First time at Proteopedia? Click on the green links: they change the 3D image. Click and drag the molecules. Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, you can edit pages in Proteopedia. Visit the Main Page to learn more.

3axk

From Proteopedia

Jump to: navigation, search
3axk, resolution 1.90Å ()
Ligands: , ,
Non-Standard Residues: ,
Activity: Ribulose-bisphosphate carboxylase, with EC number 4.1.1.39
Related: 1wdd, 3axm


Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Contents

Structure of rice Rubisco in complex with NADP(H)

Publication Abstract from PubMed

The key enzyme of plant photosynthesis, d-ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), must be activated to become catalytically competent via the carbamylation of Lys201 of the large subunit and subsequent stabilization by Mg(2+) coordination. Many biochemical studies have reported that reduced nicotinamide adenine dinucleotide phosphate (NADPH) and 6-phosphogluconate (6PG) function as positive effectors to promote activation. However, the structural mechanism remains unknown. Here, we have determined the crystal structures of activated rice Rubisco in complex with NADPH, 6PG, or 2-carboxy-d-arabinitol 1,5-bisphosphate (2CABP). The structures of the NADPH and 6PG complexes adopt open-state conformations, in which loop 6 at the catalytic site and some other loops are disordered. The structure of the 2CABP complex is in a closed state, similar to the previous 2CABP-bound activated structures from other sources. The catalytic sites of the NADPH and 6PG complexes are fully activated, despite the fact that bicarbonate (NaHCO(3)) was not added into the crystallization solution. In the catalytic site, NADPH does not interact with Mg(2+) directly but interacts with Mg(2+)-coordinated water molecules, while 6PG interacts with Mg(2+) directly. These observations suggest that the two effectors promote Rubisco activation by stabilizing the complex of Mg(2+) and the carbamylated Lys201 with unique interactions and preventing its dissociation. The structure also reveals that the relaxed complex of the effectors (NADPH or 6PG), distinct from the tight-binding mode of 2CABP, would allow rapid exchange of the effectors in the catalytic sites by substrate d-ribulose 1,5-bisphosphate for catalysis in physiological conditions.

Crystal Structure of Rice Rubisco and Implications for Activation Induced by Positive Effectors NADPH and 6-Phosphogluconate., Matsumura H, Mizohata E, Ishida H, Kogami A, Ueno T, Makino A, Inoue T, Yokota A, Mae T, Kai Y, J Mol Biol. 2012 May 17. PMID:22609438

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

Function

[RBL_ORYSJ] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. [RBS1_ORYSJ] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site (By similarity).

About this Structure

3axk is a 4 chain structure with sequence from Oryza sativa japonica group. Full crystallographic information is available from OCA.

Reference

  • Matsumura H, Mizohata E, Ishida H, Kogami A, Ueno T, Makino A, Inoue T, Yokota A, Mae T, Kai Y. Crystal Structure of Rice Rubisco and Implications for Activation Induced by Positive Effectors NADPH and 6-Phosphogluconate. J Mol Biol. 2012 May 17. PMID:22609438 doi:10.1016/j.jmb.2012.05.014

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools