PDBsum entry 1nwz

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Signaling protein PDB id
Protein chain
125 a.a. *
Waters ×156
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Pyp ultra-high resolution structure of a bacterial photorece
Structure: Photoactive yellow protein. Chain: a. Synonym: pyp. Engineered: yes
Source: Halorhodospira halophila. Organism_taxid: 1053. Gene: pyp. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
0.82Å     R-factor:   0.123     R-free:   0.144
Authors: E.D.Getzoff,K.N.Gutwin,U.K.Genick
Key ref: E.D.Getzoff et al. (2003). Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation. Nat Struct Biol, 10, 663-668. PubMed id: 12872160
07-Feb-03     Release date:   11-Mar-03    
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Protein chain
Pfam   ArchSchema ?
P16113  (PYP_HALHA) -  Photoactive yellow protein
125 a.a.
125 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to stimulus   5 terms 
  Biochemical function     signal transducer activity     2 terms  


Nat Struct Biol 10:663-668 (2003)
PubMed id: 12872160  
Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation.
E.D.Getzoff, K.N.Gutwin, U.K.Genick.
Protein photoreceptors use small-molecule cofactors called chromophores to detect light. Only under the influence of the receptors' active sites do these chromophores adopt spectral and photochemical properties that suit the receptors' functional requirements. This protein-induced change in chromophore properties is called photochemical tuning and is a prime example for the general--but poorly understood--process of chemical tuning through which proteins shape the reactivity of their active-site groups. Here we report the 0.82-A resolution X-ray structure of the bacterial light receptor photoactive yellow protein (PYP). The unusually precise structure reveals deviations from expected molecular geometries and anisotropic atomic displacements in the PYP active site. Our analysis of these deviations points directly to the intramolecular forces and active-site dynamics that tune the properties of PYP's chromophore to absorb blue light, suppress fluorescence, and favor the required light-driven double-bond isomerization.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21405157 K.Sneskov, T.Schwabe, J.Kongsted, and O.Christiansen (2011).
The polarizable embedding coupled cluster method.
  J Chem Phys, 134, 104108.  
19551213 D.Hoersch, H.Otto, M.A.Cusanovich, and M.P.Heyn (2009).
Time-resolved spectroscopy of dye-labeled photoactive yellow protein suggests a pathway of light-induced structural changes in the N-terminal cap.
  Phys Chem Chem Phys, 11, 5437-5444.  
19475175 E.M.González, L.Guidoni, and C.Molteni (2009).
Chemical and protein shifts in the spectrum of the photoactive yellow protein: a time-dependent density functional theory/molecular mechanics study.
  Phys Chem Chem Phys, 11, 4556-4563.  
19091750 J.Hendriks, and K.J.Hellingwerf (2009).
pH Dependence of the photoactive yellow protein photocycle recovery reaction reveals a new late photocycle intermediate with a deprotonated chromophore.
  J Biol Chem, 284, 5277-5288.  
19707683 K.Okamoto, N.Hamada, T.A.Okamura, N.Ueyama, and H.Yamamoto (2009).
Color regulation and stabilization of chromophore by Cys69 in photoactive yellow protein active center.
  Org Biomol Chem, 7, 3782-3791.  
19470452 P.A.Sigala, M.A.Tsuchida, and D.Herschlag (2009).
Hydrogen bond dynamics in the active site of photoactive yellow protein.
  Proc Natl Acad Sci U S A, 106, 9232-9237.  
19122140 S.Yamaguchi, H.Kamikubo, K.Kurihara, R.Kuroki, N.Niimura, N.Shimizu, Y.Yamazaki, and M.Kataoka (2009).
Low-barrier hydrogen bond in photoactive yellow protein.
  Proc Natl Acad Sci U S A, 106, 440-444.
PDB codes: 2zoh 2zoi
18399917 M.Kumauchi, M.T.Hara, P.Stalcup, A.Xie, and W.D.Hoff (2008).
Identification of six new photoactive yellow proteins--diversity and structure-function relationships in a bacterial blue light photoreceptor.
  Photochem Photobiol, 84, 956-969.  
18808119 P.A.Sigala, D.A.Kraut, J.M.Caaveiro, B.Pybus, E.A.Ruben, D.Ringe, G.A.Petsko, and D.Herschlag (2008).
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.
  J Am Chem Soc, 130, 13696-13708.
PDB codes: 2inx 3cpo
18547519 P.D.Coureux, Z.P.Fan, V.Stojanoff, and U.K.Genick (2008).
Picometer-scale conformational heterogeneity separates functional from nonfunctional states of a photoreceptor protein.
  Structure, 16, 863-872.
PDB codes: 2qj5 2qj7
18399916 Y.Imamoto, M.Harigai, T.Morimoto, and M.Kataoka (2008).
Low-temperature spectroscopy of Met100Ala mutant of photoactive yellow protein.
  Photochem Photobiol, 84, 970-976.  
18227128 Y.Imamoto, S.Tatsumi, M.Harigai, Y.Yamazaki, H.Kamikubo, and M.Kataoka (2008).
Diverse roles of glycine residues conserved in photoactive yellow proteins.
  Biophys J, 94, 3620-3628.  
17223691 A.Pandini, M.S.Denison, Y.Song, A.A.Soshilov, and L.Bonati (2007).
Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis.
  Biochemistry, 46, 696-708.  
17496031 D.Hoersch, H.Otto, C.P.Joshi, B.Borucki, M.A.Cusanovich, and M.P.Heyn (2007).
Role of a conserved salt bridge between the PAS core and the N-terminal domain in the activation of the photoreceptor photoactive yellow protein.
  Biophys J, 93, 1687-1699.  
17307829 H.Kamikubo, N.Shimizu, M.Harigai, Y.Yamazaki, Y.Imamoto, and M.Kataoka (2007).
Characterization of the solution structure of the M intermediate of photoactive yellow protein using high-angle solution x-ray scattering.
  Biophys J, 92, 3633-3642.  
17373703 K.Shirai, Y.Yamazaki, H.Kamikubo, Y.Imamoto, and M.Kataoka (2007).
Attempt to simplify the amino-acid sequence of photoactive yellow protein with a set of simple rules.
  Proteins, 67, 821-833.  
17594037 S.L.Zheng, M.Messerschmidt, and P.Coppens (2007).
Single-crystal-to-single-crystal E-->Z and Z-->E isomerizations of 3-chloroacrylic acid within the nanocavities of a supramolecular framework.
  Chem Commun (Camb), (), 2735-2737.  
17144696 Groot, W.J.Buma, E.V.Gromov, I.Burghardt, H.Köppel, and L.S.Cederbaum (2006).
Combined experimental-theoretical study of the lower excited singlet states of paravinyl phenol, an analog of the paracoumaric acid chromophore.
  J Chem Phys, 125, 204303.  
16952373 R.Brudler, C.R.Gessner, S.Li, S.Tyndall, E.D.Getzoff, and V.L.Woods (2006).
PAS domain allostery and light-induced conformational changes in photoactive yellow protein upon I2 intermediate formation, probed with enhanced hydrogen/deuterium exchange mass spectrometry.
  J Mol Biol, 363, 148-160.  
15653739 B.Nie, J.Stutzman, and A.Xie (2005).
A vibrational spectral maker for probing the hydrogen-bonding status of protonated Asp and Glu residues.
  Biophys J, 88, 2833-2847.  
16366562 K.Heyne, O.F.Mohammed, A.Usman, J.Dreyer, E.T.Nibbering, and M.A.Cusanovich (2005).
Structural evolution of the chromophore in the primary stages of trans/cis isomerization in photoactive yellow protein.
  J Am Chem Soc, 127, 18100-18106.  
15026418 R.Kort, K.J.Hellingwerf, and R.B.Ravelli (2004).
Initial events in the photocycle of photoactive yellow protein.
  J Biol Chem, 279, 26417-26424.
PDB codes: 1uwn 1uwp
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.