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PDBsum entry 1iwa

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Lyase PDB id
1iwa
Jmol
Contents
Protein chains
(+ 2 more) 473 a.a. *
(+ 2 more) 138 a.a. *
Ligands
SO4 ×8
Waters ×3112
* Residue conservation analysis

References listed in PDB file
Key reference
Title X-Ray structure of galdieria rubisco complexed with one sulfate ion per active site.
Authors Y.Okano, E.Mizohata, Y.Xie, H.Matsumura, H.Sugawara, T.Inoue, A.Yokota, Y.Kai.
Ref. FEBS Lett, 2002, 527, 33-36. [DOI no: 10.1016/S0014-5793(02)03148-4]
PubMed id 12220629
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the reactions of carboxylation and oxygenation of ribulose-1,5-bisphosphate. These reactions require that the active site should be closed by a flexible loop (loop 6) of the large subunit. Rubisco from a red alga, Galdieria partita, has the highest specificity for carboxylation reaction among the Rubiscos hitherto reported. The crystal structure of unactivated Galdieria Rubisco has been determined at 2.6 A resolution. The electron density map reveals that a sulfate binds only to the P1 anion-binding site of the active site and the loop 6 is closed. Galdieria Rubisco has a unique hydrogen bond between the main chain oxygen of Val332 on the loop 6 and the epsilon-amino group of Gln386 of the same large subunit. This interaction is likely to be crucial to understanding for stabilizing the loop 6 in the closed state and to making a higher affinity for anionic ligands.
Figure 1.
Fig. 1. Active site structure in Rubiscos structure of Galdieria metal-free Rubisco bound with SO[4]^2−. Oxygen, nitrogen, and sulfur atoms are shown in red and purple and yellow. The metal ion and the bound 2-CABP of Galdieria Rubisco(1BWV) are shown with some transparency. The loop 6 of Galdieria is shown in red.
Figure 2.
Fig. 2. The comparison in open/closed structure of the loop 6. The loop 6 structure of tobacco Rubisco (1EJ7) is shown in blue and that of Galdieria in shown red. This figure was drawn by the programs MOLSCRIPT and RASTER3D.
The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2002, 527, 33-36) copyright 2002.
Secondary reference #1
Title The transition between the open and closed states of rubisco is triggered by the inter-Phosphate distance of the bound bisphosphate.
Authors A.P.Duff, T.J.Andrews, P.M.Curmi.
Ref. J Mol Biol, 2000, 298, 903-916. [DOI no: 10.1006/jmbi.2000.3724]
PubMed id 10801357
Full text Abstract
Figure 1.
Figure 1. A schematic depicting the closed and open states of an active site of rubisco. The view is looking from above the central axis of the a/b barrel. The N-terminal domain (N terminus to residue 150) from the L[2] partner large subunit covers most of the top of the barrel. A distinct C-terminal domain exists as an appendage of the barrel domain. Two small subunits make separate contacts with the domains that form the single active site. With respect to the closed state, the N-terminal domain in the open state has moved left and correspondingly one small subunit moves up and to the left. On opening, Loop 6 of the barrel domain retracts to extend helix 6 in a stable configuration and the C-terminal strand pulls away from the active site and the barrel domain and is usually disordered in the open state crystal structures. In the closed state, there is no solvent access to the substrate and substrate binding can be divided into three distinct zones; the P1-binding site, the P2-binding site and the metal site.
Figure 4.
Figure 4. The P1 and P2 phosphate anion subsites are shown in stereo. (a) The two distinct modes of binding of phosphate in the P2 site. Inorganic phosphate (our structure) and the P2 phosphate from the Ca^2+-RuBP complex [Taylor and Andersson 1997b] bind to the upper P2 subsite consisting of interactions with Arg295 and His298 (thin lines). This is the subsite that is occupied in all open-state structures where ligands are present. CABP binds to the lower subsite, interacting with Arg295 and His327 (thin lines). This is the subsite that is occupied in all closed-state structures. (b) The three distinct modes of binding to the P1 phosphate site. All anions make hydrogen bonds to the backbone amide groups of Gly381, Gly403 and Gly404 from Loops 7 and 8 of the a/b-barrel domain (thin lines only shown for CABP and RuBP). In all closed states, the P1 phosphate occupies a proximal subsite (leftmost in Figure) where it forms a hydrogen bond to Thr65 OG1 (thin line for CABP shown). Except for Form III crystals of tobacco rubisco, all open states show the phosphate bound in a distal site, 0.7 Å further away from P2. The hydrogen bond to Thr65 is replaced by one to Trp66 (thin lines for RuBP Ca^2+ complex shown). In Form III open states, the anion is located even further away from P2 and Trp66 is dislodged by a crystal packing artefact (our inorganic phosphate structure shown).
The above figures are reproduced from the cited reference with permission from Elsevier
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