2vv6

From Proteopedia

(Difference between revisions)

Revision as of 21:10, 9 February 2016

BJFIXLH IN FERRIC FORM

Structural highlights

2vv6 is a 4 chain structure with sequence from "rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	1dp6, 1lsw, 1xj2, 1lsx, 1dp9, 1xj6, 1dp8, 1lt0, 2cmn, 1xj4, 1lsv, 1y28, 1drm, 1xj3, 2vv8, 2vv7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[FIXL_BRAJA] 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 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.

Changes in Quaternary Structure in the Signaling Mechanisms of PAS Domains(,).,Ayers RA, Moffat K Biochemistry. 2008 Oct 23. PMID:18942854^[1]

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

References

↑ Ayers RA, Moffat K. Changes in Quaternary Structure in the Signaling Mechanisms of PAS Domains(,). Biochemistry. 2008 Oct 23. PMID:18942854 doi:10.1021/bi801254c

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/2vv6"

@@ Line 2: / Line 2: @@
 <StructureSection load='2vv6' size='340' side='right' caption='[[2vv6]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VV6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vv6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VV6 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dp6|1dp6]], [[1lsw|1lsw]], [[1xj2|1xj2]], [[1lsx|1lsx]], [[1dp9|1dp9]], [[1xj6|1xj6]], [[1dp8|1dp8]], [[1lt0|1lt0]], [[2cmn|2cmn]], [[1xj4|1xj4]], [[1lsv|1lsv]], [[1y28|1y28]], [[1drm|1drm]], [[1xj3|1xj3]], [[2vv8|2vv8]], [[2vv7|2vv7]]</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=2vv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vv6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vv6 RCSB], [http://www.ebi.ac.uk/pdbsum/2vv6 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=2vv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vv6 OCA], [http://pdbe.org/2vv6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vv6 RCSB], [http://www.ebi.ac.uk/pdbsum/2vv6 PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 17: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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;">
@@ Line 27: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2vv6" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bradyrhizobium japonicum]]
+[[Category: Rhizobacterium japonicum kirchner 1896]]
 [[Category: Ayers, R A]]
 [[Category: Moffat, K]]

2vv6

From Proteopedia

Revision as of 21:10, 9 February 2016

BJFIXLH IN FERRIC FORM

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