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PDBsum entry 1rxo

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Lyase (carbon-carbon) PDB id
1rxo
Jmol
Contents
Protein chains
455 a.a. *
123 a.a. *
Ligands
RUB ×4
Metals
_CA ×4
Waters ×1024
* Residue conservation analysis

References listed in PDB file
Key reference
Title The structure of the complex between rubisco and its natural substrate ribulose 1,5-Bisphosphate.
Authors T.C.Taylor, I.Andersson.
Ref. J Mol Biol, 1997, 265, 432-444. [DOI no: 10.1006/jmbi.1996.0738]
PubMed id 9034362
Abstract
The three-dimensional structure of the complex of ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco; EC 4.1.1.39) from spinach with its natural substrate ribulose 1,5-bisphosphate (RuBP) has been determined both under activating and non-activating conditions by X-ray crystallography to a resolution of 2.1 A and 2.4 A, respectively. Under activating conditions, the use of calcium instead of magnesium as the activator metal ion enabled us to trap the substrate in a stable complex for crystallographic analysis. Comparison of the structure of the activated and the non-activated RuBP complexes shows a tighter binding for the substrate in the non-activated form of the enzyme, in line with previous solution studies. In the non-activated complex, the substrate triggers isolation of the active site by inducing movements of flexible loop regions of the catalytic subunits. In contrast, in the activated complex the active site remains partly open, probably awaiting the binding of the gaseous substrate. By inspection of the structures and by comparison with other complexes of the enzyme we were able to identify a network of hydrogen bonds that stabilise a closed active site structure during crucial steps in the reaction. The present structure underlines the central role of the carbamylated lysine 201 in both activation and catalysis, and completes available structural information for our proposal on the mechanism of the enzyme.
Figure 4.
Figure 4. Comparison of the active-site structures in the activated RuBP complex (magenta), the non-activated RuBP complex (blue) and the 2CABP complex (atoms coloured according to atom type). In the open form of the enzyme (activated RuBP complex, magenta), loop 6 of the a/b-barrel is swung away from the active site, and lies outside the image frame of the Figure. In the closed structures, the loop is folded over the active site with Lys334 at its tip, interacting with the substrate. Further differences between the open and closed forms are seen in the N-terminal loops, one beginning with Glu60 and the other centred at Asn123. Coordinates for the 2CABP complex of spinach rubisco are from the 1.6 Å resolution refined structure (8RUC, Andersson, 1996). Superposition of the structures was carried out using O (Jones et al., 1991). The picture was produced with MOLSCRIPT (Kraulis, 1991), modified by Robert Esnouf (Oxford University, unpublished). For the sake of simplicity, only key residues are labelled. See the bottom stereo pair of Figure 5 (same orientation) for further residue numbering.
Figure 7.
Figure 7. The reaction mechanism for carboxylation by rubisco based on the present structure.
The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 265, 432-444) copyright 1997.
Secondary reference #1
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
Full text Abstract
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 reproduced from the cited reference with permission from Elsevier
PROCHECK
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