Photoactive yellow protein

In molecular biology, the PYP domain (photoactive yellow protein) is a p-coumaric acid-binding protein domain. They are present in various proteins in bacteria.

PYP
Identifiers
SymbolPYP
PfamPF00989
InterProIPR012130
SMARTSM00091
PROSITEPS50112
SCOP255786 / SCOPe / SUPFAM
CDDcd00130
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

PYP is a highly soluble globular protein with an alpha/beta fold structure. It is a member of the PAS domain superfamily, which also contains a variety of other kinds of photosensory proteins.

PYP was first discovered in 1985.[1]

A recently (2016) developed chemogenetic system named FAST (Fluorescence-Activating and absorption Shifting Tag) was engineered from PYP to specifically and reversibly bind a series of hydroxybenzylidene rhodanine (HBR) derivatives for their fluorogenic properties. Upon interaction with FAST, the fluorogen is locked into a fluorescent conformation unlike when in solution. This new protein labelling system is used in a variety of microscopy and cytometry setups.[2]

p-Coumaric acid

p-Coumaric acid is a cofactor of Photoactive yellow protein|photoactive yellow proteins.[3] Adducts of p-coumaric acid bound to PYP form crystals that diffract well for x-ray crystallography experiments. These structural studies have provided insight into photosensitive proteins, e.g. the role of hydrogen bonding, molecular isomerization and photoactivity.[4][5][6][7]

Photochemical transitions

It was originally believed that due to light emissions resembling that of retinal bound rhodopsin, the photosensor molecule bound to PYP should resemble the structure of retinal bound rhodopsin, the photosensor molecule bound to PYP should resemble the structure of retinal.[8] Scientists were therefore amazed when the PYP Cys 69 was bound by a thiol ester linkage as the light sensitive prosthetic group p-coumaric acid.[3] During the photoreactive mechanism:[3][8]

  1. Light absorption yields the native protein to absorb a maximum wavelength of 446 nm, ε = 45500 M−1 cm−1.
  2. Within a nanosecond the absorbed maximum wavelength is shifted to 465 nm.
  3. Then on a sub-millisecond timescale is excited to a 355 nm state.
p-Coumaric acid exhibiting trans–cis isomerization due to absorption of light causing photochemical transitions. To the right demonstrates the molecular structure of p-coumaric acid in the ligand binding site and hydrogen bonding interactions involved in the innate oxyanion hole. To the left is a crystallographic image of p-coumaric acid in the ligand binding site based on PDB: 2PYP​ PyMOL rendering.[9]

These observed phenomena are due to the trans–cis isomerization of the vinyl trans double bond in the p-coumaric acid.[3][7][6] Scientists noted by observing the crystal structure of p-coumaric acid bound by PYP that the hydroxyl group connected to the C4 carbon of the phenyl ring appeared to be deprotonated – effectively a phenolate functional group.[7][10] This was due to abnormally short hydrogen bonding lengths observed in the protein crystal structure.[9]

Role of hydrogen bonding

Hydrogen bonds in proteins such as PYP take part in interrelated networks, where at the center of p-coumaric acid's phenolate O4 atom, there is an oxyanion hole that is crucial for photosensory function.[6][11][12] Oxyanion holes exist in enzymes to stabilize transitions states of reaction intermediates, thus stabilizing the trans–cis isomerization of p-coumaric acid.[5][13] During the transition state it is believed that the p-coumaric acid phenolate O4 takes part in a hydrogen bond network between Glu46, Tyr42 and Thr50 of PYP.[13][5] These interactions are apart from the thiol ester linkage to Cys 69 keeping p-coumaric acid in the ligand binding site.[3] Upon transitioning to the cis-isomeric form of p-coumaric acid the favorable hydrogen bonds are no longer in close interaction.

References
  1. Meyer TE (January 1985). "Isolation and characterization of soluble cytochromes, ferredoxins and other chromophoric proteins from the halophilic phototrophic bacterium Ectothiorhodospira halophila". Biochimica et Biophysica Acta (BBA) - Bioenergetics. 806 (1): 175–83. doi:10.1016/0005-2728(85)90094-5. PMID 2981543.
  2. Plamont MA, Billon-Denis E, Maurin S, Gauron C, Pimenta FM, Specht CG, et al. (January 2016). "Small fluorescence-activating and absorption-shifting tag for tunable protein imaging in vivo". Proceedings of the National Academy of Sciences of the United States of America. 113 (3): 497–502. doi:10.1073/pnas.1513094113. PMC 4725535. PMID 26711992.
  3. Hoff WD, Düx P, Hård K, Devreese B, Nugteren-Roodzant IM, Crielaard W, Boelens R, Kaptein R, van Beeumen J, Hellingwerf KJ (November 1994). "Thiol ester-linked p-coumaric acid as a new photoactive prosthetic group in a protein with rhodopsin-like photochemistry". Biochemistry. 33 (47): 13959–62. doi:10.1021/bi00251a001. PMID 7947803.
  4. "PDB101: Molecule of the Month: Photoactive Yellow Protein". RCSB: PDB-101. Retrieved 2019-03-12.
  5. Pinney MM, Natarajan A, Yabukarski F, Sanchez DM, Liu F, Liang R, Doukov T, Schwans JP, Martinez TJ, Herschlag D (August 2018). "Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein". Journal of the American Chemical Society. 140 (31): 9827–9843. doi:10.1021/jacs.8b01596. OSTI 1476146. PMID 29990421. S2CID 207190006.
  6. Hellingwerf KJ (February 2000). "Key issues in the photochemistry and signalling-state formation of photosensor proteins". Journal of Photochemistry and Photobiology B: Biology. 54 (2–3): 94–102. doi:10.1016/S1011-1344(00)00004-X. PMID 10836537.
  7. Premvardhan LL, Buda F, Van Der Horst MA, Lührs DC, Hellingwerf KJ, Van Grondelle R (2004-01-30). "Impact of Photon Absorption on the Electronic Properties of p -Coumaric Acid Derivatives of the Photoactive Yellow Protein Chromophore". The Journal of Physical Chemistry B. 108 (16): 5138–5148. doi:10.1021/jp037469b. hdl:1887/3480076.
  8. Meyer TE, Yakali E, Cusanovich MA, Tollin G (January 1987). "Properties of a water-soluble, yellow protein isolated from a halophilic phototrophic bacterium that has photochemical activity analogous to sensory rhodopsin". Biochemistry. 26 (2): 418–23. doi:10.1021/bi00376a012. PMID 3828315.
  9. Genick UK, Borgstahl GE, Ng K, Ren Z, Pradervand C, Burke PM, Srajer V, Teng TY, Schildkamp W, McRee DE, Moffat K, Getzoff ED (March 1997). "Structure of a protein photocycle intermediate by millisecond time-resolved crystallography". Science. 275 (5305): 1471–5. doi:10.1126/science.275.5305.1471. PMID 9045611. S2CID 20434371.
  10. Yamaguchi S, Kamikubo H, Kurihara K, Kuroki R, Niimura N, Shimizu N, Yamazaki Y, Kataoka M (January 2009). "Low-barrier hydrogen bond in photoactive yellow protein". Proceedings of the National Academy of Sciences of the United States of America. 106 (2): 440–4. Bibcode:2009PNAS..106..440Y. doi:10.1073/pnas.0811882106. PMC 2626721. PMID 19122140.
  11. Borgstahl GE, Williams DR, Getzoff ED (May 1995). "1.4 Å structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore". Biochemistry. 34 (19): 6278–87. doi:10.1021/bi00019a004. PMID 7756254.
  12. Stahl AD, Hospes M, Singhal K, van Stokkum I, van Grondelle R, Groot ML, Hellingwerf KJ (September 2011). "On the involvement of single-bond rotation in the primary photochemistry of photoactive yellow protein". Biophysical Journal. 101 (5): 1184–92. Bibcode:2011BpJ...101.1184S. doi:10.1016/j.bpj.2011.06.065. PMC 3164125. PMID 21889456.
  13. Herschlag D, Pinney MM (June 2018). "Hydrogen Bonds: Simple after All?". Biochemistry. 57 (24): 3338–3352. doi:10.1021/acs.biochem.8b00217. PMID 29678112.

Further reading
  • Overview of all the structural information available in the PDB for UniProt: P16113 (Photoactive yellow protein) at the PDBe-KB.
This article incorporates text from the public domain Pfam and InterPro: IPR012130
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