PDBsum entry 8ruc

Lyase (carbon-carbon)

PDB id: 8ruc

Contents

Protein chains

467 a.a. *

123 a.a. *

Ligands

CAP ×4

Metals

_MG ×4

Waters ×1520

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Large structures at high resolution: the 1.6 a crystal structure of spinach ribulose-1,5-Bisphosphate carboxylase/oxygenase complexed with 2-Carboxyarabinitol bisphosphate.

Author

I.Andersson.

Ref.

J Mol Biol, 1996, 259, 160-174. [DOI no: 10.1006/jmbi.1996.0310]

PubMed id

8648644

Abstract

Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from spinach is a hexadecamer (L8S8, Mr = 550,000) consisting of eight large (L, 475 residues) and eight small subunits (S, 123 residues). High-resolution data collection on crystals with large unit cells is not a trivial task due to the effect of radiation damage and the large number of overlapping reflections when conventional data collection methods are used. In order to minimise these effects, data on rubisco were collected with a giant Weissenberg camera at long crystal to image-plate distances at the synchrotron of the Photon Factory, Japan. Relative to conventional data sets, this experimental arrangement allowed a 20 to 30-fold reduction of the X-ray dose/exposure time for data collection. This paper describes the refined 1.6 A crystal structure of activated rubisco complexed with a transition state analogue, 2-carboxyarabinitol-bisphosphate. The crystallographic asymmetric unit contains an L4S4 unit, representing half of the molecule. The structure presented here is currently the highest resolution structure for any protein of comparable size. Refinement of the model was carried out by restrained least squares techniques without non-crystallographic symmetry averaging. The results show that all L and S subunits have identical three-dimensional structures, and their arrangement within the hexadecamer has no intrinsic asymmetry. A detailed analysis of the high-resolution maps identified 30 differences in the sequence of the small subunit, indicating a larger than usual heterogeneity for this nuclear encoded protein in spinach. No such differences were found in the sequence of the chloroplast encoded large subunit. The transition state analogue is in the cis conformation at the active site suggesting a key role for the carbamate of Lys201 in catalysis. Analysis of the active site around the catalytically essential magnesium ion further indicates that residues in the second liganding sphere of the metal play a role in fine-tuning the acid-base character and the position of the residues directly liganded to the metal.

Figure 1.
Figure 1. Reactions catalysed by rubisco.

Figure 7.
Figure 7. Overview of the active site of spinach rubisco showing 2-CABP, Mg 2+ and residues within hydrogen-bonding distance to these ligands. The hydroxyl groups at C2 and C3 of 2-CABP are in cis conformation. The two views in (a) and (b) are related by 180° with respect to the vertical axis.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 259, 160-174) copyright 1996.

Secondary reference #1

Title

Crystallographic analysis of ribulose 1,5-Bisphosphate carboxylase from spinach at 2.4 a resolution. Subunit interactions and active site.

Authors

S.Knight, I.Andersson, C.I.Brändén.

Ref.

J Mol Biol, 1990, 215, 113-160.

PubMed id

2118958

Secondary reference #2

Title

Crystal structure of the active site of ribulose-Bisphosphate carboxylase

Authors

I.Andersson, S.Knight, G.Schneider, Y.Lindqvist, T.Lundqvist, C.-I.Branden, G.H.Lorimer.

Ref.

nature, 1989, 337, 229.

Secondary reference #3

Title

Reexamination of the three-Dimensional structure of the small subunit of rubisco from higher plants

Authors

S.Knight, I.Andersson, C.-I.Branden.

Ref.

science, 1989, 244, 702.