1d06

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:47, 7 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1d06.gif|left|200px]]
 
-
<!--
+
==STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION==
-
The line below this paragraph, containing "STRUCTURE_1d06", creates the "Structure Box" on the page.
+
<StructureSection load='1d06' size='340' side='right'caption='[[1d06]], [[Resolution|resolution]] 1.40&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'>[[1d06]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D06 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]] 1.4&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-
{{STRUCTURE_1d06| PDB=1d06 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [https://pdbe.org/1d06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [https://www.ebi.ac.uk/pdbsum/1d06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d06 ProSAT]</span></td></tr>
-
 
+
</table>
-
'''STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/FIXL_RHIME FIXL_RHIME] Putative oxygen sensor; modulates the activity of FixJ, a transcriptional activator of nitrogen fixation fixK gene. FixL probably acts as a kinase that phosphorylates FixJ.
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
FixL of Rhizobium meliloti (RmFixL) is a sensor histidine kinase of the two-component system, which regulates the expression of the genes related to nitrogen fixation in the root nodule in response to the O(2) levels. The crystal structure of the sensor domain of FixL (RmFixLH), which contains a heme (Fe-porphyrin) as a sensing site, was determined at 1.4 A resolution. Based on the structural and spectroscopic analyses, we propose the O(2) sensing mechanism that differs from the case proposed in BjFixLH as follows; conformational changes in the F/G loop, which are induced by steric repulsion between the bent-bound O(2) and the Ile209 side-chain, would be transmitted to the histidine kinase domain. Interaction between the iron-bound O(2) and Ile209 was also observed in the resonance Raman spectra of RmFixLH as evidenced by the fact that the Fe-O(2) and Fe-CN stretching frequencies were shifted from 575 to 570 cm(-1) (Fe-O(2)), and 504 to 499 cm(-1), respectively, as the result of the replacement of Ile209 with an Ala residue. In the I209A mutant of RmFixL, the O(2) sensing activity was destroyed, thus confirming our proposed mechanism.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/1d06_consurf.spt"</scriptWhenChecked>
-
1D06 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies., Miyatake H, Mukai M, Park SY, Adachi S, Tamura K, Nakamura H, Nakamura K, Tsuchiya T, Iizuka T, Shiro Y, J Mol Biol. 2000 Aug 11;301(2):415-31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10926518 10926518]
+
</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=1d06 ConSurf].
-
[[Category: Single protein]]
+
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Sinorhizobium meliloti]]
[[Category: Sinorhizobium meliloti]]
-
[[Category: Adachi, S.]]
+
[[Category: Adachi S]]
-
[[Category: Iizuka, T.]]
+
[[Category: Iizuka T]]
-
[[Category: Miyatake, H.]]
+
[[Category: Miyatake H]]
-
[[Category: Mukai, M.]]
+
[[Category: Mukai M]]
-
[[Category: Nakamura, H.]]
+
[[Category: Nakamura H]]
-
[[Category: Nakamura, K.]]
+
[[Category: Nakamura K]]
-
[[Category: Park, S Y.]]
+
[[Category: Park S-Y]]
-
[[Category: Shiro, Y.]]
+
[[Category: Shiro Y]]
-
[[Category: Tamura, K.]]
+
[[Category: Tamura K]]
-
[[Category: Tsuchiya, T.]]
+
[[Category: Tsuchiya T]]
-
[[Category: High-resolution]]
+
-
[[Category: Histidine kinase]]
+
-
[[Category: Oxygen sensor]]
+
-
[[Category: Pa]]
+
-
[[Category: Two-component system]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:17:50 2008''
+

Current revision

STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION

PDB ID 1d06

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/1d06"
Personal tools