum/1rw4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rw4 ProSAT]</span></td></tr>
</table>
== Function ==
[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 ==
[[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/rw/1rw4_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=1rw4 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of a nitrogenase Fe protein single site deletion variant reveals a distinctly new conformation of the Fe protein and indicates that, upon binding of MgATP, the Fe protein undergoes a dramatic conformational change that is largely manifested in the rigid-body reorientation of the homodimeric Fe protein subunits with respect to one another. The observed conformational state allows the rationalization of a model of structurally and chemically complementary interactions that occur upon initial complex formation with the MoFe protein component that are distinct from the protein-protein interactions that have been characterized previously for stabilized nitrogenase complexes. The crystallographic results, in combination with complementary UV-visible absorption, EPR, and resonance Raman spectroscopic data, indicate that the [4Fe-4S] cluster of both the Fe protein deletion variant and the native Fe protein in the presence of MgATP can reversibly cycle between a regular cubane-type [4Fe-4S] cluster in the reduced state and a cleaved form involving two [2Fe-2S] fragments in the oxidized state. Resonance Raman studies indicate that this novel cluster conversion is induced by glycerol, and the crystallographic data suggest that glycerol is bound as a bridging bidentate ligand to both [2Fe-2S] cluster fragments in the oxidized state.


==About this Structure==
A conformational mimic of the MgATP-bound "on state" of the nitrogenase iron protein.,Sen S, Igarashi R, Smith A, Johnson MK, Seefeldt LC, Peters JW Biochemistry. 2004 Feb 24;43(7):1787-97. PMID:14967020<ref>PMID:14967020</ref>
1RW4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii] with SF4 and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RW4 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
A conformational mimic of the MgATP-bound "on state" of the nitrogenase iron protein., Sen S, Igarashi R, Smith A, Johnson MK, Seefeldt LC, Peters JW, Biochemistry. 2004 Feb 24;43(7):1787-97. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14967020 14967020]
</div>
<div class="pdbe-citations 1rw4" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Nitrogenase 3D structures|Nitrogenase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Azotobacter vinelandii]]
[[Category: Azotobacter vinelandii]]
[[Category: Nitrogenase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Igarashi R]]
[[Category: Igarashi, R.]]
[[Category: Johnson MK]]
[[Category: Johnson, M.K.]]
[[Category: Peters JW]]
[[Category: Peters, J.W.]]
[[Category: Seefeldt LC]]
[[Category: Seefeldt, L.C.]]
[[Category: Sen S]]
[[Category: Sen, S.]]
[[Category: Smith A]]
[[Category: Smith, A.]]
[[Category: GOL]]
[[Category: SF4]]
[[Category: oxidoreductase]]
 
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