Crystal structure of the unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate.
Abstract
The crystal structure of unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase from Nicotiana tabacum complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate, was determined to 2.7 A resolution by X-ray crystallography. The transition state analog binds at the active site in an extended conformation. As compared to the binding of the same analog in the activated enzyme, the analog binds in a reverse orientation. The active site Lys 201 is within hydrogen bonding distance of the carboxyl oxygen of the analog. Loop 6 (residues 330-339) remains open and flexible upon binding of the analog in the unactivated enzyme, in contrast to the closed and ordered loop 6 in the activated enzyme complex. The transition state analog is exposed to solvent due to the open conformation of loop 6.
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- Baker TS, Suh SW, Eisenberg D. Structure of ribulose-1,5-bisphosphate carboxylase-oxygenase: Form III crystals. Proc Natl Acad Sci U S A. 1977 Mar;74(3):1037–1041.[PMC free article] [PubMed] [Google Scholar]
- Brändén CI, Lindqvist Y, Schneider G. Protein engineering of Rubisco. Acta Crystallogr B. 1991 Dec 1;47(Pt 6):824–835. [PubMed] [Google Scholar]
- Brünger AT, Kuriyan J, Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 1987 Jan 23;235(4787):458–460. [PubMed] [Google Scholar]
- Chan PH, Sakano K, Singh S, Wildman SG. Crystalline fraction I protein: preparation in large yield. Science. 1972 Jun 9;176(4039):1145–1146. [PubMed] [Google Scholar]
- Chapman MS, Smith WW, Suh SW, Cascio D, Howard A, Hamlin R, Xuong NH, Eisenberg D. Structural studies of Rubisco from tobacco. Philos Trans R Soc Lond B Biol Sci. 1986 Oct 14;313(1162):367–378. [PubMed] [Google Scholar]
- Chapman MS, Suh SW, Cascio D, Smith WW, Eisenberg D. Sliding-layer conformational change limited by the quaternary structure of plant RuBisCO. Nature. 1987 Sep 24;329(6137):354–356. [PubMed] [Google Scholar]
- Chapman MS, Suh SW, Curmi PM, Cascio D, Smith WW, Eisenberg DS. Tertiary structure of plant RuBisCO: domains and their contacts. Science. 1988 Jul 1;241(4861):71–74. [PubMed] [Google Scholar]
- Curmi PM, Cascio D, Sweet RM, Eisenberg D, Schreuder H. Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-A resolution. J Biol Chem. 1992 Aug 25;267(24):16980–16989. [PubMed] [Google Scholar]
- Estelle M, Hanks J, McIntosh L, Somerville C. Site-specific mutagenesis of ribulose-1,5-bisphosphate carboxylase/oxygenase. Evidence that carbamate formation at Lys 191 is required for catalytic activity. J Biol Chem. 1985 Aug 15;260(17):9523–9526. [PubMed] [Google Scholar]
- Jones TA. Diffraction methods for biological macromolecules. Interactive computer graphics: FRODO. Methods Enzymol. 1985;115:157–171. [PubMed] [Google Scholar]
- Lorimer GH. Ribulosebisphosphate carboxylase: amino acid sequence of a peptide bearing the activator carbon dioxide. Biochemistry. 1981 Mar 3;20(5):1236–1240. [PubMed] [Google Scholar]
- Lorimer GH, Badger MR, Andrews TJ. The activation of ribulose-1,5-bisphosphate carboxylase by carbon dioxide and magnesium ions. Equilibria, kinetics, a suggested mechanism, and physiological implications. Biochemistry. 1976 Feb 10;15(3):529–536. [PubMed] [Google Scholar]
- Lorimer GH, Hartman FC. Evidence supporting lysine 166 of Rhodospirillum rubrum ribulosebisphosphate carboxylase as the essential base which initiates catalysis. J Biol Chem. 1988 May 15;263(14):6468–6471. [PubMed] [Google Scholar]
- Pierce J, Andrews TJ, Lorimer GH. Reaction intermediate partitioning by ribulose-bisphosphate carboxylases with differing substrate specificities. J Biol Chem. 1986 Aug 5;261(22):10248–10256. [PubMed] [Google Scholar]
- Pierce J, Tolbert NE, Barker R. Interaction of ribulosebisphosphate carboxylase/oxygenase with transition-state analogues. Biochemistry. 1980 Mar 4;19(5):934–942. [PubMed] [Google Scholar]
- Ray WJ, Jr, Bolin JT, Puvathingal JM, Minor W, Liu YW, Muchmore SW. Removal of salt from a salt-induced protein crystal without cross-linking. Preliminary examination of "desalted" crystals of phosphoglucomutase by X-ray crystallography at low temperature. Biochemistry. 1991 Jul 16;30(28):6866–6875. [PubMed] [Google Scholar]
- Schneider G, Lindqvist Y, Brändén CI, Lorimer G. Three-dimensional structure of ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum at 2.9 A resolution. EMBO J. 1986 Dec 20;5(13):3409–3415.[PMC free article] [PubMed] [Google Scholar]
- Schreuder HA, Knight S, Curmi PM, Andersson I, Cascio D, Sweet RM, Brändén CI, Eisenberg D. Crystal structure of activated tobacco rubisco complexed with the reaction-intermediate analogue 2-carboxy-arabinitol 1,5-bisphosphate. Protein Sci. 1993 Jul;2(7):1136–1146.[PMC free article] [PubMed] [Google Scholar]
Abstract
The crystal structure of unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase from Nicotiana tabacum complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate, was determined to 2.7 A resolution by X-ray crystallography. The transition state analog binds at the active site in an extended conformation. As compared to the binding of the same analog in the activated enzyme, the analog binds in a reverse orientation. The active site Lys 201 is within hydrogen bonding distance of the carboxyl oxygen of the analog. Loop 6 (residues 330-339) remains open and flexible upon binding of the analog in the unactivated enzyme, in contrast to the closed and ordered loop 6 in the activated enzyme complex. The transition state analog is exposed to solvent due to the open conformation of loop 6.