PDBsum entry 2ool

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protein ligands Protein-protein interface(s) links
Signaling protein PDB id
Protein chains
304 a.a. *
LBV ×2
Waters ×215
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Crystal structure of the chromophore-binding domain of an un bacteriophytochrome rpbphp3 from r. Palustris
Structure: Sensor protein. Chain: a, b. Fragment: chormophore binding domain (residues: 1-337). Engineered: yes
Source: Rhodopseudomonas palustris. Organism_taxid: 258594. Strain: cga009. Gene: phyb2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.20Å     R-factor:   0.192     R-free:   0.231
Authors: X.Yang,E.A.Stojkovic,J.Kuk,K.Moffat
Key ref:
X.Yang et al. (2007). Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion. Proc Natl Acad Sci U S A, 104, 12571-12576. PubMed id: 17640891 DOI: 10.1073/pnas.0701737104
25-Jan-07     Release date:   10-Jul-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q6N5G2  (Q6N5G2_RHOPA) -  Bacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB2
775 a.a.
304 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     signal transduction   4 terms 
  Biochemical function     signal transducer activity     1 term  


DOI no: 10.1073/pnas.0701737104 Proc Natl Acad Sci U S A 104:12571-12576 (2007)
PubMed id: 17640891  
Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion.
X.Yang, E.A.Stojkovic, J.Kuk, K.Moffat.
Bacteriophytochromes RpBphP2 and RpBphP3 from the photosynthetic bacterium Rhodopseudomonas palustris work in tandem to modulate synthesis of the light-harvesting complex LH4 in response to light. Although RpBphP2 and RpBphP3 share the same domain structure with 52% sequence identity, they demonstrate distinct photoconversion behaviors. RpBphP2 exhibits the "classical" phytochrome behavior of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states, whereas RpBphP3 exhibits novel photoconversion between Pr and a near-red (Pnr) light-absorbing states. We have determined the crystal structure at 2.2-A resolution of the chromophore binding domains of RpBphP3, covalently bound with chromophore biliverdin IXalpha. By combining structural and sequence analyses with site-directed mutagenesis, we identify key residues that directly modulate the photochemical properties of RpBphP3 and RpBphP2. Remarkably, we identify a region spanning residues 207-212 in RpBphP3, in which a single mutation, L207Y, causes this unusual bacteriophytochrome to revert to the classical phenotype that undergoes reversible photoconversion between the Pr and Pfr states. The reverse mutation, Y193L, in the corresponding region in RpBphP2 significantly diminishes the formation of the Pfr state. We propose that residues 207-212 and the spatially adjacent conserved residues, Asp-216 and Tyr-272, interact with the chromophore and form part of the interface between the chromophore binding domains and the PHY domain that modulates photoconversion.
  Selected figure(s)  
Figure 1.
Fig. 1. Crystal structure of RpBphP3-CBD. (a) Domain structure of the full-length Bph RpBphP3. (b) Ribbon diagram of the two RpBphP3-CBD molecules in the asymmetric unit. The PAS domain is in yellow, and the GAF domain is in green. (c) Superposition of the crystal structures of RpBphP3-CBD (PDB ID code 2OOL, in yellow and green) and DrBphP-CBD (PDB ID code 2O9C, in light blue). (d) The F[o] – F[c] omit map in the region of chromophore. The chromophore is shown as 2(S),3(E)-P B covalently linked to Cys-28.
Figure 4.
Fig. 4. VDW surface of the RpBphP3-CBD structure. Residues Tyr-272, Asp-216, and Leu-207-Phe-210-Phe-212 in the 15Ea pocket (colored in maroon) form a continuous surface patch and shield ring D of the chromophore (in cyan) in the GAF domain.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21352235 A.Losi, and W.Gärtner (2011).
Old chromophores, new photoactivation paradigms, trendy applications: flavins in blue light-sensing photoreceptors.
  Photochem Photobiol, 87, 491-510.  
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.  
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
20534495 H.Li, J.Zhang, R.D.Vierstra, and H.Li (2010).
Quaternary organization of a phytochrome dimer as revealed by cryoelectron microscopy.
  Proc Natl Acad Sci U S A, 107, 10872-10877.  
20437037 I.Baca, D.Sprockett, and V.Dvornyk (2010).
Circadian input kinases and their homologs in cyanobacteria: evolutionary constraints versus architectural diversification.
  J Mol Evol, 70, 453-465.  
20441366 I.Rajkovic, J.Hallmann, S.Grübel, R.More, W.Quevedo, M.Petri, and S.Techert (2010).
Development of a multipurpose vacuum chamber for serial optical and diffraction experiments with free electron laser radiation.
  Rev Sci Instrum, 81, 045105.  
20223701 J.Cheung, and W.A.Hendrickson (2010).
Sensor domains of two-component regulatory systems.
  Curr Opin Microbiol, 13, 116-123.  
19967442 J.Wang, B.Yan, G.Chen, Y.Su, and T.Wang (2010).
Adaptive evolution in the GAF domain of phytochromes in gymnosperms.
  Biochem Genet, 48, 236-247.  
20435909 K.C.Toh, E.A.Stojkovic, I.H.van Stokkum, K.Moffat, and J.T.Kennis (2010).
Proton-transfer and hydrogen-bond interactions determine fluorescence quantum yield and photochemical efficiency of bacteriophytochrome.
  Proc Natl Acad Sci U S A, 107, 9170-9175.  
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.  
20333618 P.Piwowarski, E.Ritter, K.P.Hofmann, P.Hildebrandt, D.von Stetten, P.Scheerer, N.Michael, T.Lamparter, and F.Bartl (2010).
Light-induced activation of bacterial phytochrome Agp1 monitored by static and time-resolved FTIR spectroscopy.
  Chemphyschem, 11, 1207-1214.  
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.  
20492561 T.Rohmer, C.Lang, W.Gärtner, J.Hughes, and J.Matysik (2010).
Role of the protein cavity in phytochrome chromoprotein assembly and double-bond isomerization: a comparison with model compounds.
  Photochem Photobiol, 86, 856-861.  
19671704 A.T.Ulijasz, G.Cornilescu, D.von Stetten, C.Cornilescu, F.Velazquez Escobar, J.Zhang, R.J.Stankey, M.Rivera, P.Hildebrandt, and R.D.Vierstra (2009).
Cyanochromes are blue/green light photoreversible photoreceptors defined by a stable double cysteine linkage to a phycoviolobilin-type chromophore.
  J Biol Chem, 284, 29757-29772.  
19640848 B.Borucki, and T.Lamparter (2009).
A polarity probe for monitoring light-induced structural changes at the entrance of the chromophore pocket in a bacterial phytochrome.
  J Biol Chem, 284, 26005-26016.  
19224036 B.Durbeej (2009).
On the primary event of phytochrome: quantum chemical comparison of photoreactions at C(4), C(10) and C(15).
  Phys Chem Chem Phys, 11, 1354-1361.  
19450486 M.A.Mroginski, D.von Stetten, F.V.Escobar, H.M.Strauss, S.Kaminski, P.Scheerer, M.Günther, D.H.Murgida, P.Schmieder, C.Bongards, W.Gärtner, J.Mailliet, J.Hughes, L.O.Essen, and P.Hildebrandt (2009).
Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: reconciling structural and spectroscopic data by QM/MM calculations.
  Biophys J, 96, 4153-4163.  
19339496 N.C.Rockwell, L.Shang, S.S.Martin, and J.C.Lagarias (2009).
Distinct classes of red/far-red photochemistry within the phytochrome superfamily.
  Proc Natl Acad Sci U S A, 106, 6123-6127.  
  19194010 R.Narikawa, N.Muraki, T.Shiba, M.Ikeuchi, and G.Kurisu (2009).
Crystallization and preliminary X-ray studies of the chromophore-binding domain of cyanobacteriochrome AnPixJ from Anabaena sp. PCC 7120.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 159-162.  
19720999 X.Yang, J.Kuk, and K.Moffat (2009).
Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome.
  Proc Natl Acad Sci U S A, 106, 15639-15644.
PDB codes: 3g6o 3ibr
18192363 C.Schumann, R.Gross, M.M.Wolf, R.Diller, N.Michael, and T.Lamparter (2008).
Subpicosecond midinfrared spectroscopy of the Pfr reaction of phytochrome Agp1 from Agrobacterium tumefaciens.
  Biophys J, 94, 3189-3197.  
18612842 E.Giraud, and A.Verméglio (2008).
Bacteriophytochromes in anoxygenic photosynthetic bacteria.
  Photosynth Res, 97, 141-153.  
18762196 G.Cornilescu, A.T.Ulijasz, C.C.Cornilescu, J.L.Markley, and R.D.Vierstra (2008).
Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state.
  J Mol Biol, 383, 403-413.
PDB codes: 2k2n 2lb9
18708494 J.M.Lee, H.Y.Cho, H.J.Cho, I.J.Ko, S.W.Park, H.S.Baik, J.H.Oh, C.Y.Eom, Y.M.Kim, B.S.Kang, and J.I.Oh (2008).
O2- and NO-sensing mechanism through the DevSR two-component system in Mycobacterium smegmatis.
  J Bacteriol, 190, 6795-6804.
PDB codes: 2vjw 2vks
18192276 J.R.Wagner, J.Zhang, D.von Stetten, M.Günther, D.H.Murgida, M.A.Mroginski, J.M.Walker, K.T.Forest, P.Hildebrandt, and R.D.Vierstra (2008).
Mutational analysis of Deinococcus radiodurans bacteriophytochrome reveals key amino acids necessary for the photochromicity and proton exchange cycle of phytochromes.
  J Biol Chem, 283, 12212-12226.  
18799745 L.O.Essen, J.Mailliet, and J.Hughes (2008).
The structure of a complete phytochrome sensory module in the Pr ground state.
  Proc Natl Acad Sci U S A, 105, 14709-14714.
PDB code: 2vea
18846279 M.Ikeuchi, and T.Ishizuka (2008).
Cyanobacteriochromes: a new superfamily of tetrapyrrole-binding photoreceptors in cyanobacteria.
  Photochem Photobiol Sci, 7, 1159-1167.  
18549244 N.C.Rockwell, S.L.Njuguna, L.Roberts, E.Castillo, V.L.Parson, S.Dwojak, J.C.Lagarias, and S.C.Spiller (2008).
A second conserved GAF domain cysteine is required for the blue/green photoreversibility of cyanobacteriochrome Tlr0924 from Thermosynechococcus elongatus.
  Biochemistry, 47, 7304-7316.  
18446253 O.Anders Borg, and B.Durbeej (2008).
Which factors determine the acidity of the phytochromobilin chromophore of plant phytochrome?
  Phys Chem Chem Phys, 10, 2528-2537.  
18390618 P.Schwinté, H.Foerstendorf, Z.Hussain, W.Gärtner, M.A.Mroginski, P.Hildebrandt, and F.Siebert (2008).
FTIR study of the photoinduced processes of plant phytochrome phyA using isotope-labeled bilins and density functional theory calculations.
  Biophys J, 95, 1256-1267.  
18771590 R.A.Sharrock (2008).
The phytochrome red/far-red photoreceptor superfamily.
  Genome Biol, 9, 230.  
18846291 R.Narikawa, T.Kohchi, and M.Ikeuchi (2008).
Characterization of the photoactive GAF domain of the CikA homolog (SyCikA, Slr1969) of the cyanobacterium Synechocystis sp. PCC 6803.
  Photochem Photobiol Sci, 7, 1253-1259.  
18832155 T.Rohmer, C.Lang, J.Hughes, L.O.Essen, W.Gärtner, and J.Matysik (2008).
Light-induced chromophore activity and signal transduction in phytochromes observed by 13C and 15N magic-angle spinning NMR.
  Proc Natl Acad Sci U S A, 105, 15229-15234.  
18799746 X.Yang, J.Kuk, and K.Moffat (2008).
Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: photoconversion and signal transduction.
  Proc Natl Acad Sci U S A, 105, 14715-14720.
PDB code: 3c2w
18621684 Y.Hirose, T.Shimada, R.Narikawa, M.Katayama, and M.Ikeuchi (2008).
Cyanobacteriochrome CcaS is the green light receptor that induces the expression of phycobilisome linker protein.
  Proc Natl Acad Sci U S A, 105, 9528-9533.  
18024131 M.A.van der Horst, J.Key, and K.J.Hellingwerf (2007).
Photosensing in chemotrophic, non-phototrophic bacteria: let there be light sensing too.
  Trends Microbiol, 15, 554-562.  
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.