3KDO

Crystal structure of Type III Rubisco SP6 mutant complexed with 2-CABP

Summary for 3KDO

• Entry DOI: 10.2210/pdb3kdo/pdb
• Related: 1GEH 3A12 3A13 3KBN
• Descriptor: Ribulose bisphosphate carboxylase, 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: ribulose-1, 5-bisphosphate carboxylase/oxygenase, rubisco, carbon dioxide fixation, lyase, magnesium, metal-binding, monooxygenase
• Biological source: Thermococcus kodakaraensis
• Total number of polymer chains: 10
• Total formula weight: 501768.30

Authors

Nishitani, Y.,Fujihashi, M.,Doi, T.,Yoshida, S.,Atomi, H.,Imanaka, T.,Miki, K. (deposition date: 2009-10-23, release date: 2010-10-06, Last modification date: 2023-11-22)

Primary citation

Nishitani, Y.,Yoshida, S.,Fujihashi, M.,Kitagawa, K.,Doi, T.,Atomi, H.,Imanaka, T.,Miki, K.
Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile
J.Biol.Chem., 285:39339-39347, 2010

PubMed Abstract: The Calvin-Benson-Bassham cycle is responsible for carbon dioxide fixation in all plants, algae, and cyanobacteria. The enzyme that catalyzes the carbon dioxide-fixing reaction is ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Rubisco from a hyperthermophilic archaeon Thermococcus kodakarensis (Tk-Rubisco) belongs to the type III group, and shows high activity at high temperatures. We have previously found that replacement of the entire α-helix 6 of Tk-Rubisco with the corresponding region of the spinach enzyme (SP6 mutant) results in an improvement of catalytic performance at mesophilic temperatures, both in vivo and in vitro, whereas the former and latter half-replacements of the α-helix 6 (SP4 and SP5 mutants) do not yield such improvement. We report here the crystal structures of the wild-type Tk-Rubisco and the mutants SP4 and SP6, and discuss the relationships between their structures and enzymatic activities. A comparison among these structures shows the movement and the increase of temperature factors of α-helix 6 induced by four essential factors. We thus supposed that an increase in the flexibility of the α-helix 6 and loop 6 regions was important to increase the catalytic activity of Tk-Rubisco at ambient temperatures. Based on this structural information, we constructed a new mutant, SP5-V330T, which was designed to have significantly greater flexibility in the above region, and it proved to exhibit the highest activity among all mutants examined to date. The thermostability of the SP5-V330T mutant was lower than that of wild-type Tk-Rubisco, providing further support on the relationship between flexibility and activity at ambient temperatures.

PubMed: 20926376
DOI: 10.1074/jbc.M110.147587

Experimental method

X-RAY DIFFRACTION (2.36 Å)