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2c8v

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Revision as of 06:50, 1 December 2021

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

Structural highlights

2c8v is a 1 chain structure with sequence from Azotobacter vinelandii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	1de0, 1fp6, 1g1m, 1g20, 1g21, 1g5p, 1m1y, 1m34, 1n2c, 1nip, 1rw4, 1xcp, 1xd8, 1xd9, 1xdb, 2afh, 2afi, 2afk, 2nip
Activity:	Nitrogenase, with EC number 1.18.6.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sen S, Krishnakumar A, McClead J, Johnson MK, Seefeldt LC, Szilagyi RK, Peters JW. 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. J Inorg Biochem. 2006 May;100(5-6):1041-52. Epub 2006 Mar 3. PMID:16616373 doi:10.1016/j.jinorgbio.2006.02.016

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2c8v"

@@ Line 3: / Line 3: @@
 <StructureSection load='2c8v' size='340' side='right'caption='[[2c8v]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2c8v]] is a 1 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C8V FirstGlance]. <br>
+<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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</td></tr><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>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1de0|1de0]], [[1fp6|1fp6]], [[1g1m|1g1m]], [[1g20|1g20]], [[1g21|1g21]], [[1g5p|1g5p]], [[1m1y|1m1y]], [[1m34|1m34]], [[1n2c|1n2c]], [[1nip|1nip]], [[1rw4|1rw4]], [[1xcp|1xcp]], [[1xd8|1xd8]], [[1xd9|1xd9]], [[1xdb|1xdb]], [[2afh|2afh]], [[2afi|2afi]], [[2afk|2afk]], [[2nip|2nip]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1de0|1de0]], [[1fp6|1fp6]], [[1g1m|1g1m]], [[1g20|1g20]], [[1g21|1g21]], [[1g5p|1g5p]], [[1m1y|1m1y]], [[1m34|1m34]], [[1n2c|1n2c]], [[1nip|1nip]], [[1rw4|1rw4]], [[1xcp|1xcp]], [[1xd8|1xd8]], [[1xd9|1xd9]], [[1xdb|1xdb]], [[2afh|2afh]], [[2afi|2afi]], [[2afk|2afk]], [[2nip|2nip]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/2c8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB], [http://www.ebi.ac.uk/pdbsum/2c8v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2c8v ProSAT]</span></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=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>
 </table>
 == Function ==
-[[http://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]
+[[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]]

2c8v

From Proteopedia

Revision as of 06:50, 1 December 2021

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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