4LF1

Hexameric Form II RuBisCO from Rhodopseudomonas palustris, activated and complexed with 2-CABP

Summary for 4LF1

• Entry DOI: 10.2210/pdb4lf1/pdb
• Related: 4LF1
• Descriptor: Ribulose bisphosphate carboxylase, 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: form ii, cbbm, protein, 2-cabp, transition-state analog, reaction intermediate analogue, carbon fixation, enzyme activation, activated, carbamylation, photosynthesis, lyase, oxidoreductase
• Biological source: Rhodopseudomonas palustris
• Total number of polymer chains: 6
• Total formula weight: 318826.56

Authors

Chan, S.,Satagopan, S.,Sawaya, M.R.,Eisenberg, D.,Tabita, F.R.,Perry, L.J. (deposition date: 2013-06-26, release date: 2014-06-25, Last modification date: 2025-03-26)

Primary citation

Satagopan, S.,Chan, S.,Perry, L.J.,Tabita, F.R.
Structure-function studies with the unique hexameric form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Rhodopseudomonas palustris.
J.Biol.Chem., 289:21433-21450, 2014

PubMed Abstract: The first x-ray crystal structure has been solved for an activated transition-state analog-bound form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). This enzyme, from Rhodopseudomonas palustris, assembles as a unique hexamer with three pairs of catalytic large subunit homodimers around a central 3-fold symmetry axis. This oligomer arrangement is unique among all known Rubisco structures, including the form II homolog from Rhodospirillum rubrum. The presence of a transition-state analog in the active site locked the activated enzyme in a "closed" conformation and revealed the positions of critical active site residues during catalysis. Functional roles of two form II-specific residues (Ile(165) and Met(331)) near the active site were examined via site-directed mutagenesis. Substitutions at these residues affect function but not the ability of the enzyme to assemble. Random mutagenesis and suppressor selection in a Rubisco deletion strain of Rhodobacter capsulatus identified a residue in the amino terminus of one subunit (Ala(47)) that compensated for a negative change near the active site of a neighboring subunit. In addition, substitution of the native carboxyl-terminal sequence with the last few dissimilar residues from the related R. rubrum homolog increased the enzyme's kcat for carboxylation. However, replacement of a longer carboxyl-terminal sequence with termini from either a form III or a form I enzyme, which varied both in length and sequence, resulted in complete loss of function. From these studies, it is evident that a number of subtle interactions near the active site and the carboxyl terminus account for functional differences between the different forms of Rubiscos found in nature.

PubMed: 24942737
DOI: 10.1074/jbc.M114.578625

Experimental method

X-RAY DIFFRACTION (2.38 Å)