Motion in Photoactive Yellow Protein (PYP) [pyp]

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Classification Known Fragment Motion, Unclassifiable [F-?-2]

2PHY Dark state [ PartsList ]
2PYP Intermediate, 50% bleached [ PartsList ]
2PYR 1 Nanosecond Intermediate
3PYP Early light cycle intermediate
3PHY Dark state, NMR [ PartsList ]

Photoactive Yellow Protein (PYP) is apparantly responsible for the negatively phototactic photoresponse of Ectohiorhodospira halophila. It is believed to be a simple bacterial photosensor that binds a small chromophore and then interacts with a secondary receptor. Aspects of the PYP photocycle make it suitable for study on the millisecond time-scale with time-resolved crystallographic methods (Gennick et al.). The conformation of one of the longest-lived intermediate photoexcited species in the photocycle has been determined (PDB ID 2PYP; Gennick et al., see also Krebs). Upon photoexcitation, the chromophore (covalently bondend to cysteine) has its chromophore significantly displaced, triggering subtle displacements in the protein backbone (Gennick et al., Krebs). Kaptein et al. have found the timescale of the motion to be in the millisecond range.

Particular values describing motion
Creation Date = 19971130
Experimental Methods = tx (Time-resolved and traditional X-ray Structures)
Modification Date = 2000-01-14 15:49:24.000

G E O Borgstahl, D R Williams, E D Getzoff (1995). 1.4 A Structure of Photoactive Yellow Protein, a Cytosolic Photoreceptor: Unusual Fold, Active Site, and Chromophore. Biochem. 34:6278-6287. [Medline info for 95063908]
K Ng, E D Getzoff, K Moffat (1995). Optical studies of a bacterial photoreceptor protein, photoactive yellow protein, in single crystals. Biochem. 34:879-90. [Medline info for 95127666]
Rubinstenn G, Vuister GW, Mulder FA, Dux PE, Boelens R, Hellingwerf KJ, Kaptein R (1998). Structural and dynamic changes of photoactive yellow protein during its photocycle in solution.Nat Struct Biol Jul;5(7):568-70 [Medline info for 98328107]
U K Genick, G E Borgstahl, K Ng, Z Ren, C Pradervand, P M Burke, V Srajer, T Y Teng, W Schildkamp, D E McRee, K Moffat, E D Getzoff (1997). Structure of a protein photocycle intermediate by millisecond time-resolved crystallography. Sci. 275:1471-5. [Medline info for 97197907]
W G Krebs (1996). Kinetic Analysis and Intermediate Structure Determination From High-Speed Time-Resolved Crystallography. University of Chicago: MS Thesis.
Y Imamoto, M Kataoka, F Tokunaga (1996). Photoreaction cycle of photoactive yellow protein from Ectothiorhodospira halophila studied by low-temperature spectroscopy. Biochem. 35:14047-53. [Medline info for 97074462]

Data and Graphics
Experimental method: Time-resolved x-ray crystallography Information on the time-resolved x-ray crystallography method

GO terms associated with structures
Molecular functionsignal transducer activity
Biological processsignal transduction


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Best representative
Morph Morph name Structure #1 Structure #2 Residues
Photoactive Yellow Protein 2phy [ A ] 3pyp [ A ] 125

User-submitted morphs
Morph Morph name Structure #1 Structure #2 Residues
245750-6361 Photoactive Yellow Protein 2phy [ A ] 2pyp [ A ] 125
246675-9692 Photoactive Yellow Protein 2phy [ A ] 2pyr [ A ] 125
81333-3767 Via_align 1byw [ A ] 2phy [ A ] 125

Automatic morphs
Morph Morph name Structure #1 Structure #2 Residues
va2phyA-3phyA Photoactive Yellow Protein 2phy [ A ] 3phy [ A ] 125
va3phyA-1f9iA Photoactive Yellow Protein 3phy [ A ] 1f9i [ A ] 125
va3phyA-1f98A Photoactive Yellow Protein 3phy [ A ] 1f98 [ A ] 125

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Copyright 1995-2005 M. Gerstein, W. Krebs, S. Flores, N. Echols, and others
Email: Mark.Gerstein _at_