1m34: Difference between revisions

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-[[Image:1m34.gif|left|200px]]
-<!--
+==Nitrogenase Complex From Azotobacter Vinelandii Stabilized By ADP-Tetrafluoroaluminate==
-The line below this paragraph, containing "STRUCTURE_1m34", creates the "Structure Box" on the page.
+<StructureSection load='1m34' size='340' side='right'caption='[[1m34]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1m34]] 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=1M34 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M34 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</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=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-{{STRUCTURE_1m34|  PDB=1m34  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m34 OCA], [https://pdbe.org/1m34 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m34 RCSB], [https://www.ebi.ac.uk/pdbsum/1m34 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m34 ProSAT]</span></td></tr>
+</table>
+== 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.
+== 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/m3/1m34_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/main_output.php?pdb_ID=1m34 ConSurf].
+<div style="clear:both"></div>
-'''Nitrogenase Complex From Azotobacter Vinelandii Stabilized By ADP-Tetrafluoroaluminate'''
+==See Also==
+*[[Nitrogenase 3D structures|Nitrogenase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-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.
-==About this Structure==
-M34 is a [[Protein complex]] structure of sequences 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=1M34 OCA].
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/12501184 12501184]
 [[Category: Azotobacter vinelandii]]
-[[Category: Nitrogenase]]
+[[Category: Large Structures]]
-[[Category: Protein complex]]
+[[Category: Chiu H-J]]
-[[Category: Chiu, H J.]]
+[[Category: Einsle O]]
-[[Category: Einsle, O.]]
+[[Category: Howard JB]]
-[[Category: Howard, J B.]]
+[[Category: Rees DC]]
-[[Category: Howard, J B.Rees, D C.]]
+[[Category: Schmid B]]
-[[Category: Schmid, B.]]
+[[Category: Willing A]]
-[[Category: Willing, A.]]
+[[Category: Yoshida M]]
-[[Category: Yoshida, M.]]
-[[Category: Atp hydrolysis]]
-[[Category: Complex of nitrogenase protein]]
-[[Category: Electron transfer]]
-[[Category: Nitrogen fixation]]
-[[Category: Nitrogenase]]
-[[Category: Signal transduction]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 00:34:35 2008''