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Crystal structure of carboxylase reaction-oriented ribulose 1, 5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita.

Sugawara H, Yamamoto H, Shibata N, Inoue T, Okada S, Miyake C, Yokota A, Kai Y
J Biol Chem 274 15655-61 (1999)
Cited: 36 times
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Abstract

Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco, EC 4.1.1. 39) obtained from a thermophilic red alga Galdieria partita has the highest specificity factor of 238 among the Rubiscos hitherto reported. Crystal structure of activated Rubisco from G. partita complexed with the reaction intermediate analogue, 2-carboxyarabinitol 1,5-bisphosphate (2-CABP) has been determined at 2.4-A resolution. Compared with other Rubiscos, different amino residues bring the structural differences in active site, which are marked around the binding sites of P-2 phosphate of 2-CABP. Especially, side chains of His-327 and Arg-295 show the significant differences from those of spinach Rubisco. Moreover, the side chains of Asn-123 and His-294 which are reported to bind the substrate, ribulose 1,5-bisphosphate, form hydrogen bonds characteristic of Galdieria Rubisco. Small subunits of Galdieria Rubisco have more than 30 extra amino acid residues on the C terminus, which make up a hairpin-loop structure to form many interactions with the neighboring small subunits. When the structures of Galdieria and spinach Rubiscos are superimposed, the hairpin region of the neighboring small subunit in Galdieria enzyme and apical portion of insertion residues 52-63 characteristic of small subunits in higher plant enzymes are almost overlapped to each other.

Reviews - 1bwv mentioned but not cited (2)

  1. The small subunit of Rubisco and its potential as an engineering target. Mao Y, Catherall E, Díaz-Ramos A, Greiff GRL, Azinas S, Gunn L, McCormick AJ. J Exp Bot 74 543-561 (2023)
  2. Red Rubiscos and opportunities for engineering green plants. Oh ZG, Askey B, Gunn LH. J Exp Bot 74 520-542 (2023)

Articles - 1bwv mentioned but not cited (6)

  1. Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree. Kacar B, Hanson-Smith V, Adam ZR, Boekelheide N. Geobiology 15 628-640 (2017)
  2. Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications. Valegård K, Andralojc PJ, Haslam RP, Pearce FG, Eriksen GK, Madgwick PJ, Kristoffersen AK, van Lun M, Klein U, Eilertsen HC, Parry MAJ, Andersson I. J Biol Chem 293 13033-13043 (2018)
  3. Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bisphosphate. Valegård K, Hasse D, Andersson I, Gunn LH. Acta Crystallogr D Struct Biol 74 1-9 (2018)
  4. Comparison of Protein Extracts from Various Unicellular Green Sources. Teuling E, Wierenga PA, Schrama JW, Gruppen H. J Agric Food Chem 65 7989-8002 (2017)
  5. Reversible post-translational carboxylation modulates the enzymatic activity of N-acetyl-L-ornithine transcarbamylase. Li Y, Yu X, Ho J, Fushman D, Allewell NM, Tuchman M, Shi D. Biochemistry 49 6887-6895 (2010)
  6. Deriving and Using Descriptors of Elementary Functions in Rational Protein Design. Yin M, Goncearenco A, Berezovsky IN. Front Bioinform 1 657529 (2021)


Reviews citing this publication (4)

  1. Rubisco: structure, regulatory interactions, and possibilities for a better enzyme. Spreitzer RJ, Salvucci ME. Annu Rev Plant Biol 53 449-475 (2002)
  2. Structure and function of Rubisco. Andersson I, Backlund A. Plant Physiol Biochem 46 275-291 (2008)
  3. Role of the small subunit in ribulose-1,5-bisphosphate carboxylase/oxygenase. Spreitzer RJ. Arch Biochem Biophys 414 141-149 (2003)
  4. Structural framework for catalysis and regulation in ribulose-1,5-bisphosphate carboxylase/oxygenase. Andersson I, Taylor TC. Arch Biochem Biophys 414 130-140 (2003)

Articles citing this publication (24)

  1. Form I Rubiscos from non-green algae are expressed abundantly but not assembled in tobacco chloroplasts. Whitney SM, Baldet P, Hudson GS, Andrews TJ. Plant J 26 535-547 (2001)
  2. Structure and function of the AAA+ protein CbbX, a red-type Rubisco activase. Mueller-Cajar O, Stotz M, Wendler P, Hartl FU, Bracher A, Hayer-Hartl M. Nature 479 194-199 (2011)
  3. EST-analysis of the thermo-acidophilic red microalga Galdieria sulphuraria reveals potential for lipid A biosynthesis and unveils the pathway of carbon export from rhodoplasts. Weber AP, Oesterhelt C, Gross W, Bräutigam A, Imboden LA, Krassovskaya I, Linka N, Truchina J, Schneidereit J, Voll H, Voll LM, Zimmermann M, Jamai A, Riekhof WR, Yu B, Garavito RM, Benning C. Plant Mol Biol 55 17-32 (2004)
  4. Catalytic by-product formation and ligand binding by ribulose bisphosphate carboxylases from different phylogenies. Pearce FG. Biochem J 399 525-534 (2006)
  5. Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry. Kitano K, Maeda N, Fukui T, Atomi H, Imanaka T, Miki K. Structure 9 473-481 (2001)
  6. Structural mechanism of RuBisCO activation by carbamylation of the active site lysine. Stec B. Proc Natl Acad Sci U S A 109 18785-18790 (2012)
  7. Highly conserved small subunit residues influence rubisco large subunit catalysis. Genkov T, Spreitzer RJ. J Biol Chem 284 30105-30112 (2009)
  8. A conserved mechanism controls translation of Rubisco large subunit in different photosynthetic organisms. Cohen I, Sapir Y, Shapira M. Plant Physiol 141 1089-1097 (2006)
  9. Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate. Mizohata E, Matsumura H, Okano Y, Kumei M, Takuma H, Onodera J, Kato K, Shibata N, Inoue T, Yokota A, Kai Y. J Mol Biol 316 679-691 (2002)
  10. Structure-function studies with the unique hexameric form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Rhodopseudomonas palustris. Satagopan S, Chan S, Perry LJ, Tabita FR. J Biol Chem 289 21433-21450 (2014)
  11. Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum. Li H, Sawaya MR, Tabita FR, Eisenberg D. Structure 13 779-789 (2005)
  12. Role of small subunit in mediating assembly of red-type form I Rubisco. Joshi J, Mueller-Cajar O, Tsai YC, Hartl FU, Hayer-Hartl M. J Biol Chem 290 1066-1074 (2015)
  13. RbcS suppressor mutations improve the thermal stability and CO2/O2 specificity of rbcL- mutant ribulose-1,5-bisphosphate carboxylase/oxygenase. Du YC, Hong S, Spreitzer RJ. Proc Natl Acad Sci U S A 97 14206-14211 (2000)
  14. The kinetics of conformation change as determinant of Rubisco's specificity. Schlitter J, Wildner GF. Photosynth Res 65 7-13 (2000)
  15. X-ray structure of Galdieria Rubisco complexed with one sulfate ion per active site. Okano Y, Mizohata E, Xie Y, Matsumura H, Sugawara H, Inoue T, Yokota A, Kai Y. FEBS Lett 527 33-36 (2002)
  16. Immobilization of D-ribulose-1,5-bisphosphate carboxylase/oxygenase: a step toward carbon dioxide fixation bioprocess. Chakrabarti S, Bhattacharya S, Bhattacharya SK. Biotechnol Bioeng 81 705-711 (2003)
  17. Ribulose-1,5-bisphosphate carboxylase/oxygenase from thermophilic cyanobacterium Thermosynechococcus elongatus. Gubernator B, Bartoszewski R, Kroliczewski J, Wildner G, Szczepaniak A. Photosynth Res 95 101-109 (2008)
  18. Calcium supports loop closure but not catalysis in Rubisco. Karkehabadi S, Taylor TC, Andersson I. J Mol Biol 334 65-73 (2003)
  19. Identification of major zinc-binding proteins from a marine cyanobacterium: insight into metal uptake in oligotrophic environments. Barnett JP, Scanlan DJ, Blindauer CA. Metallomics 6 1254-1268 (2014)
  20. Mixotrophic growth of the extremophile Galdieria sulphuraria reveals the flexibility of its carbon assimilation metabolism. Curien G, Lyska D, Guglielmino E, Westhoff P, Janetzko J, Tardif M, Hallopeau C, Brugière S, Dal Bo D, Decelle J, Gallet B, Falconet D, Carone M, Remacle C, Ferro M, Weber APM, Finazzi G. New Phytol 231 326-338 (2021)
  21. Substitutions at the opening of the Rubisco central solvent channel affect holoenzyme stability and CO2/O 2 specificity but not activation by Rubisco activase. Esquivel MG, Genkov T, Nogueira AS, Salvucci ME, Spreitzer RJ. Photosynth Res 118 209-218 (2013)
  22. Ab initio study of molecular interactions in higher plant and Galdieria partita Rubiscos with the fragment molecular orbital method. Watanabe H, Enomoto T, Tanaka S. Biochem Biophys Res Commun 361 367-372 (2007)
  23. Deletion of nine carboxy-terminal residues of the Rubisco small subunit decreases thermal stability but does not eliminate function. Esquível MG, Anwaruzzaman M, Spreitzer RJ. FEBS Lett 520 73-76 (2002)
  24. An Insight of RuBisCO Evolution through a Multilevel Approach. Camel V, Zolla G. Biomolecules 11 1761 (2021)


Related citations provided by authors (1)

  1. Large Structures at High Resolution: The 1.6 A Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Complexed with 2- Carboxyarabinitol Bisphosphate. Andersson I J. Mol. Biol. 259 160- (1996)

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