2c8v

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[[Image:2c8v.gif|left|200px]]
 
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{{Structure
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==Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP==
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|PDB= 2c8v |SIZE=350|CAPTION= <scene name='initialview01'>2c8v</scene>, resolution 2.5&Aring;
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<StructureSection load='2c8v' size='340' side='right'caption='[[2c8v]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Atp+Binding+Site+For+Chain+A'>AC1</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ATP:ADENOSINE-5&#39;-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FS1:IRON/SULFUR+CLUSTER'>FS1</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
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<table><tr><td colspan='2'>[[2c8v]] 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=2C8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C8V FirstGlance]. <br>
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|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>
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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]] 2.5&#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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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|DOMAIN=
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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=2c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8v OCA], [https://pdbe.org/2c8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB], [https://www.ebi.ac.uk/pdbsum/2c8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c8v ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8v OCA], [http://www.ebi.ac.uk/pdbsum/2c8v PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB]</span>
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== Function ==
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}}
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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/c8/2c8v_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=2c8v ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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In the present work, determination of the structure of the nitrogenase Leu 127 deletion variant Fe protein with MgATP bound is presented, along with density functional theory calculations, to provide insights into the roles of MgATP in the nitrogenase reaction mechanism. Comparison of the MgATP-bound structure of this Fe protein to the nucleotide-free form indicates that the binding of MgATP does not alter the overall structure of the variant significantly with only small differences in the conformation of amino acids in direct contact with the two bound MgATP molecules being seen. The earlier observation of splitting of the [4Fe-4S] cluster into two [2Fe-2S] clusters was observed to be unaltered upon binding MgATP. Density functional theory was used to probe the assignment of ligands to the two [2Fe-2S] rhombs. The Mg(2+) environment in the MgATP-bound structure of the Leu127 deletion Fe protein is similar to that observed for the Fe protein in the nitrogenase Fe protein: MoFe protein complex stabilized by MgADP and tetrafluoroaluminate suggesting that large scale conformational change implicated for the Fe protein may not be mediated by changes in the Mg(2+) coordination. The results presented here indicated that MgATP may enhance the stability of an open conformation and prohibit intersubunit interactions, which have been implicated in promoting nucleotide hydrolysis. This could be critical to the tight control of MgATP hydrolysis observed within the nitrogenase complex and may be important for maintaining unidirectional electron flow toward substrate reduction.
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'''INSIGHTS INTO THE ROLE OF NUCLEOTIDE-DEPENDENT CONFORMATIONAL CHANGE IN NITROGENASE CATALYSIS: STRUCTURAL CHARACTERIZATION OF THE NITROGENASE FE PROTEIN LEU127 DELETION VARIANT WITH BOUND MGATP'''
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Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP.,Sen S, Krishnakumar A, McClead J, Johnson MK, Seefeldt LC, Szilagyi RK, Peters JW J Inorg Biochem. 2006 May;100(5-6):1041-52. Epub 2006 Mar 3. PMID:16616373<ref>PMID:16616373</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2c8v" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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In the present work, determination of the structure of the nitrogenase Leu 127 deletion variant Fe protein with MgATP bound is presented, along with density functional theory calculations, to provide insights into the roles of MgATP in the nitrogenase reaction mechanism. Comparison of the MgATP-bound structure of this Fe protein to the nucleotide-free form indicates that the binding of MgATP does not alter the overall structure of the variant significantly with only small differences in the conformation of amino acids in direct contact with the two bound MgATP molecules being seen. The earlier observation of splitting of the [4Fe-4S] cluster into two [2Fe-2S] clusters was observed to be unaltered upon binding MgATP. Density functional theory was used to probe the assignment of ligands to the two [2Fe-2S] rhombs. The Mg(2+) environment in the MgATP-bound structure of the Leu127 deletion Fe protein is similar to that observed for the Fe protein in the nitrogenase Fe protein: MoFe protein complex stabilized by MgADP and tetrafluoroaluminate suggesting that large scale conformational change implicated for the Fe protein may not be mediated by changes in the Mg(2+) coordination. The results presented here indicated that MgATP may enhance the stability of an open conformation and prohibit intersubunit interactions, which have been implicated in promoting nucleotide hydrolysis. This could be critical to the tight control of MgATP hydrolysis observed within the nitrogenase complex and may be important for maintaining unidirectional electron flow toward substrate reduction.
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*[[Nitrogenase 3D structures|Nitrogenase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2C8V 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=2C8V OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP., Sen S, Krishnakumar A, McClead J, Johnson MK, Seefeldt LC, Szilagyi RK, Peters JW, J Inorg Biochem. 2006 May;100(5-6):1041-52. Epub 2006 Mar 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16616373 16616373]
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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: Johnson MK]]
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[[Category: Johnson, M K.]]
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[[Category: Krishnakumar A]]
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[[Category: Krishnakumar, A.]]
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[[Category: McClead J]]
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[[Category: Mcclead, J.]]
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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: Sen S]]
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[[Category: Sen, S.]]
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[[Category: Szilagyi RK]]
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[[Category: Szilagyi, R K.]]
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[[Category: 4fe-4]]
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[[Category: atp-binding]]
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[[Category: av2]]
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[[Category: fe protein]]
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[[Category: iron]]
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[[Category: iron-sulfur]]
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[[Category: metal-binding]]
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[[Category: mgadp]]
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[[Category: nitrogen fixation]]
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[[Category: nitrogenase]]
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[[Category: nucleotide-binding]]
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[[Category: oxidoreductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:18:03 2008''
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Current revision

Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP

PDB ID 2c8v

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