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PDBsum entry 3ibr
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protein ligands Protein-protein interface(s) links
Transferase PDB id
3ibr

 

 

 

 

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Contents
Protein chains
457 a.a. *
Ligands
BLA ×2
Waters ×2
* Residue conservation analysis
PDB id:
3ibr
Name: Transferase
Title: Crystal structure of p. Aeruginosa bacteriophytochrome photosensory core module mutant q188l in the mixed pr/pfr state
Structure: Bacteriophytochrome. Chain: a, b. Fragment: unp residues 1-497. Synonym: phytochrome-like protein. Engineered: yes. Mutation: yes
Source: Pseudomonas aeruginosa. Organism_taxid: 287. Strain: pa01. Gene: bphp, pa4117. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.97Å     R-factor:   0.236     R-free:   0.307
Authors: X.Yang,J.Kuk,K.Moffat
Key ref: X.Yang et al. (2009). Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome. Proc Natl Acad Sci U S A, 106, 15639-15644. PubMed id: 19720999
Date:
16-Jul-09     Release date:   22-Sep-09    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9HWR3  (BPHY_PSEAE) -  Bacteriophytochrome from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Seq:
Struc: 		 
Seq:
Struc: 		728 a.a.
457 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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    
 
 
Proc Natl Acad Sci U S A 106:15639-15644 (2009)
PubMed id: 19720999  
 
 
Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome.
X.Yang, J.Kuk, K.Moffat.
 
  ABSTRACT  
 
Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria by means of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here, we report the crystal structure of the Q188L mutant of Pseudomonas aeruginosa bacteriophytochrome (PaBphP) photosensory core module, which exhibits altered photoconversion behavior and different crystal packing from wild type. We observe two distinct chromophore conformations in the Q188L crystal structure that we identify with the Pfr and Pr states. The Pr/Pfr compositions, varying from crystal to crystal, seem to correlate with light conditions under which the Q188L crystals are cryoprotected. We also compare all known Pr and Pfr structures. Using site-directed mutagenesis, we identify residues that are involved in stabilizing the 15Ea (Pfr) and 15Za (Pr) configurations of the biliverdin chromophore. Specifically, Ser-261 appears to be essential to form a stable Pr state in PaBphP, possibly by means of its interaction with the propionate group of ring C. We propose a "flip-and-rotate" model that summarizes the major conformational differences between the Pr and Pfr states of the chromophore and its binding pocket.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21253657 A.Strambi, and B.Durbeej (2011).
Initial excited-state relaxation of the bilin chromophores of phytochromes: a computational study.
  Photochem Photobiol Sci, 10, 569-579.  
21325055 C.Song, G.Psakis, C.Lang, J.Mailliet, W.Gärtner, J.Hughes, and J.Matysik (2011).
Two ground state isoforms and a chromophore D-ring photoflip triggering extensive intramolecular changes in a canonical phytochrome.
  Proc Natl Acad Sci U S A, 108, 3842-3847.  
21347487 J.Perry, K.Koteva, and G.Wright (2011).
Receptor domains of two-component signal transduction systems.
  Mol Biosyst, 7, 1388-1398.  
21250783 M.E.Auldridge, and K.T.Forest (2011).
Bacterial phytochromes: more than meets the light.
  Crit Rev Biochem Mol Biol, 46, 67-88.  
22002602 X.Yang, Z.Ren, J.Kuk, and K.Moffat (2011).
Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome.
  Nature, 479, 428-432.
PDB codes: 3nhq 3nop 3not 3nou
20192744 A.Möglich, X.Yang, R.A.Ayers, and K.Moffat (2010).
Structure and function of plant photoreceptors.
  Annu Rev Plant Biol, 61, 21-47.  
20075921 A.T.Ulijasz, G.Cornilescu, C.C.Cornilescu, J.Zhang, M.Rivera, J.L.Markley, and R.D.Vierstra (2010).
Structural basis for the photoconversion of a phytochrome to the activated Pfr form.
  Nature, 463, 250-254.
PDB codes: 2kli 2koi 2lb5
20223701 J.Cheung, and W.A.Hendrickson (2010).
Sensor domains of two-component regulatory systems.
  Curr Opin Microbiol, 13, 116-123.  
20340123 M.Röben, J.Hahn, E.Klein, T.Lamparter, G.Psakis, J.Hughes, and P.Schmieder (2010).
NMR spectroscopic investigation of mobility and hydrogen bonding of the chromophore in the binding pocket of phytochrome proteins.
  Chemphyschem, 11, 1248-1257.  
20155775 N.C.Rockwell, and J.C.Lagarias (2010).
A brief history of phytochromes.
  Chemphyschem, 11, 1172-1180.  
20373318 P.Scheerer, N.Michael, J.H.Park, S.Nagano, H.W.Choe, K.Inomata, B.Borucki, N.Krauss, and T.Lamparter (2010).
Light-induced conformational changes of the chromophore and the protein in phytochromes: bacterial phytochromes as model systems.
  Chemphyschem, 11, 1090-1105.  
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 codes are shown on the right.

 

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