This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2gj3

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:28, 14 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2gj3.jpg|left|200px]]<br /><applet load="2gj3" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2gj3, resolution 1.040&Aring;" />
 
-
'''Crystal structure of the FAD-containing PAS domain of the protein NifL from Azotobacter vinelandii.'''<br />
 
-
==Overview==
+
==Crystal structure of the FAD-containing PAS domain of the protein NifL from Azotobacter vinelandii.==
-
NifL is a multidomain sensor protein responsible for the transcriptional regulation of genes involved in response to changes in cellular redox state and ADP concentration. Cellular redox is monitored by the N-terminal PAS domain of NifL which contains an FAD cofactor. Flavin-based PAS domains of this type have also been referred to as LOV domains. To explore the mechanism of signal recognition and transduction in NifL, we determined the crystal structure of the FAD-bound PAS domain of NifL from Azotobacter vinelandii to 1.04 A resolution. The structure reveals a novel cavity within the PAS domain which contains two water molecules directly coordinated to the FAD. This cavity is connected to solvent by multiple access channels which may facilitate the oxidation of the FAD by molecular oxygen and the release of hydrogen peroxide. The structure contains a dimer of the NifL PAS domain that is structurally very similar to those described in other crystal structures of PAS domains and identifies a conserved dimerization motif. An N-terminal amphipathic helix constitutes part of the dimerization interface, and similar N-terminal helices are identified in other PAS domain proteins. The structure suggests a model for redox-mediated signaling in which a conformational change is initiated by redox-dependent changes in protonation at the N5 atom of FAD that lead to reorganization of hydrogen bonds within the flavin binding pocket. A structural signal is subsequently transmitted to the beta-sheet interface between the monomers of the PAS domain.
+
<StructureSection load='2gj3' size='340' side='right'caption='[[2gj3]], [[Resolution|resolution]] 1.04&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[2gj3]] is a 2 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=2GJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GJ3 FirstGlance]. <br>
-
2GJ3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii] with <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=FAD:'>FAD</scene> and <scene name='pdbligand=EOH:'>EOH</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GJ3 OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.04&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gj3 OCA], [https://pdbe.org/2gj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gj3 RCSB], [https://www.ebi.ac.uk/pdbsum/2gj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gj3 ProSAT]</span></td></tr>
-
Structure of the redox sensor domain of Azotobacter vinelandii NifL at atomic resolution: signaling, dimerization, and mechanism., Key J, Hefti M, Purcell EB, Moffat K, Biochemistry. 2007 Mar 27;46(12):3614-23. Epub 2007 Feb 24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17319691 17319691]
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/NIFL_AZOVI NIFL_AZOVI] Required for the inhibition of NifA activity in response to oxygen and low level of fixed nitrogen.
 +
== 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/gj/2gj3_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=2gj3 ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
[[Category: Azotobacter vinelandii]]
[[Category: Azotobacter vinelandii]]
-
[[Category: Histidine kinase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Hefti M]]
-
[[Category: Hefti, M.]]
+
[[Category: Key J]]
-
[[Category: Key, J.]]
+
[[Category: Moffat K]]
-
[[Category: Moffat, K.]]
+
[[Category: Purcell E]]
-
[[Category: Purcell, E.]]
+
-
[[Category: EOH]]
+
-
[[Category: FAD]]
+
-
[[Category: SO4]]
+
-
[[Category: atomic resolution]]
+
-
[[Category: fad]]
+
-
[[Category: pas domain]]
+
-
[[Category: redox sensor]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:32:12 2008''
+

Current revision

Crystal structure of the FAD-containing PAS domain of the protein NifL from Azotobacter vinelandii.

PDB ID 2gj3

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2gj3"
Personal tools