3min: Difference between revisions

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-[[Image:3min.gif|left|200px]]
- {{Structure
+==NITROGENASE MOFE PROTEIN FROM AZOTOBACTER VINELANDII, OXIDIZED STATE==
-|PDB= 3min |SIZE=350|CAPTION= <scene name='initialview01'>3min</scene>, resolution 2.03&Aring;
+<StructureSection load='3min' size='340' side='right'caption='[[3min]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <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>
+<table><tr><td colspan='2'>[[3min]] is a 4 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=3MIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MIN FirstGlance]. <br>
-|ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.03&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3min FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3min OCA], [https://pdbe.org/3min PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3min RCSB], [https://www.ebi.ac.uk/pdbsum/3min PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3min ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3min FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3min OCA], [http://www.ebi.ac.uk/pdbsum/3min PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3min RCSB]</span>
+== 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/mi/3min_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=3min ConSurf].
+<div style="clear:both"></div>
-'''NITROGENASE MOFE PROTEIN FROM AZOTOBACTER VINELANDII, OXIDIZED STATE'''
+==See Also==
+*[[Nitrogenase 3D structures|Nitrogenase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The structure of the nitrogenase MoFe-protein from Azotobacter vinelandii has been refined to 2.0 A resolution in two oxidation states. EPR studies on the crystals indicate that the structures correspond to the spectroscopically assigned oxidized (P(OX)/M(OX)) and the native or dithionite-reduced (P(N)/M(N)) forms of the enzyme. Both MoFe-protein structures are essentially identical, with the exception of the P-cluster. The MoFe-protein P-cluster in each state is found to contain eight Fe and seven S atoms. Interconversion between the two redox states involves movement of two Fe atoms and an exchange of protein coordination for ligands supplied by a central S atom. In the oxidized P(OX) state, the cluster is coordinated by the protein through six cysteine ligands, Ser-beta188 O gamma, and the backbone amide of Cys-alpha88. In the native P(N) state, Ser-beta188 O gamma and the amide N of Cys-alpha88 no longer coordinate the cluster due to movement of their coordinated Fe atoms toward the central sulfur. Consequently, this central sulfur adopts a distorted octahedral environment with six surrounding Fe atoms. A previously described model of the P-cluster containing 8Fe-8S likely reflects the inappropriate modeling of a single structure to a mixture of these two P-cluster redox states. These observed redox-mediated structural changes of the P-cluster suggest a role for this cluster in coupling electron transfer and proton transfer in nitrogenase.
-==About this Structure==
-MIN 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=3MIN OCA].
-==Reference==
-Redox-dependent structural changes in the nitrogenase P-cluster., Peters JW, Stowell MH, Soltis SM, Finnegan MG, Johnson MK, Rees DC, Biochemistry. 1997 Feb 11;36(6):1181-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9063865 9063865]
 [[Category: Azotobacter vinelandii]]
-[[Category: Nitrogenase]]
+[[Category: Large Structures]]
-[[Category: Protein complex]]
+[[Category: Day MW]]
-[[Category: Day, M W.]]
+[[Category: Kim J]]
-[[Category: Kim, J.]]
+[[Category: Peters JW]]
-[[Category: Peters, J W.]]
+[[Category: Rees DC]]
-[[Category: Rees, D C.]]
+[[Category: Soltis SM]]
-[[Category: Soltis, S M.]]
+[[Category: Stowell MHB]]
-[[Category: Stowell, M H.B.]]
-[[Category: biological nitrogen fixation]]
-[[Category: molybdoenzyme]]
-[[Category: nitrogen fixation]]
-[[Category: nitrogen metabolism]]
-[[Category: oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:34:40 2008''