2afh: Difference between revisions

Latest revision as of 07:46, 13 August 2026

Crystal Structure of Nucleotide-Free Av2-Av1 Complex

Structural highlights

2afh is a 6 chain structure with sequence from Azotobacter vinelandii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	1PE, CA, HCA, NA, P6G, PEG, PG4, PGE, TRS
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NIFD_AZOVI This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.

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

Adenosine triphosphate (ATP) hydrolysis in the nitrogenase complex controls the cycle of association and dissociation between the electron donor adenosine triphosphatase (ATPase) (Fe-protein) and its target catalytic protein (MoFe-protein), driving the reduction of dinitrogen into ammonia. Crystal structures in different nucleotide states have been determined that identify conformational changes in the nitrogenase complex during ATP turnover. These structures reveal distinct and mutually exclusive interaction sites on the MoFe-protein surface that are selectively populated, depending on the Fe-protein nucleotide state. A consequence of these different docking geometries is that the distance between redox cofactors, a critical determinant of the intermolecular electron transfer rate, is coupled to the nucleotide state. More generally, stabilization of distinct docking geometries by different nucleotide states, as seen for nitrogenase, could enable nucleotide hydrolysis to drive the relative motion of protein partners in molecular motors and other systems.

Nitrogenase complexes: multiple docking sites for a nucleotide switch protein.,Tezcan FA, Kaiser JT, Mustafi D, Walton MY, Howard JB, Rees DC Science. 2005 Aug 26;309(5739):1377-80. PMID:16123301^[1]

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

References

↑ Tezcan FA, Kaiser JT, Mustafi D, Walton MY, Howard JB, Rees DC. Nitrogenase complexes: multiple docking sites for a nucleotide switch protein. Science. 2005 Aug 26;309(5739):1377-80. PMID:16123301 doi:309/5739/1377

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Tezcan FA, Kaiser JT, Mustafi D, Walton MY, Howard JB, Rees DC. Nitrogenase complexes: multiple docking sites for a nucleotide switch protein. Science. 2005 Aug 26;309(5739):1377-80. PMID:16123301 doi:309/5739/1377

[1]

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Nucleotide-Free Av2-Av1 Complex==
-<StructureSection load='2afh' size='340' side='right' caption='[[2afh]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='2afh' size='340' side='right'caption='[[2afh]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2afh]] is a 6 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=2AFH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AFH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2afh]] is a 6 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=2AFH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AFH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CFN:FE(7)-MO-S(9)-N+CLUSTER'>CFN</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2afi|2afi]], [[2afk|2afk]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2afh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2afh OCA], [https://pdbe.org/2afh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2afh RCSB], [https://www.ebi.ac.uk/pdbsum/2afh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2afh ProSAT]</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=2afh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2afh OCA], [http://pdbe.org/2afh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2afh RCSB], [http://www.ebi.ac.uk/pdbsum/2afh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2afh ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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. [[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] [[http://www.uniprot.org/uniprot/NIFK_AZOVI NIFK_AZOVI]] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.
+[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]]
@@ Line 16: / Line 15: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/af/2afh_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 32: / Line 31: @@
 ==See Also==
-*[[Nitrogenase|Nitrogenase]]
+*[[Nitrogenase 3D structures|Nitrogenase 3D structures]]
 == References ==
 <references/>
@@ Line 38: / Line 37: @@
 </StructureSection>
 [[Category: Azotobacter vinelandii]]
-[[Category: Nitrogenase]]
+[[Category: Large Structures]]
-[[Category: Howard, J B]]
+[[Category: Howard JB]]
-[[Category: Kaiser, J T]]
+[[Category: Kaiser JT]]
-[[Category: Mustafi, D]]
+[[Category: Mustafi D]]
-[[Category: Rees, D C]]
+[[Category: Rees DC]]
-[[Category: Tezcan, F A]]
+[[Category: Tezcan FA]]
-[[Category: Walton, M Y]]
+[[Category: Walton MY]]
-[[Category: Iron-sulfur]]
-[[Category: Metal-binding]]
-[[Category: Molybdenum]]
-[[Category: Nitrogen fixation]]
-[[Category: Oxidoreductase]]

2afh: Difference between revisions

Latest revision as of 07:46, 13 August 2026

Crystal Structure of Nucleotide-Free Av2-Av1 Complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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