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.

1d06

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:37, 6 December 2017

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

Structural highlights

1d06 is a 1 chain structure with sequence from Atcc 9930. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

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

Publication Abstract from PubMed

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.

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:10926518^[1]

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

References

↑ Miyatake H, Mukai M, Park SY, Adachi S, Tamura K, Nakamura H, Nakamura K, Tsuchiya T, Iizuka T, Shiro Y. Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies. J Mol Biol. 2000 Aug 11;301(2):415-31. PMID:10926518 doi:10.1006/jmbi.2000.3954

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1d06"

@@ Line 1: / Line 1: @@
 ==STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION==
 <StructureSection load='1d06' size='340' side='right' caption='[[1d06]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
@@ Line 4: / Line 5: @@
 <table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D06 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [http://pdbe.org/1d06 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [http://www.ebi.ac.uk/pdbsum/1d06 PDBsum]</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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [http://pdbe.org/1d06 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [http://www.ebi.ac.uk/pdbsum/1d06 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1d06 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 12: / Line 13: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/1d06_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/1d06_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1d06

From Proteopedia

Revision as of 08:37, 6 December 2017

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox