2vv6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:33, 13 December 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2vv6.png|left|200px]]
 
-
<!--
+
==BJFIXLH IN FERRIC FORM==
-
The line below this paragraph, containing "STRUCTURE_2vv6", creates the "Structure Box" on the page.
+
<StructureSection load='2vv6' size='340' side='right'caption='[[2vv6]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2vv6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VV6 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-
{{STRUCTURE_2vv6| PDB=2vv6 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vv6 OCA], [https://pdbe.org/2vv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vv6 RCSB], [https://www.ebi.ac.uk/pdbsum/2vv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vv6 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/FIXL_BRADU FIXL_BRADU]
 +
== 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/vv/2vv6_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=2vv6 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
FixL from Bradyrhizobium japonicum is a PAS sensor protein in which two PAS domains covalently linked to a histidine kinase domain are responsible for regulating nitrogen fixation in an oxygen-dependent manner. The more C-terminal PAS domain, denoted bjFixLH, contains a heme cofactor that binds diatomic molecules such as carbon monoxide and oxygen and regulates the activity of the FixL histidine kinase as part of a two-component signaling system. We present the structures of ferric, deoxy, and carbon monoxide-bound bjFixLH in a new space group ( P1) and at resolutions (1.5-1.8 A) higher than the resolutions of those previously obtained. Interestingly, bjFixLH can form two different dimers (in P1 and R32 crystal forms) in the same crystallization solution, where the monomers in one dimer are rotated approximately 175 degrees relative to the second. This suggests that PAS monomers are plastic and that two quite distinct quaternary structures are closely similar in free energy. We use screw rotation analysis to carry out a quantitative pairwise comparison of PAS quaternary structures, which identifies five different relative orientations adopted by isolated PAS monomers. We conclude that PAS monomer arrangement is context-dependent and could differ depending on whether the PAS domains are isolated or are part of a full-length protein. Structurally homologous residues comprise a conserved dimer interface. Using network analysis, we find that the architecture of the PAS dimer interface is continuous rather than modular; the network of residues comprising the interface is strongly connected. A continuous dimer interface is consistent with the low dimer-monomer dissociation equilibrium constant. Finally, we quantitate quaternary structural changes induced by carbon monoxide binding to a bjFixLH dimer, in which monomers rotate by up to approximately 2 degrees relative to each other. We relate these changes to those in other dimeric PAS domains and discuss the role of quaternary structural changes in the signaling mechanisms of PAS sensor proteins.
-
===BJFIXLH IN FERRIC FORM===
+
Changes in Quaternary Structure in the Signaling Mechanisms of PAS Domains(,).,Ayers RA, Moffat K Biochemistry. 2008 Oct 23. PMID:18942854<ref>PMID:18942854</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_18942854}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2vv6" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 18942854 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18942854}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
[[2vv6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VV6 OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:018942854</ref><references group="xtra"/>
+
[[Category: Bradyrhizobium japonicum]]
[[Category: Bradyrhizobium japonicum]]
-
[[Category: Ayers, R A.]]
+
[[Category: Large Structures]]
-
[[Category: Moffat, K.]]
+
[[Category: Ayers RA]]
-
[[Category: Fixl]]
+
[[Category: Moffat K]]
-
[[Category: Heme]]
+
-
[[Category: Iron]]
+
-
[[Category: Kinase]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Nitrogen fixation]]
+
-
[[Category: Pa]]
+
-
[[Category: Per-arnt-sim]]
+
-
[[Category: Phosphoprotein]]
+
-
[[Category: Signaling protein]]
+
-
[[Category: Transferase]]
+
-
[[Category: Two-component regulatory system]]
+

Current revision

BJFIXLH IN FERRIC FORM

PDB ID 2vv6

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/2vv6"
Personal tools