5rub
CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE FROM RHODOSPIRILLUM RUBRUM AT 1.7 ANGSTROMS RESOLUTION
|
OverviewOverview
The amino acid sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase, from Rhodospirillum rubrum has been fitted to the electron density maps., The resulting protein model has been refined to a nominal resolution of, 1.7 A using the constrained-restrained least-squares refinement program of, Sussman and the restrained least-squares refinement program of Hendrickson, & Konnert. The crystallographic refinement, based on 76,452 reflections, with F greater than sigma (F) in the resolution range 5.5 to 1.7 A, resulted in a crystallographic R-factor of 18.0%. The asymmetric unit, contains one dimeric ribulose-1,5-biphosphate carboxylase molecule, consisting of 869 amino acid residues and 736 water molecules. The, geometry of the refined model is close to ideal, with root-mean-square, deviations of 0.018 A in bond lengths and 2.7 degrees in bond angles. Two, loop regions, comprising residues 54 to 63 and 324 to 335, and the last, ten amino acid residues at the C terminus are disordered in our crystals., The expected trimodal distribution is obtained for the side-chain chi, 1-angles with a marked preference for staggered conformation. The, hydrogen-bonding pattern in the N-terminal beta-sheet and the parallel, sheet in the beta/alpha-barrel is described. A number of hydrogen bonds, and salt bridges are involved in domain-domain and subunit-subunit, interactions. The subunit-subunit interface in the dimer covers an area of, 2800 A2. Considerable deviations from the local 2-fold symmetry are found, at both the N terminus (residues 2 to 5) and the C terminus (residues 422, to 457). Furthermore, loop 8 in the beta/alpha-barrel domain has a, different conformation in the two subunits. A number of amino acid, side-chains have different conformations in the two subunits. Most of, these residues are located at the surface of the protein. An analysis of, the individual temperature factors indicates a high mobility of the, C-terminal region and for some of the loops at the active site. The, positions and B-factors for 736 solvent sites have been refined (average, B: 45.9 A2). Most of the solvent molecules are bound as clusters to the, protein. The active site of the enzyme, especially the environment of the, activator Lys191 in the non-activated enzyme is described., Crystallographic refinement at 1.7 A resolution clearly revealed the, presence of a cis-proline at the active site. This residue is part of the, highly conserved region Lys166-Pro167-Lys168.
About this StructureAbout this Structure
5RUB is a Single protein structure of sequence from Rhodospirillum rubrum. This structure superseeds the now removed PDB entry 2RUB. Active as Ribulose-bisphosphate carboxylase, with EC number 4.1.1.39 Full crystallographic information is available from OCA.
ReferenceReference
Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 A resolution., Schneider G, Lindqvist Y, Lundqvist T, J Mol Biol. 1990 Feb 20;211(4):989-1008. PMID:2107319
Page seeded by OCA on Tue Nov 20 19:41:25 2007