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PDBsum entry 2vv6
Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Signaling protein, transferase PDB id
2vv6

 

 

 

 

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Contents
Protein chains
106 a.a. *
Ligands
HEM ×4
Metals
_CL ×4
_NA ×3
Waters ×576
* Residue conservation analysis
PDB id:
2vv6
Name: Signaling protein, transferase
Title: Bjfixlh in ferric form
Structure: Sensor protein fixl. Chain: a, b, c, d. Fragment: heme domain, residues 151-269. Synonym: fixl. Engineered: yes
Source: Bradyrhizobium japonicum. Organism_taxid: 375. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.50Å     R-factor:   0.183     R-free:   0.211
Authors: R.A.Ayers,K.Moffat
Key ref: R.A.Ayers and K.Moffat (2008). Changes in quaternary structure in the signaling mechanisms of PAS domains. Biochemistry, 47, 12078-12086. PubMed id: 18942854
Date:
04-Jun-08     Release date:   04-Nov-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23222  (FIXL_BRADU) -  Sensor protein FixL from Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)
Seq:
Struc: 		505 a.a.
106 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.13.3  - histidine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
ATP
 + protein L-histidine
 = ADP
 + protein N-phospho-L-histidine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Biochemistry 47:12078-12086 (2008)
PubMed id: 18942854  
 
 
Changes in quaternary structure in the signaling mechanisms of PAS domains.
R.A.Ayers, K.Moffat.
 
  ABSTRACT  
 
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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21443850 J.D.Satterlee (2011).
Origins of aging mass loss in recombinant N-terminus and C-terminus deletion mutants of the heme-PAS biosensor domain BjFixLH(140-270).
  J Inorg Biochem, 105, 609-615.  
21347487 J.Perry, K.Koteva, and G.Wright (2011).
Receptor domains of two-component signal transduction systems.
  Mol Biosyst, 7, 1388-1398.  
20223701 J.Cheung, and W.A.Hendrickson (2010).
Sensor domains of two-component regulatory systems.
  Curr Opin Microbiol, 13, 116-123.  
20544970 L.J.Smith, A.Kahraman, and J.M.Thornton (2010).
Heme proteins--diversity in structural characteristics, function, and folding.
  Proteins, 78, 2349-2368.  
19906177 P.Slavny, R.Little, P.Salinas, T.A.Clarke, and R.Dixon (2010).
Quaternary structure changes in a second Per-Arnt-Sim domain mediate intramolecular redox signal relay in the NifL regulatory protein.
  Mol Microbiol, 75, 61-75.  
19836329 A.Möglich, R.A.Ayers, and K.Moffat (2009).
Structure and signaling mechanism of Per-ARNT-Sim domains.
  Structure, 17, 1282-1294.  
19864414 C.Lechauve, L.Bouzhir-Sima, T.Yamashita, M.C.Marden, M.H.Vos, U.Liebl, and L.Kiger (2009).
Heme ligand binding properties and intradimer interactions in the full-length sensor protein dos from Escherichia coli and its isolated heme domain.
  J Biol Chem, 284, 36146-36159.  
19712683 J.S.Lamb, B.D.Zoltowski, S.A.Pabit, L.Li, B.R.Crane, and L.Pollack (2009).
Illuminating solution responses of a LOV domain protein with photocoupled small-angle X-ray scattering.
  J Mol Biol, 393, 909-919.
PDB code: 3is2
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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