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1xdb

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[[Image:1xdb.gif|left|200px]]
 
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{{Structure
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==Crystal Structure of the Nitrogenase Fe protein Asp129Glu==
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|PDB= 1xdb |SIZE=350|CAPTION= <scene name='initialview01'>1xdb</scene>, resolution 2.8&Aring;
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<StructureSection load='1xdb' size='340' side='right'caption='[[1xdb]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=SF4:IRON/SULFUR CLUSTER'>SF4</scene>
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<table><tr><td colspan='2'>[[1xdb]] is a 2 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=1XDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XDB FirstGlance]. <br>
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|ACTIVITY= [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]
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdb OCA], [https://pdbe.org/1xdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xdb RCSB], [https://www.ebi.ac.uk/pdbsum/1xdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xdb ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xd/1xdb_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1xdb ConSurf].
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<div style="clear:both"></div>
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'''Crystal Structure of the Nitrogenase Fe protein Asp129Glu'''
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==See Also==
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*[[Nitrogenase 3D structures|Nitrogenase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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The structures of nitrogenase Fe proteins with defined amino acid substitutions in the previously implicated nucleotide-dependent signal transduction pathways termed switch I and switch II have been determined by X-ray diffraction methods. In the Fe protein of nitrogenase the nucleotide-dependent switch regions are responsible for communication between the sites responsible for nucleotide binding and hydrolysis and the [4Fe-4S] cluster of the Fe protein and the docking interface that interacts with the MoFe protein upon macromolecular complex formation. In this study the structural characterization of the Azotobacter vinelandii nitrogenase Fe protein with Asp at position 39 substituted by Asn in MgADP-bound and nucleotide-free states provides an explanation for the experimental observation that the altered Fe proteins form a trapped complex subsequent to a single electron transfer event. The structures reveal that the substitution allows the formation of a hydrogen bond between the switch I Asn39 and the switch II Asp125. In the structure of the native enzyme the analogous interaction between the side chains of Asp39 and Asp125 is precluded due to electrostatic repulsion. These results suggest that the electrostatic repulsion between Asp39 and Asp125 is important for dissociation of the Fe protein:MoFe protein complex during catalysis. In a separate study, the structural characterization of the Fe protein with Asp129 substituted by Glu provides the structural basis for the observation that the Glu129-substituted variant in the absence of bound nucleotides has biochemical properties in common with the native Fe protein with bound MgADP. Interactions of the longer Glu side chain with the phosphate binding loop (P-loop) results in a similar conformation of the switch II region as the conformation that results from the binding of the phosphate of ADP to the P-loop.
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==About this Structure==
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1XDB is a [[Single protein]] structure of 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=1XDB OCA].
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==Reference==
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Structural and biochemical implications of single amino acid substitutions in the nucleotide-dependent switch regions of the nitrogenase Fe protein from Azotobacter vinelandii., Jang SB, Jeong MS, Seefeldt LC, Peters JW, J Biol Inorg Chem. 2004 Dec;9(8):1028-33. Epub 2004 Nov 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15549494 15549494]
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[[Category: Azotobacter vinelandii]]
[[Category: Azotobacter vinelandii]]
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[[Category: Nitrogenase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Jang SB]]
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[[Category: Jang, S B.]]
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[[Category: Jeong MS]]
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[[Category: Jeong, M S.]]
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[[Category: Peters JW]]
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[[Category: Peters, J W.]]
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[[Category: Seefeldt LC]]
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[[Category: Seefeldt, L C.]]
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[[Category: SF4]]
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[[Category: [fes] cluster]]
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[[Category: fe protein]]
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[[Category: signal transduction]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:08:17 2008''
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Current revision

Crystal Structure of the Nitrogenase Fe protein Asp129Glu

PDB ID 1xdb

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