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Refined structure of c-phycocyanin from the cyanobacterium Synechococcus vulcanus at 1.6 A: insights into the role of solvent molecules in thermal stability and co-factor structure.

Adir N, Vainer R, Lerner N
Biochim Biophys Acta 1556 168-74 (2002)
Cited: 27 times
EuropePMC logo PMID: 12460674

Abstract

The crystal structure of the light-harvesting phycobiliprotein, c-phycocyanin from the thermophilic cyanobacterium Synechococcus vulcanus has been refined to 1.6 A resolution based on the previously determined lower resolution structure (PDB entry 1I7Y). The improved data was collected using synchrotron radiation at 100 K. The significantly improved crystallographic data has lead to improved calculated electron density maps, allowing the unambiguous positioning of all protein and co-factor atoms and the positioning of 377 solvent molecules. The positions of solvent molecules at specific sites important for stabilization of different levels of self-assembly of the phycobilisome structure were identified and the bonding network is described. The presence of solvent molecules in the vicinity of the co-factors and in intermolecular spaces is identified and their possible roles are suggested. All three of the phycocyanobilin co-factors bind water molecules at specific sites between the propionic acid side chains. Molecular dynamic (MD) simulations support that these special waters have a role in stabilization of this conformation. On the basis of the crystal packing reported here and in comparison to other phycobiliprotein crystal forms, we have analyzed the roles of specific sites on the formation of the phycobilisome complex.

Reviews - 1ktp mentioned but not cited (1)

  1. Phycobiliproteins: Structural aspects, functional characteristics, and biotechnological perspectives. Dagnino-Leone J, Figueroa CP, Castañeda ML, Youlton AD, Vallejos-Almirall A, Agurto-Muñoz A, Pavón Pérez J, Agurto-Muñoz C. Comput Struct Biotechnol J 20 1506-1527 (2022)

Articles - 1ktp mentioned but not cited (3)

  1. The structure of allophycocyanin B from Synechocystis PCC 6803 reveals the structural basis for the extreme redshift of the terminal emitter in phycobilisomes. Peng PP, Dong LL, Sun YF, Zeng XL, Ding WL, Scheer H, Yang X, Zhao KH. Acta Crystallogr D Biol Crystallogr 70 2558-2569 (2014)
  2. Structural, functional, and mutational analysis of the NblA protein provides insight into possible modes of interaction with the phycobilisome. Dines M, Sendersky E, David L, Schwarz R, Adir N. J Biol Chem 283 30330-30340 (2008)
  3. Non-conventional octameric structure of C-phycocyanin. Minato T, Teramoto T, Adachi N, Hung NK, Yamada K, Kawasaki M, Akutsu M, Moriya T, Senda T, Ogo S, Kakuta Y, Yoon KS. Commun Biol 4 1238 (2021)


Reviews citing this publication (5)

  1. Elucidation of the molecular structures of components of the phycobilisome: reconstructing a giant. Adir N. Photosynth Res 85 15-32 (2005)
  2. Production of phycocyanin--a pigment with applications in biology, biotechnology, foods and medicine. Eriksen NT. Appl Microbiol Biotechnol 80 1-14 (2008)
  3. Biliprotein maturation: the chromophore attachment. Scheer H, Zhao KH. Mol Microbiol 68 263-276 (2008)
  4. Phycocyanin: A Potential Drug for Cancer Treatment. Jiang L, Wang Y, Yin Q, Liu G, Liu H, Huang Y, Li B. J Cancer 8 3416-3429 (2017)
  5. Exploring the structural aspects and therapeutic perspectives of cyanobacterial phycobiliproteins. Patel SN, Sonani RR, Roy D, Singh NK, Subudhi S, Pabbi S, Madamwar D. 3 Biotech 12 224 (2022)

Articles citing this publication (18)

  1. Phycobilin:cystein-84 biliprotein lyase, a near-universal lyase for cysteine-84-binding sites in cyanobacterial phycobiliproteins. Zhao KH, Su P, Tu JM, Wang X, Liu H, Plöscher M, Eichacker L, Yang B, Zhou M, Scheer H. Proc Natl Acad Sci U S A 104 14300-14305 (2007)
  2. High-resolution crystal structures of trimeric and rod phycocyanin. David L, Marx A, Adir N. J Mol Biol 405 201-213 (2011)
  3. Allophycocyanin and phycocyanin crystal structures reveal facets of phycobilisome assembly. Marx A, Adir N. Biochim Biophys Acta 1827 311-318 (2013)
  4. Allophycocyanin trimer stability and functionality are primarily due to polar enhanced hydrophobicity of the phycocyanobilin binding pocket. McGregor A, Klartag M, David L, Adir N. J Mol Biol 384 406-421 (2008)
  5. Quantum chemical description of absorption properties and excited-state processes in photosynthetic systems. König C, Neugebauer J. Chemphyschem 13 386-425 (2012)
  6. The structure at 2 A resolution of Phycocyanin from Gracilaria chilensis and the energy transfer network in a PC-PC complex. Contreras-Martel C, Matamala A, Bruna C, Poo-Caamaño G, Almonacid D, Figueroa M, Martínez-Oyanedel J, Bunster M. Biophys Chem 125 388-396 (2007)
  7. Chromophore attachment in phycocyanin. Functional amino acids of phycocyanobilin--alpha-phycocyanin lyase and evidence for chromophore binding. Zhao KH, Wu D, Zhang L, Zhou M, Böhm S, Bubenzer C, Scheer H. FEBS J 273 1262-1274 (2006)
  8. CpeS is a lyase specific for attachment of 3Z-PEB to Cys82 of {beta}-phycoerythrin from Prochlorococcus marinus MED4. Wiethaus J, Busch AW, Kock K, Leichert LI, Herrmann C, Frankenberg-Dinkel N. J Biol Chem 285 37561-37569 (2010)
  9. Structure and mechanism of the phycobiliprotein lyase CpcT. Zhou W, Ding WL, Zeng XL, Dong LL, Zhao B, Zhou M, Scheer H, Zhao KH, Yang X. J Biol Chem 289 26677-26689 (2014)
  10. C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening. Sarrou I, Feiler CG, Falke S, Peard N, Yefanov O, Chapman H. Acta Crystallogr D Struct Biol 77 224-236 (2021)
  11. Crystallization of sparingly soluble stress-related proteins from cyanobacteria by controlled urea solublization. Dines M, Sendersky E, Schwarz R, Adir N. J Struct Biol 158 116-121 (2007)
  12. Confined water dynamics in a hydrated photosynthetic pigment-protein complex. Kurzweil-Segev Y, Popov I, Eisenberg I, Yochelis S, Keren N, Paltiel Y, Feldman Y. Phys Chem Chem Phys 19 28063-28070 (2017)
  13. Anti-Stokes fluorescence excitation reveals conformational mobility of the C-phycocyanin chromophores. Tsoraev GV, Protasova EA, Klimanova EA, Ryzhykau YL, Kuklin AI, Semenov YS, Ge B, Li W, Qin S, Friedrich T, Sluchanko NN, Maksimov EG. Struct Dyn 9 054701 (2022)
  14. Revisiting high-resolution crystal structure of Phormidium rubidum phycocyanin. Sonani RR, Roszak AW, Liu H, Gross ML, Blankenship RE, Madamwar D, Cogdell RJ. Photosynth Res 144 349-360 (2020)
  15. Crystal structure of Synechococcus phycocyanin: implications of light-harvesting and antioxidant properties. Patel SN, Sonani RR, Chaubey MG, Gupta GD, Singh NK, Kumar V, Madamwar D. 3 Biotech 13 247 (2023)
  16. Estimation of the relative contributions to the electronic energy transfer rates based on Förster theory: The case of C-phycocyanin chromophores. Mishima K, Shoji M, Umena Y, Boero M, Shigeta Y. Biophys Physicobiol 18 196-214 (2021)
  17. Structural comparison of allophycocyanin variants reveals the molecular basis for their spectral differences. Gisriel CJ, Elias E, Shen G, Soulier NT, Brudvig GW, Croce R, Bryant DA. Photosynth Res (2023)
  18. Water in the hydrated protein powders: Dynamic and structure. Sasaki K, Popov I, Feldman Y. J Chem Phys 150 204504 (2019)


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